Query 004939
Match_columns 722
No_of_seqs 214 out of 1087
Neff 8.6
Searched_HMMs 46136
Date Thu Mar 28 15:24:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004939.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004939hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166 Cullins [Cell cycle co 100.0 2E-119 5E-124 1013.3 65.4 703 2-720 4-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 3E-112 7E-117 910.9 62.2 706 3-722 15-773 (773)
3 KOG2167 Cullins [Cell cycle co 100.0 1E-107 3E-112 855.2 46.8 631 62-722 2-661 (661)
4 KOG2284 E3 ubiquitin ligase, C 100.0 7E-106 2E-110 805.6 46.8 664 2-722 5-728 (728)
5 KOG2285 E3 ubiquitin ligase, C 100.0 1.8E-89 4E-94 693.5 55.1 697 5-722 10-777 (777)
6 PF00888 Cullin: Cullin family 100.0 1.3E-89 2.8E-94 794.2 60.1 581 12-626 1-588 (588)
7 smart00182 CULLIN Cullin. 100.0 1.6E-32 3.5E-37 255.8 17.8 141 406-547 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 3.9E-26 8.5E-31 245.6 40.5 303 399-711 441-757 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 1.1E-19 2.3E-24 145.4 2.2 68 649-716 1-68 (68)
10 PF08539 HbrB: HbrB-like; Int 95.9 0.2 4.4E-06 47.1 13.5 126 5-138 2-145 (158)
11 TIGR01610 phage_O_Nterm phage 93.5 0.24 5.1E-06 42.5 6.5 65 554-626 21-93 (95)
12 PF09339 HTH_IclR: IclR helix- 91.6 0.3 6.6E-06 36.5 4.2 45 561-607 6-51 (52)
13 PF13412 HTH_24: Winged helix- 91.6 0.39 8.4E-06 35.2 4.7 42 557-598 2-43 (48)
14 PF02082 Rrf2: Transcriptional 91.5 0.57 1.2E-05 38.9 6.2 59 559-624 11-70 (83)
15 PF12802 MarR_2: MarR family; 90.2 0.39 8.4E-06 37.2 3.8 51 556-608 3-55 (62)
16 PF08220 HTH_DeoR: DeoR-like h 89.5 0.92 2E-05 34.7 5.2 46 560-607 2-47 (57)
17 KOG2167 Cullins [Cell cycle co 88.0 29 0.00063 39.1 17.2 186 10-215 112-324 (661)
18 PF01047 MarR: MarR family; I 86.5 0.77 1.7E-05 35.2 3.3 50 556-607 1-50 (59)
19 PF13463 HTH_27: Winged helix 86.2 1.2 2.6E-05 35.1 4.4 50 556-607 1-51 (68)
20 PF01022 HTH_5: Bacterial regu 86.0 1.9 4.1E-05 31.4 4.9 44 559-605 3-46 (47)
21 PF12840 HTH_20: Helix-turn-he 85.9 1.1 2.3E-05 34.8 3.7 49 557-607 9-57 (61)
22 TIGR02337 HpaR homoprotocatech 85.3 1.7 3.6E-05 38.8 5.3 52 555-608 25-76 (118)
23 smart00550 Zalpha Z-DNA-bindin 84.1 2.2 4.7E-05 34.0 4.8 47 559-607 7-55 (68)
24 COG3682 Predicted transcriptio 84.0 1 2.3E-05 40.0 3.2 62 656-722 6-67 (123)
25 PRK11512 DNA-binding transcrip 83.2 2.4 5.3E-05 39.3 5.5 52 555-608 37-88 (144)
26 PF08279 HTH_11: HTH domain; 81.6 2.9 6.3E-05 31.4 4.5 37 562-598 4-41 (55)
27 TIGR02698 CopY_TcrY copper tra 81.3 1.7 3.8E-05 39.5 3.7 60 658-722 6-65 (130)
28 PF09012 FeoC: FeoC like trans 81.2 0.7 1.5E-05 36.9 1.0 45 661-713 5-49 (69)
29 PRK11920 rirA iron-responsive 79.2 5.9 0.00013 37.2 6.6 56 561-623 13-68 (153)
30 TIGR01889 Staph_reg_Sar staphy 78.9 5.2 0.00011 35.1 5.8 52 555-608 22-77 (109)
31 PRK10857 DNA-binding transcrip 78.3 6.6 0.00014 37.3 6.7 45 560-606 12-57 (164)
32 PF03965 Penicillinase_R: Peni 77.8 2.1 4.5E-05 38.1 3.0 60 658-722 5-64 (115)
33 smart00347 HTH_MARR helix_turn 77.7 4.4 9.5E-05 34.4 5.0 52 554-607 6-57 (101)
34 smart00346 HTH_ICLR helix_turn 76.1 6.1 0.00013 33.1 5.3 45 561-607 8-53 (91)
35 PF01978 TrmB: Sugar-specific 75.8 2.3 5.1E-05 33.6 2.5 49 557-607 7-55 (68)
36 smart00420 HTH_DEOR helix_turn 75.7 5.8 0.00012 29.1 4.6 44 561-606 3-46 (53)
37 COG3355 Predicted transcriptio 74.6 7.5 0.00016 34.9 5.5 39 568-608 38-76 (126)
38 TIGR02010 IscR iron-sulfur clu 74.4 8.8 0.00019 35.1 6.3 44 561-606 13-57 (135)
39 PF04492 Phage_rep_O: Bacterio 74.2 11 0.00024 32.6 6.3 62 555-626 29-98 (100)
40 COG1959 Predicted transcriptio 73.7 8.7 0.00019 35.9 6.1 59 559-624 11-70 (150)
41 PF13404 HTH_AsnC-type: AsnC-t 73.6 5 0.00011 28.5 3.4 36 561-596 6-41 (42)
42 PRK15090 DNA-binding transcrip 72.2 8.3 0.00018 39.6 6.2 47 560-608 16-62 (257)
43 PRK13777 transcriptional regul 71.7 8.4 0.00018 37.4 5.6 53 554-608 41-93 (185)
44 PF05584 Sulfolobus_pRN: Sulfo 71.4 10 0.00022 30.4 5.0 42 562-606 9-50 (72)
45 PHA00738 putative HTH transcri 71.4 10 0.00022 32.9 5.4 68 553-626 7-74 (108)
46 PRK03573 transcriptional regul 70.1 8.9 0.00019 35.4 5.4 53 554-608 27-80 (144)
47 PF05732 RepL: Firmicute plasm 69.4 9 0.0002 36.4 5.2 50 572-630 75-124 (165)
48 PF08280 HTH_Mga: M protein tr 67.9 6.8 0.00015 30.1 3.4 38 560-597 7-44 (59)
49 PF08784 RPA_C: Replication pr 66.5 9.4 0.0002 33.0 4.4 44 555-598 44-91 (102)
50 smart00419 HTH_CRP helix_turn_ 66.5 14 0.00029 26.5 4.7 34 572-607 8-41 (48)
51 PRK10870 transcriptional repre 65.8 15 0.00032 35.4 6.0 51 556-608 53-105 (176)
52 TIGR00738 rrf2_super rrf2 fami 65.4 17 0.00036 32.9 6.1 45 560-606 12-57 (132)
53 TIGR01884 cas_HTH CRISPR locus 64.6 11 0.00024 37.2 5.0 52 555-608 140-191 (203)
54 PRK10141 DNA-binding transcrip 63.8 15 0.00033 32.7 5.2 58 560-623 18-75 (117)
55 PF04703 FaeA: FaeA-like prote 63.3 9.7 0.00021 29.7 3.4 45 563-609 5-50 (62)
56 smart00345 HTH_GNTR helix_turn 62.9 17 0.00036 27.3 4.8 39 567-607 14-53 (60)
57 TIGR03879 near_KaiC_dom probab 62.3 9.1 0.0002 30.9 3.2 28 570-597 30-57 (73)
58 PF08220 HTH_DeoR: DeoR-like h 61.3 4.9 0.00011 30.7 1.4 46 659-712 3-48 (57)
59 PF01978 TrmB: Sugar-specific 60.8 3.8 8.3E-05 32.4 0.8 55 659-721 11-65 (68)
60 smart00550 Zalpha Z-DNA-bindin 60.7 9.8 0.00021 30.2 3.1 53 658-718 8-62 (68)
61 cd00090 HTH_ARSR Arsenical Res 60.6 19 0.00042 28.2 5.1 47 557-606 6-52 (78)
62 PRK11569 transcriptional repre 60.6 17 0.00038 37.7 5.9 47 560-608 30-77 (274)
63 PF13463 HTH_27: Winged helix 60.0 10 0.00022 29.6 3.2 53 658-718 5-60 (68)
64 smart00344 HTH_ASNC helix_turn 59.8 16 0.00035 31.7 4.7 45 559-605 4-48 (108)
65 TIGR02944 suf_reg_Xantho FeS a 59.7 23 0.00049 32.1 5.8 44 561-606 12-57 (130)
66 COG1414 IclR Transcriptional r 59.5 20 0.00044 36.5 6.0 46 561-608 7-53 (246)
67 COG2345 Predicted transcriptio 59.1 13 0.00028 36.9 4.3 43 561-605 14-56 (218)
68 PRK10163 DNA-binding transcrip 58.8 21 0.00045 37.0 6.1 47 560-608 27-74 (271)
69 PF13601 HTH_34: Winged helix 57.9 9.5 0.00021 31.4 2.7 43 561-605 3-45 (80)
70 PF09756 DDRGK: DDRGK domain; 57.7 5.1 0.00011 38.8 1.2 58 657-722 100-157 (188)
71 TIGR02431 pcaR_pcaU beta-ketoa 57.5 23 0.00049 36.1 6.1 44 561-606 12-56 (248)
72 PF08318 COG4: COG4 transport 56.4 2.8E+02 0.006 29.6 16.7 163 254-430 15-214 (331)
73 PF01325 Fe_dep_repress: Iron 56.3 25 0.00055 27.1 4.7 44 563-608 13-56 (60)
74 PRK11014 transcriptional repre 55.9 35 0.00075 31.4 6.4 40 567-608 20-59 (141)
75 PRK09834 DNA-binding transcrip 55.7 23 0.0005 36.5 5.8 46 561-608 14-60 (263)
76 PF10771 DUF2582: Protein of u 55.4 24 0.00052 27.8 4.3 38 561-598 11-48 (65)
77 smart00418 HTH_ARSR helix_turn 54.9 25 0.00053 26.6 4.6 35 570-606 8-42 (66)
78 PF04545 Sigma70_r4: Sigma-70, 54.0 31 0.00067 25.2 4.7 33 561-595 11-43 (50)
79 COG1846 MarR Transcriptional r 53.9 25 0.00055 30.7 5.2 51 556-608 20-70 (126)
80 PF08221 HTH_9: RNA polymerase 51.9 20 0.00044 27.9 3.5 34 569-604 24-57 (62)
81 PF13730 HTH_36: Helix-turn-he 51.7 35 0.00077 25.4 4.8 24 574-597 27-50 (55)
82 cd00092 HTH_CRP helix_turn_hel 50.8 37 0.0008 26.2 5.0 35 571-607 24-58 (67)
83 PF12324 HTH_15: Helix-turn-he 49.6 41 0.00089 27.4 4.9 39 559-597 25-63 (77)
84 PF02002 TFIIE_alpha: TFIIE al 48.0 15 0.00033 31.9 2.6 45 559-605 14-58 (105)
85 smart00418 HTH_ARSR helix_turn 47.6 20 0.00044 27.0 3.0 44 663-715 4-47 (66)
86 PF05158 RNA_pol_Rpc34: RNA po 47.5 14 0.0003 39.4 2.6 143 555-714 81-260 (327)
87 TIGR02844 spore_III_D sporulat 46.4 33 0.00071 28.3 4.0 35 559-594 7-41 (80)
88 PRK10434 srlR DNA-bindng trans 46.2 26 0.00056 36.0 4.3 47 559-607 6-52 (256)
89 PF11994 DUF3489: Protein of u 45.8 47 0.001 26.7 4.6 47 557-603 9-55 (72)
90 PF14394 DUF4423: Domain of un 44.6 58 0.0013 31.1 6.2 54 553-608 19-75 (171)
91 PF09012 FeoC: FeoC like trans 44.6 24 0.00051 28.0 3.0 35 564-598 6-40 (69)
92 smart00421 HTH_LUXR helix_turn 44.3 46 0.001 24.3 4.5 39 557-597 5-43 (58)
93 TIGR00373 conserved hypothetic 43.9 40 0.00088 31.8 4.9 44 560-605 16-59 (158)
94 PF02796 HTH_7: Helix-turn-hel 43.7 38 0.00083 24.3 3.7 31 562-594 13-43 (45)
95 PRK06266 transcription initiat 42.8 35 0.00077 32.9 4.4 45 559-605 23-67 (178)
96 PRK11169 leucine-responsive tr 42.7 38 0.00082 32.1 4.6 48 556-605 12-59 (164)
97 cd06170 LuxR_C_like C-terminal 42.7 51 0.0011 24.2 4.5 39 557-597 2-40 (57)
98 cd07153 Fur_like Ferric uptake 42.6 26 0.00057 30.8 3.3 57 661-720 6-63 (116)
99 COG1349 GlpR Transcriptional r 42.6 33 0.00072 35.1 4.5 47 559-607 6-52 (253)
100 PF08281 Sigma70_r4_2: Sigma-7 41.9 46 0.00099 24.6 4.1 24 571-594 25-48 (54)
101 PF01853 MOZ_SAS: MOZ/SAS fami 40.7 27 0.00059 33.7 3.1 26 572-597 150-175 (188)
102 PF01726 LexA_DNA_bind: LexA D 40.2 66 0.0014 25.3 4.8 51 556-608 4-60 (65)
103 COG1318 Predicted transcriptio 40.1 42 0.0009 31.7 4.1 50 526-596 36-85 (182)
104 PF13412 HTH_24: Winged helix- 39.5 18 0.0004 26.1 1.5 44 658-709 5-48 (48)
105 COG4189 Predicted transcriptio 39.1 47 0.001 32.9 4.5 49 557-607 22-70 (308)
106 PF01726 LexA_DNA_bind: LexA D 38.8 53 0.0011 25.8 4.0 56 653-715 7-63 (65)
107 TIGR02702 SufR_cyano iron-sulf 38.7 68 0.0015 31.5 5.9 44 562-607 5-48 (203)
108 PRK11179 DNA-binding transcrip 38.6 48 0.001 31.0 4.5 48 556-605 7-54 (153)
109 PF00325 Crp: Bacterial regula 38.5 45 0.00098 22.2 3.0 26 572-597 2-27 (32)
110 cd07377 WHTH_GntR Winged helix 38.4 74 0.0016 24.2 5.0 38 568-607 20-58 (66)
111 PF07106 TBPIP: Tat binding pr 38.2 2.5E+02 0.0054 26.6 9.5 59 560-624 3-64 (169)
112 PF00196 GerE: Bacterial regul 37.6 52 0.0011 24.9 3.8 40 556-597 4-43 (58)
113 PRK13509 transcriptional repre 37.5 52 0.0011 33.6 5.0 47 559-607 6-52 (251)
114 PF02186 TFIIE_beta: TFIIE bet 36.6 22 0.00049 28.0 1.6 54 658-722 7-61 (65)
115 PRK10681 DNA-binding transcrip 36.4 48 0.001 33.9 4.5 39 559-597 8-46 (252)
116 COG1522 Lrp Transcriptional re 36.2 63 0.0014 29.9 5.0 49 556-606 6-54 (154)
117 PRK00215 LexA repressor; Valid 36.1 75 0.0016 31.2 5.7 51 556-608 2-58 (205)
118 COG1654 BirA Biotin operon rep 35.9 1.1E+02 0.0023 25.2 5.5 41 565-605 12-52 (79)
119 smart00344 HTH_ASNC helix_turn 35.0 26 0.00057 30.3 2.0 46 657-710 4-49 (108)
120 KOG1086 Cytosolic sorting prot 33.5 1.2E+02 0.0027 32.9 6.8 92 8-114 22-121 (594)
121 PF12802 MarR_2: MarR family; 33.5 21 0.00045 27.2 1.0 45 661-713 10-56 (62)
122 COG4190 Predicted transcriptio 33.5 1.3E+02 0.0029 27.2 6.0 67 558-626 64-133 (144)
123 PRK13239 alkylmercury lyase; P 33.2 75 0.0016 31.3 4.9 40 558-597 22-61 (206)
124 smart00762 Cog4 COG4 transport 33.1 6.2E+02 0.013 26.9 15.8 160 254-427 15-205 (324)
125 KOG2747 Histone acetyltransfer 33.0 54 0.0012 35.5 4.2 64 532-597 282-354 (396)
126 TIGR02404 trehalos_R_Bsub treh 32.8 27 0.00059 35.1 2.0 35 684-719 30-64 (233)
127 PF01047 MarR: MarR family; I 32.2 17 0.00036 27.6 0.3 44 661-712 8-51 (59)
128 PF04967 HTH_10: HTH DNA bindi 32.1 90 0.0019 23.5 4.1 31 566-596 17-47 (53)
129 cd06171 Sigma70_r4 Sigma70, re 32.1 95 0.0021 22.0 4.5 40 556-596 11-50 (55)
130 PF06784 UPF0240: Uncharacteri 31.9 79 0.0017 30.5 4.8 64 529-597 96-161 (179)
131 PF00165 HTH_AraC: Bacterial r 31.7 65 0.0014 22.5 3.3 28 570-597 6-33 (42)
132 PRK09802 DNA-binding transcrip 31.5 63 0.0014 33.4 4.5 48 558-607 17-64 (269)
133 smart00420 HTH_DEOR helix_turn 31.5 33 0.00071 24.8 1.8 43 662-712 6-48 (53)
134 PRK10906 DNA-binding transcrip 31.4 67 0.0014 32.9 4.6 47 559-607 6-52 (252)
135 PF00392 GntR: Bacterial regul 31.1 27 0.00059 27.1 1.3 34 684-718 30-63 (64)
136 PF13542 HTH_Tnp_ISL3: Helix-t 30.8 1.1E+02 0.0025 22.2 4.6 35 559-595 16-50 (52)
137 PRK09334 30S ribosomal protein 30.8 35 0.00075 28.5 1.9 37 686-722 49-85 (86)
138 KOG3054 Uncharacterized conser 30.8 44 0.00095 33.3 2.8 54 661-722 205-258 (299)
139 PRK04424 fatty acid biosynthes 30.6 63 0.0014 31.3 4.0 40 558-597 7-46 (185)
140 PF06163 DUF977: Bacterial pro 30.5 47 0.001 29.8 2.7 52 654-713 10-61 (127)
141 PLN03238 probable histone acet 30.5 79 0.0017 32.7 4.8 38 559-596 209-247 (290)
142 TIGR00498 lexA SOS regulatory 30.4 1E+02 0.0022 30.1 5.5 50 556-607 4-59 (199)
143 PRK11402 DNA-binding transcrip 30.1 32 0.00069 34.8 2.0 35 684-719 39-73 (241)
144 PHA03103 double-strand RNA-bin 29.8 1.1E+02 0.0024 29.6 5.3 45 562-608 17-61 (183)
145 smart00531 TFIIE Transcription 29.6 62 0.0013 30.0 3.7 30 569-598 12-41 (147)
146 PF13384 HTH_23: Homeodomain-l 29.5 59 0.0013 23.5 2.9 32 563-596 10-41 (50)
147 PRK04172 pheS phenylalanyl-tRN 29.1 77 0.0017 35.9 5.0 50 555-606 3-52 (489)
148 smart00345 HTH_GNTR helix_turn 28.8 38 0.00083 25.3 1.8 28 686-713 28-55 (60)
149 PF01638 HxlR: HxlR-like helix 28.6 95 0.0021 26.0 4.3 45 560-607 7-52 (90)
150 TIGR01714 phage_rep_org_N phag 28.0 91 0.002 27.8 4.2 48 558-607 29-84 (119)
151 PF09681 Phage_rep_org_N: N-te 27.9 74 0.0016 28.5 3.7 38 568-607 49-86 (121)
152 TIGR02325 C_P_lyase_phnF phosp 27.9 36 0.00078 34.2 1.9 34 685-719 39-72 (238)
153 PHA02591 hypothetical protein; 27.9 73 0.0016 25.9 3.1 25 571-595 58-82 (83)
154 PRK10079 phosphonate metabolis 27.7 37 0.0008 34.3 2.0 51 661-719 25-75 (241)
155 PF09904 HTH_43: Winged helix- 27.7 1E+02 0.0022 25.9 4.1 38 565-603 15-52 (90)
156 PF03444 HrcA_DNA-bdg: Winged 27.6 2.1E+02 0.0045 23.5 5.7 48 559-608 10-57 (78)
157 PRK10411 DNA-binding transcrip 26.5 89 0.0019 31.7 4.5 40 559-598 5-44 (240)
158 cd07977 TFIIE_beta_winged_heli 26.4 48 0.001 26.9 2.0 58 655-722 8-70 (75)
159 TIGR03433 padR_acidobact trans 26.3 1E+02 0.0022 26.5 4.1 53 657-710 5-57 (100)
160 PF09763 Sec3_C: Exocyst compl 26.3 1.2E+03 0.025 27.9 20.0 132 179-343 551-701 (701)
161 PF06163 DUF977: Bacterial pro 25.4 1.3E+02 0.0028 27.1 4.5 48 558-607 12-59 (127)
162 COG2188 PhnF Transcriptional r 25.4 42 0.0009 34.0 1.8 36 683-719 36-71 (236)
163 PF04182 B-block_TFIIIC: B-blo 25.3 1.1E+02 0.0023 24.8 3.9 48 558-607 2-51 (75)
164 PRK14999 histidine utilization 25.3 41 0.0009 34.0 1.8 47 664-719 29-76 (241)
165 COG4742 Predicted transcriptio 25.2 1.2E+02 0.0027 31.0 5.1 42 563-607 18-59 (260)
166 PF04760 IF2_N: Translation in 25.1 48 0.001 24.8 1.7 23 571-593 2-24 (54)
167 PF08672 APC2: Anaphase promot 24.7 61 0.0013 25.1 2.2 52 661-712 2-55 (60)
168 COG3355 Predicted transcriptio 24.4 92 0.002 28.1 3.6 40 665-712 37-76 (126)
169 TIGR01889 Staph_reg_Sar staphy 24.3 56 0.0012 28.5 2.2 42 667-716 40-83 (109)
170 PF13730 HTH_36: Helix-turn-he 24.3 48 0.001 24.6 1.6 21 688-708 35-55 (55)
171 PF02270 TFIIF_beta: Transcrip 24.3 99 0.0021 32.1 4.4 57 559-625 217-273 (275)
172 PRK11050 manganese transport r 23.8 1.3E+02 0.0029 28.0 4.7 43 562-606 41-83 (152)
173 PLN02999 photosystem II oxygen 23.7 5.6E+02 0.012 24.6 8.6 62 42-115 126-189 (190)
174 PF14947 HTH_45: Winged helix- 23.7 1.7E+02 0.0036 23.7 4.8 43 560-605 8-50 (77)
175 PRK03902 manganese transport t 23.3 1.4E+02 0.0029 27.4 4.7 43 562-606 12-54 (142)
176 PLN03239 histone acetyltransfe 23.1 1.2E+02 0.0025 32.5 4.5 38 559-596 267-308 (351)
177 PF12395 DUF3658: Protein of u 23.0 1.1E+02 0.0024 26.9 3.8 48 671-720 62-109 (111)
178 PF10007 DUF2250: Uncharacteri 22.7 1.6E+02 0.0035 25.0 4.5 53 554-608 3-55 (92)
179 TIGR00721 tfx DNA-binding prot 22.7 1.5E+02 0.0032 27.2 4.6 39 556-596 7-45 (137)
180 PRK13719 conjugal transfer tra 22.4 1.5E+02 0.0032 29.5 4.9 41 555-597 143-183 (217)
181 PF00356 LacI: Bacterial regul 22.4 1.1E+02 0.0023 22.3 2.9 21 574-594 1-21 (46)
182 COG1522 Lrp Transcriptional re 22.1 65 0.0014 29.8 2.3 50 655-712 7-56 (154)
183 smart00347 HTH_MARR helix_turn 22.0 93 0.002 25.9 3.1 47 658-712 12-58 (101)
184 PHA02701 ORF020 dsRNA-binding 22.0 1.9E+02 0.0042 27.8 5.4 45 561-607 7-52 (183)
185 TIGR02018 his_ut_repres histid 21.8 54 0.0012 32.9 1.8 33 686-719 33-65 (230)
186 PRK03573 transcriptional regul 21.7 62 0.0013 29.7 2.1 26 687-712 55-80 (144)
187 KOG2905 Transcription initiati 21.6 1.2E+02 0.0026 30.4 4.0 56 561-626 189-244 (254)
188 PF00392 GntR: Bacterial regul 21.6 1.3E+02 0.0029 23.1 3.7 39 568-608 19-58 (64)
189 PF09860 DUF2087: Uncharacteri 21.6 1.1E+02 0.0025 24.5 3.2 45 665-718 24-68 (71)
190 PF13545 HTH_Crp_2: Crp-like h 21.4 1.7E+02 0.0038 23.1 4.5 34 572-607 28-61 (76)
191 COG2197 CitB Response regulato 21.3 1.4E+02 0.0031 29.4 4.8 42 555-598 148-189 (211)
192 cd07377 WHTH_GntR Winged helix 21.1 68 0.0015 24.4 1.9 28 685-712 32-59 (66)
193 PF09114 MotA_activ: Transcrip 21.0 1.5E+02 0.0033 24.8 3.8 47 561-609 19-67 (96)
194 PF01399 PCI: PCI domain; Int 21.0 1.6E+02 0.0035 24.7 4.5 40 559-598 47-86 (105)
195 COG1321 TroR Mn-dependent tran 21.0 1.7E+02 0.0038 27.4 4.9 45 562-608 14-58 (154)
196 PRK09764 DNA-binding transcrip 20.9 61 0.0013 32.7 2.0 33 686-719 37-69 (240)
197 PF04539 Sigma70_r3: Sigma-70 20.6 1E+02 0.0022 24.8 2.9 26 571-596 19-44 (78)
198 COG2771 CsgD DNA-binding HTH d 20.4 2.4E+02 0.0052 21.2 5.0 41 555-597 4-44 (65)
199 TIGR02989 Sig-70_gvs1 RNA poly 20.4 1.3E+02 0.0029 27.6 4.1 38 556-595 112-150 (159)
200 PF09107 SelB-wing_3: Elongati 20.4 2.1E+02 0.0045 21.3 4.1 41 565-607 3-43 (50)
201 PF10668 Phage_terminase: Phag 20.1 1.4E+02 0.003 23.2 3.2 22 569-590 19-40 (60)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.4e-119 Score=1013.31 Aligned_cols=703 Identities=67% Similarity=1.104 Sum_probs=651.2
Q ss_pred CCCCCCHHHhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhccccc
Q 004939 2 DRKTIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPS 81 (722)
Q Consensus 2 ~~~~~~fd~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~~~LY~~l~~~l~~~l~~~~~~~ 81 (722)
-+.+.+|+..|+.++++++++.+..++-....++.-+++.+|+++|++|+++++.+..++||+++++++.+|+.+.+.+.
T Consensus 4 ~~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~ 83 (725)
T KOG2166|consen 4 APKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPA 83 (725)
T ss_pred cccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 35778999999999999999998876433335778889999999999999996555569999999999999999988777
Q ss_pred ccccCchHHHHHHHHHHHHHHHHHHHHHHhhchhhHhhhhcC-CCCcHHHHH-HHHHHH-----------------HHHH
Q 004939 82 LSEKHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARR-SLPALNEVG-LTCFRE-----------------QIDK 142 (722)
Q Consensus 82 l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~-~~~~i~~l~-l~lf~~-----------------~I~~ 142 (722)
.....++.+|..+...|.+|+.++.+++++|+||||+||++. +..++++++ +.+|+. +|..
T Consensus 84 ~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~~ 163 (725)
T KOG2166|consen 84 LREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIHK 163 (725)
T ss_pred HHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHHh
Confidence 777788899999999999999999999999999999999865 555555544 333322 7899
Q ss_pred HhcCCccCHHHHHHHHHHHHHhcccchhchHHHHHHHHHHHHHHHHHHHHHhhHhcCChhHHHHHHHHHHHHHHHHHchh
Q 004939 143 EREGEQIDRALLKNVLDIFVEIGMGQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHY 222 (722)
Q Consensus 143 ~R~g~~i~~~~i~~~i~~~~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~ 222 (722)
+|.|+.||+..|+++++|++.+|.+..++|...||++|++.|..||..+++.|+...++++|+.+|+.++.+|..|+..|
T Consensus 164 eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~y 243 (725)
T KOG2166|consen 164 EREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHY 243 (725)
T ss_pred hcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999988999999999999999999999999999998899999999999999999999999
Q ss_pred cCCCchHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhhcCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHHHHHHHh
Q 004939 223 LHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQ 302 (722)
Q Consensus 223 l~~~t~~~l~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~i~~~ 302 (722)
++..+.+++.+.+...++..+++.+++..++|+..|+.+++.++|.+||+|++++++|++++++.|+.|++.+|..++..
T Consensus 244 l~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r 323 (725)
T KOG2166|consen 244 LHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVAR 323 (725)
T ss_pred hhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999888877
Q ss_pred hHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHhhc
Q 004939 303 AEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKK 382 (722)
Q Consensus 303 ~~~~~~~~~~~~~~~~~~~~I~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~e~La~y~d~~lk~ 382 (722)
..... ..+|..++..+++++++|..++..||.++..|..+++.||..|+|.+... .+|+||+|||.++|+
T Consensus 324 ~~~~~--------~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~--~~E~la~y~D~~lkk 393 (725)
T KOG2166|consen 324 PAETA--------ATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVAT--SAELLATYCDDILKK 393 (725)
T ss_pred hhhhc--------ccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCC--cHHHHHHHhHHHhcc
Confidence 65432 15789999999999999999999999999999999999999999998632 269999999999999
Q ss_pred CCCCCCChHHHHHHHHHHhhheecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcchhhHhHHHHHHhH
Q 004939 383 GGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDL 462 (722)
Q Consensus 383 ~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~ 462 (722)
+ ..+.++++++..+++++.+|+|+.+||+|+.+|+++||+|||+++|.|+++|+.||.+|+++||.+||.+|++|++|+
T Consensus 394 ~-~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~ 472 (725)
T KOG2166|consen 394 G-SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDL 472 (725)
T ss_pred c-ccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccH
Confidence 4 466789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEE
Q 004939 463 TLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCN 542 (722)
Q Consensus 463 ~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~ 542 (722)
..|++++..|.++. +.....+++|.|.|||.|+||.+++.++.||++|.++++.|.+||..+|+||+|.|+|++|.|+
T Consensus 473 ~~s~~l~~~F~~~~--~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~e 550 (725)
T KOG2166|consen 473 TLSRELQTAFADYA--NYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGE 550 (725)
T ss_pred HHHHHHHHHHHhhh--chhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceE
Confidence 99999999999871 1222357999999999999999888889999999999999999999999999999999999999
Q ss_pred EEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEec
Q 004939 543 INGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFN 622 (722)
Q Consensus 543 i~~~~~~~~~~l~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N 622 (722)
|.++|.+++++|+|||+||+||++||+.+.+|+++|.+.|+++.+++.++|+||++.|.+++.+ |.++. ++++.|.+|
T Consensus 551 i~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N 628 (725)
T KOG2166|consen 551 INGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFN 628 (725)
T ss_pred EEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEee
Confidence 9999999999999999999999999999999999999999999999999999999888677766 66666 889999999
Q ss_pred ccCCCCCcceeccCCChhhhhhHHHhHHHhhhhhhhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhh
Q 004939 623 SKFTDRMRRIKIPLPPVDERKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDL 702 (722)
Q Consensus 623 ~~f~~~~~~i~i~~~~~~e~~~~~~~v~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~L 702 (722)
.+|+++++|++++.++.++.+.+.+.+++||+..|+||||||||+||.+.|++|+.||++|++++|.|++.+||+|||.|
T Consensus 629 ~~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~L 708 (725)
T KOG2166|consen 629 SKFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDL 708 (725)
T ss_pred ccccCcceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHH
Confidence 99999999999998887788888999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcccCCCCCceee
Q 004939 703 ITRDYLERDKENPNMFRY 720 (722)
Q Consensus 703 iereyl~r~~~d~~~y~Y 720 (722)
||||||+|| +|+++|+|
T Consensus 709 IEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 709 IEREYLERD-ENPNIYRY 725 (725)
T ss_pred HHHHHHhcc-CCCCcccC
Confidence 999999999 89999998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.4e-112 Score=910.85 Aligned_cols=706 Identities=31% Similarity=0.532 Sum_probs=619.0
Q ss_pred CCCCCHHHhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHhhhhccCCCCC------------chHHHHHHHHHHH
Q 004939 3 RKTIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHD------------YSQQLYDKYKQAF 70 (722)
Q Consensus 3 ~~~~~fd~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~------------~~~~LY~~l~~~l 70 (722)
.+..||+.+|..+++||++|+.-|.. ++....||++|+.+|+.|+++.+.- .+..||+++....
T Consensus 15 ~~~~df~~~W~~i~~~I~~I~~~l~~----~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~ 90 (773)
T COG5647 15 LSEEDFESTWEFIERAIGQIFERLYD----SMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYA 90 (773)
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHHh----hhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999865543 3556779999999999999985421 3888999999999
Q ss_pred HHHHHhcccccccccCchHHHHHHHHHHHHHHHHHHHHHHhhchhhHhhhhcCC-----CCcHHHHHHHHHHH-------
Q 004939 71 EEYISSMVLPSLSEKHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARRS-----LPALNEVGLTCFRE------- 138 (722)
Q Consensus 71 ~~~l~~~~~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~-----~~~i~~l~l~lf~~------- 138 (722)
+.|+...-. ..+....+.||..++..|++|..++.+++.+|.||||+|++..+ ...++++++..|+.
T Consensus 91 k~~i~~~~~-~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~ 169 (773)
T COG5647 91 KNYIEEYNR-GRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIV 169 (773)
T ss_pred HHHHHHhcc-cccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhh
Confidence 999987532 23333457899999999999999999999999999999999322 23455667766665
Q ss_pred ---------HHHHHhcCCccCHHHHHHHHHHHHHhcc------cchhchHHHHHHHHHHHHHHHHHHHHHhhHhcCChhH
Q 004939 139 ---------QIDKEREGEQIDRALLKNVLDIFVEIGM------GQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPE 203 (722)
Q Consensus 139 ---------~I~~~R~g~~i~~~~i~~~i~~~~~l~~------~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~ 203 (722)
.+.+.|.|+.||+..+..++.|+..++. .++.+|.+.|||.||+.|.+||..++++.+...++.+
T Consensus 170 ~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~e 249 (773)
T COG5647 170 DSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTE 249 (773)
T ss_pred HHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHH
Confidence 5788999999999999999999999964 3468999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHchhcCCCchHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhhcCcHHHHHHHHHhhccCCCChHH
Q 004939 204 YMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEP 283 (722)
Q Consensus 204 Yl~~v~~~l~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~~~l~~ 283 (722)
||.+|..++++|..+++.|++.++..++.++++++||..|.+.|.+.. +|+..++.....+.|+.||+++++++.++.+
T Consensus 250 yL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~-s~f~~~~d~~~~e~l~~lY~l~se~~~~v~p 328 (773)
T COG5647 250 YLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQG-SGFREALDASNLEKLQVLYRLLSETKYGVQP 328 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhch-HHHHHHHHhhhHHHHHHHHHHhhhhhhhhhh
Confidence 999999999999999999999999999999999999999999997654 8999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhHHHhhh-cC----CCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHH
Q 004939 284 VANVFKQHITAEGTVLVQQAEDAATN-QG----GSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIF 358 (722)
Q Consensus 284 l~~~~~~~i~~~g~~i~~~~~~~~~~-~~----~~~~~~~~~~~I~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~ 358 (722)
|.+.|..||...|.-+ +.....+.. +. -......+..+++.++++++.+..++.+.|.+|..+..++++||..|
T Consensus 329 l~~~f~~yV~~~g~~~-~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~f 407 (773)
T COG5647 329 LQEVFERYVKDEGVLI-NIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTF 407 (773)
T ss_pred HHHHHHHHHHhhchhh-hhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHH
Confidence 9999999999999222 222111110 00 00013468899999999999999999999999999999999999999
Q ss_pred hhCCCC-CCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhheecccChhHHHHHHHHHHHHHhcCCCCCChHHHH
Q 004939 359 CNKAVG-GSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHER 437 (722)
Q Consensus 359 ~N~~~~-~~~~~e~La~y~d~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~ 437 (722)
+|.+.+ ...++|+||+|+|.+||++++ ......++..+.+++.||+|+.+||+|+++|+++||||||+++|++.+.|.
T Consensus 408 in~~~sa~~~~~e~Laky~D~~lkk~~k-~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~ 486 (773)
T COG5647 408 INGNESADSGPSEYLAKYIDGLLKKDGK-QSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAEL 486 (773)
T ss_pred hccccccccccHHHHHHHhHHHhhcccc-ccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHH
Confidence 998542 357899999999999998652 222345777889999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcchhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCccCChhHHHHH
Q 004939 438 SILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKS-SDLNLPSEMVKCV 516 (722)
Q Consensus 438 ~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~-~~~~lP~~l~~~~ 516 (722)
.||++||+.||.+||+|+++||+||..|.++...|++...+ ..+.+++.|.||+..+||..|. ..+.||++|.+.+
T Consensus 487 ~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s---~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~l 563 (773)
T COG5647 487 KMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQS---YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPIL 563 (773)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchh---hccccchhHHHHHHhcCCCCccccccCCChHHHHHH
Confidence 99999999999999999999999999999999998764321 1257899999999999996554 5799999999999
Q ss_pred HHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEE---EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHH
Q 004939 517 EVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELI---VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLL 593 (722)
Q Consensus 517 ~~F~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~---~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L 593 (722)
+.|++||..+|+||+|.|.|+||+|+|++.|+.+++.+. ++++|+.|+++||+++++|+++|.+.|+++.++++++|
T Consensus 564 e~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L 643 (773)
T COG5647 564 EGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVL 643 (773)
T ss_pred HHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHH
Confidence 999999999999999999999999999999997754444 56789999999999999999999999999999999999
Q ss_pred hHhhhcccceeecCCCCCCCCCCCeEEecccCCCCCcceeccCCCh----hhhhhHHHhHHHhhhhhhhhheeeccccCc
Q 004939 594 HSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV----DERKKIVEDVDKDRRYAIDAALVRIMKSRK 669 (722)
Q Consensus 594 ~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~v~~~r~~~i~A~IVRimK~~k 669 (722)
+||+++|..++.+ +++.+++++.|.+|.+|+++..+|+++.+.. ++...+++.+++||+..++||||||||+||
T Consensus 644 ~sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk 721 (773)
T COG5647 644 QSLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARK 721 (773)
T ss_pred HHHHhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999876555554 4778899999999999999999999987654 345567788999999999999999999999
Q ss_pred cCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 670 VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 670 ~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
+|+|++|+++|+.+.+.||.|++.+||++|+.|||||||+|.++| .+|+|+|
T Consensus 722 ~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 722 KLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred cCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999999999999999999999999999999999999988 8999997
No 3
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.5e-107 Score=855.21 Aligned_cols=631 Identities=35% Similarity=0.618 Sum_probs=587.9
Q ss_pred HHHHHHHHHHHHHHhccccccccc-CchHHHHHHHHHHHHHHHHHHHHHHhhchhhHhhhhcC--CCCcHHHHHHHHHHH
Q 004939 62 LYDKYKQAFEEYISSMVLPSLSEK-HDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARR--SLPALNEVGLTCFRE 138 (722)
Q Consensus 62 LY~~l~~~l~~~l~~~~~~~l~~~-~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~--~~~~i~~l~l~lf~~ 138 (722)
||+.++..+++|+.+.+...-.+. +...+|..+.++|..|...+.+++.+|.||||.|+... .++|+|++++.+||.
T Consensus 2 ly~~l~~~~~~~~~~~~~q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp~v~siWem~l~LFR~ 81 (661)
T KOG2167|consen 2 LYKQLRQICEQHIKAQIEQLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNPYVLSIWEMGLQLFRA 81 (661)
T ss_pred hHHHHHHHHHHHHHHHHhhCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCCCcCCHHHhhHHHHHH
Confidence 899999999999987654222222 23579999999999999999999999999999999873 478999999999998
Q ss_pred --------------------HHHHHhcCCccCHHHHHHHHHHHHHhcccchhchHHHHHHHHHHHHHHHHHHHHHhhHhc
Q 004939 139 --------------------QIDKEREGEQIDRALLKNVLDIFVEIGMGQMDSYEKDFEEHMLQDTGAYYSRKASNWILE 198 (722)
Q Consensus 139 --------------------~I~~~R~g~~i~~~~i~~~i~~~~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~ 198 (722)
.+.++|.|+++|+.+++.++.|+.++ ..|.+.|++.|++.+.++|.+++....++
T Consensus 82 ~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~-----~iY~esF~~~fls~f~~lY~aE~~d~~Qe 156 (661)
T KOG2167|consen 82 HFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDL-----QIYKESFELTFLSLFRELYAAEGQDKRQE 156 (661)
T ss_pred HhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHH-----HhhhhhhHHHHHHHHHHHHHHHhcchhhh
Confidence 68999999999999999999999984 68999999999999999999999999999
Q ss_pred CChhHHHHHHHHHHHHHHHHHchhcCCCchHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhhcCcHHHHHHHHHhhccCC
Q 004939 199 DSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKIP 278 (722)
Q Consensus 199 ~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~ 278 (722)
..+++||++++.++.+|..|+..+++.+|...+..+++..|+..|++.|+.+ |+..+++.++..++.+||.|++++.
T Consensus 157 l~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~k---gl~~lvDm~q~~d~~rly~L~~r~~ 233 (661)
T KOG2167|consen 157 LEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTK---GLDSLVDMRQTSDLTRLYMLFSRVQ 233 (661)
T ss_pred cccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhc---chHHhhhhhhccchHhHHHHHHHHh
Confidence 9999999999999999999999999999977799999999999999999876 8999999999999999999999998
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCC--hHHHHHHHHHHH
Q 004939 279 KGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINH--TLFHKALKEAFE 356 (722)
Q Consensus 279 ~~l~~l~~~~~~~i~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~I~~ll~l~~~~~~l~~~~F~~~--~~f~~~l~~af~ 356 (722)
++...++..|++|+++.|..++.... .+..+|+.+++++++.+-++..||..+ ..|..++++||+
T Consensus 234 ~g~l~l~qq~sdylk~~G~KlV~de~-------------kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe 300 (661)
T KOG2167|consen 234 GGQLSLLQQWSDYLKKPGFKLVIDEE-------------KDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFE 300 (661)
T ss_pred cchHHHHHHHHHHHhcccceeccCch-------------hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 89899999999999999999986432 256899999999999999999999988 899999999999
Q ss_pred HHhhCCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhheecccChhHHHHHHHHHHHHHhcCCCCCChHHH
Q 004939 357 IFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHE 436 (722)
Q Consensus 357 ~~~N~~~~~~~~~e~La~y~d~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E 436 (722)
.|+|+.. +++|++||+|.|..|+.|. ...++++++..++.++.||+||..||+|+.+|++.||+|||.++|++.++|
T Consensus 301 ~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae 377 (661)
T KOG2167|consen 301 TFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAE 377 (661)
T ss_pred HHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcch
Confidence 9999764 5799999999999999864 456788899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcchhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCChhHHHHH
Q 004939 437 RSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCV 516 (722)
Q Consensus 437 ~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~ 516 (722)
.+|+.+|+.+||..||++|++|++||..|++++..|+.+..++.....++ +.+.|+|.++||.+++.++.||++|.+++
T Consensus 378 ~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~ 456 (661)
T KOG2167|consen 378 KSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQ 456 (661)
T ss_pred hHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHH
Confidence 99999999999999999999999999999999999999865544333445 99999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 517 EVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 517 ~~F~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
+.|..||..+|.||+|.|.+++|+|.+++.|..|+.+|.+|++|++||++||+++++|++||.+.|+|.+.+|.++|+||
T Consensus 457 e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl 536 (661)
T KOG2167|consen 457 EIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSL 536 (661)
T ss_pred HHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccceeecCCCCCCCCCCCeEEecccCCCCCcceeccCCCh----hhhhhHHHhHHHhhhhhhhhheeeccccCccCC
Q 004939 597 SCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV----DERKKIVEDVDKDRRYAIDAALVRIMKSRKVLG 672 (722)
Q Consensus 597 ~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~v~~~r~~~i~A~IVRimK~~k~l~ 672 (722)
.|+|.++|.+.|.|+.+.+++.|.+|..|+++..||+|+.+.. +|.+.|.++|.+||.+.||||||||||+||+|+
T Consensus 537 ~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~ 616 (661)
T KOG2167|consen 537 ACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLS 616 (661)
T ss_pred hcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999999999999999999999987654 456778899999999999999999999999999
Q ss_pred hhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 673 HQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 673 ~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
|+.|+.++.++++ |+..+ ++|+|||+||+|||++|| +| +.|.|||
T Consensus 617 h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 617 HNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred hhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 9999999999997 98888 999999999999999999 44 9999998
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7e-106 Score=805.57 Aligned_cols=664 Identities=28% Similarity=0.521 Sum_probs=604.7
Q ss_pred CCCCCCHHHhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhccccc
Q 004939 2 DRKTIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPS 81 (722)
Q Consensus 2 ~~~~~~fd~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~~~LY~~l~~~l~~~l~~~~~~~ 81 (722)
-|++++||++|..|.+.|..|... +.+.+..|..-|+.||.+|... |.+-|+.||+..+.++++|++.+....
T Consensus 5 kp~vv~fd~~w~~l~~si~~ii~l------~~i~~~~w~~~fsdvy~icvs~-p~pl~erly~e~k~~i~~hvrq~~~~~ 77 (728)
T KOG2284|consen 5 KPKVVEFDKVWVQLRPSIIDIINL------RPITNVQWHHKFSDVYDICVSI-PTPLSERLYNEVKACIQEHVRQKRQDI 77 (728)
T ss_pred CceeeeHHHHHHHHHHHHHHHHhc------cchhccccccchhhHHHHHHhC-CCchhHHHHHHHHHHHHHHHHHHhhhh
Confidence 478899999999999999887542 3577888999999999999998 677899999999999999999765433
Q ss_pred ccccCchHHHHHHHHHHHHHHHHHHHHHHhhchhhHhhhhcCCC---------------Cc---HHHHHHHHHHH-----
Q 004939 82 LSEKHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARRSL---------------PA---LNEVGLTCFRE----- 138 (722)
Q Consensus 82 l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~~---------------~~---i~~l~l~lf~~----- 138 (722)
. ..+++.+|..|.+.|+.|..+..++..+|.||+..|++.++. ++ |..+|+.+||+
T Consensus 78 v-~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~~ 156 (728)
T KOG2284|consen 78 V-DVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVKT 156 (728)
T ss_pred h-cCCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHHH
Confidence 3 334456999999999999999999999999999999998642 33 44678999998
Q ss_pred -----------HHHHHhcCCccC-HHHHHHHHHHHHHhcc-----------------cchhchHHHHHHHHHHHHHHHHH
Q 004939 139 -----------QIDKEREGEQID-RALLKNVLDIFVEIGM-----------------GQMDSYEKDFEEHMLQDTGAYYS 189 (722)
Q Consensus 139 -----------~I~~~R~g~~i~-~~~i~~~i~~~~~l~~-----------------~~~~~Y~~~FE~~~L~~t~~yY~ 189 (722)
.|.++|.|+..+ ...+.++|+.|+.+.. ....+|++.||.|||.+|.+||+
T Consensus 157 i~~~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~ 236 (728)
T KOG2284|consen 157 ILPQLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYS 236 (728)
T ss_pred HHHHHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHH
Confidence 478899999887 6689999999998753 13578999999999999999999
Q ss_pred HHHHhhHhcCChhHHHHHHHHHHHHHHHHHchhcCCCchHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhhcCcHHHHHH
Q 004939 190 RKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSR 269 (722)
Q Consensus 190 ~~s~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ 269 (722)
++++..+.+.+|++|+.+|..++++|+-||+.|||+|+..+++..|++.+|..|.+.|- ..|+.++.+.+..|++.
T Consensus 237 ~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~lh----a~ch~~i~~e~~~d~~n 312 (728)
T KOG2284|consen 237 ALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKLH----AVCHDLITNEENKDLRN 312 (728)
T ss_pred HHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHH----HHHHHHHhhhhhhhHHH
Confidence 99999999999999999999999999999999999999999999999999999998873 46899999999999999
Q ss_pred HHHhhccCCCChHHHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHH
Q 004939 270 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHK 349 (722)
Q Consensus 270 ly~L~~~~~~~l~~l~~~~~~~i~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~I~~ll~l~~~~~~l~~~~F~~~~~f~~ 349 (722)
||+|++.+..|+..+.+.|..||...|...++....+ +-|..||+.++.+|.+|.+++...|.+|..|..
T Consensus 313 my~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~e----------n~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s 382 (728)
T KOG2284|consen 313 MYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGE----------NVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSS 382 (728)
T ss_pred HHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhccc----------cchHHHHHHHHHHHHHHHHHHHHHhcCchhhhH
Confidence 9999999999999999999999999999999876443 458999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCC---CCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhheecccChhHHHHHHHHHHHHHhc
Q 004939 350 ALKEAFEIFCNKAVG---GSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLL 426 (722)
Q Consensus 350 ~l~~af~~~~N~~~~---~~~~~e~La~y~d~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL 426 (722)
+++.|+..++|...+ -.+.+|.||+|||.+|+++. .++++.+++..|+..+.+|+|++|||+|.++|.++||+||+
T Consensus 383 ~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~-kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli 461 (728)
T KOG2284|consen 383 GLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKST-KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLI 461 (728)
T ss_pred HHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhh-cCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHH
Confidence 999999999997764 34789999999999999964 57899999999999999999999999999999999999999
Q ss_pred CCCCCChHHHHHHHHHHHHhhcchhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCc
Q 004939 427 FDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDL 506 (722)
Q Consensus 427 ~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~ 506 (722)
.+.|.|.|.|..||++||+.||++||+++- +.|++.|.+++++|.+.+. +|
T Consensus 462 ~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~---------------------------nf 512 (728)
T KOG2284|consen 462 ASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIA---------------------------NF 512 (728)
T ss_pred hhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHH---------------------------hc
Confidence 999999999999999999999999999998 9999999999999987654 27
Q ss_pred cCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCH
Q 004939 507 NLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTH 586 (722)
Q Consensus 507 ~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~ 586 (722)
.+|.+|+...+.|+.||..+|+||+|+|++.++++++++++-++.|.-.+.++||++||+||..+.+++.||.+.+|++.
T Consensus 513 ~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~ 592 (728)
T KOG2284|consen 513 HLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSG 592 (728)
T ss_pred cchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccH
Confidence 89999999999999999999999999999999999999999989998899999999999999999999999999999999
Q ss_pred HHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccCCCCCcceeccCCCh-----hhhhhHHHhHHHhhhhhhhhhe
Q 004939 587 DDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV-----DERKKIVEDVDKDRRYAIDAAL 661 (722)
Q Consensus 587 ~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~-----~e~~~~~~~v~~~r~~~i~A~I 661 (722)
+.|.+.+.++.. .++|... +..+..+..|++|.+|+++..+.++..|.. +|.+.+...+.+||++.++|||
T Consensus 593 ~~l~kti~tild--v~~~~~d--~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~ai 668 (728)
T KOG2284|consen 593 DYLLKTIRTILD--VTLLTCD--DQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAI 668 (728)
T ss_pred HHHHHHHHHHHh--ceeeccc--ccccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHH
Confidence 999999999974 5677654 345667788999999999999999987653 3455567789999999999999
Q ss_pred eeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 662 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 662 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
|||||+||.+.|+.|+.+|+.|.+++|.|++++||+|||.||++-||+|.+.+ +.|.|+|
T Consensus 669 vrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 669 VRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 99999999999999999999999999999999999999999999999999875 8999997
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.8e-89 Score=693.47 Aligned_cols=697 Identities=27% Similarity=0.462 Sum_probs=614.0
Q ss_pred CCCHHHhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccc
Q 004939 5 TIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPSLSE 84 (722)
Q Consensus 5 ~~~fd~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~~~LY~~l~~~l~~~l~~~~~~~l~~ 84 (722)
..-||+.|+...|.+.++.+ +++++++.|..||.+||.+|.+. .....++|+.++..+.+|+.+.-.+..+.
T Consensus 10 r~qFee~W~~~rpIVlkLLr------Q~sVt~~~WqDLF~~Vh~vclWd--dkGpaKI~d~L~~dI~efi~qAq~rv~s~ 81 (777)
T KOG2285|consen 10 RDQFEEEWSKARPIVLKLLR------QKSVTPAAWQDLFYHVHKVCLWD--DKGPAKIRDILTRDINEFIHQAQKRVRSL 81 (777)
T ss_pred hhhhhhhccccchHHHHHHh------hccCCHHHHHHHHhhheeeeeec--CCCcHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34799999999999999877 34699999999999999999997 44678899999999999998753333344
Q ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHhhchhhHhhhhcCC--------CCcHHHHHHHHHHH----------------HH
Q 004939 85 KHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARRS--------LPALNEVGLTCFRE----------------QI 140 (722)
Q Consensus 85 ~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~--------~~~i~~l~l~lf~~----------------~I 140 (722)
..+..+|..|+.+|.+|..+..++...|.-|+..-.-..+ -.+|+.+.+.-|.+ ++
T Consensus 82 q~d~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAmklV 161 (777)
T KOG2285|consen 82 QTDGALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAMKLV 161 (777)
T ss_pred ccccHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5567899999999999999999999999999988554322 13678888888877 68
Q ss_pred HHHhcCCccCHHHHHHHHHHHHHhcc---cchhchHHHHHHHHHHHHHHHHHHHHHhhHhcCChhHHHHHHHHHHHHHHH
Q 004939 141 DKEREGEQIDRALLKNVLDIFVEIGM---GQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERD 217 (722)
Q Consensus 141 ~~~R~g~~i~~~~i~~~i~~~~~l~~---~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~eE~~ 217 (722)
..||+|+.+|.+.+-++-++|+.++. +.+.+|++.||..||++|.+||+..+..+++++++.+|++.|..-+++|+.
T Consensus 162 haER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~ 241 (777)
T KOG2285|consen 162 HAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQ 241 (777)
T ss_pred HHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHH
Confidence 89999999999999999999999975 567899999999999999999999999999999999999999999999999
Q ss_pred HHchhcCC--CchHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhhcCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHHH
Q 004939 218 RVSHYLHS--SSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAE 295 (722)
Q Consensus 218 r~~~~l~~--~t~~~l~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~ 295 (722)
|+.+||.. +|..+++..+.++||.++.+.|+. .|..|+...+++.|++||+|+.++..|++++.+.+..||...
T Consensus 242 RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~sa 317 (777)
T KOG2285|consen 242 RAKRYLEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSA 317 (777)
T ss_pred HHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhh
Confidence 99999976 678899999999999999999986 478899999999999999999999999999999999999999
Q ss_pred HHHHHHhhHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhCCC------------
Q 004939 296 GTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAV------------ 363 (722)
Q Consensus 296 g~~i~~~~~~~~~~~~~~~~~~~~~~~I~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~------------ 363 (722)
|..-+....+.+ +.++..||++|+.++++|..++.++|++||.|..|-+.||..++|...
T Consensus 318 GLaDM~~aaE~i--------ttDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kg 389 (777)
T KOG2285|consen 318 GLADMRNAAENI--------TTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKG 389 (777)
T ss_pred hHHHHHhhhhhc--------cCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcC
Confidence 987765544433 467889999999999999999999999999999999999999999763
Q ss_pred ------CCCCcHHHHHHHHHHHhhcCC-CCCCChHHHHHHHHHHhhheecccChhHHHHHHHHHHHHHhcCCCCCChHHH
Q 004939 364 ------GGSSSSELLATFCDNILKKGG-NEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHE 436 (722)
Q Consensus 364 ------~~~~~~e~La~y~d~~lk~~~-~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E 436 (722)
..++.||+||.|||.+||+.. +.+++.++++..|++|+-+++|+.+||+|..+++.+|++||+...|++.+.|
T Consensus 390 rglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkE 469 (777)
T KOG2285|consen 390 RGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKE 469 (777)
T ss_pred CccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHH
Confidence 135789999999999999853 4578889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhc--chhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCccCChhHH
Q 004939 437 RSILTKLKQQCG--GQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKS-SDLNLPSEMV 513 (722)
Q Consensus 437 ~~~i~~Lk~~~G--~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~-~~~~lP~~l~ 513 (722)
..|++.|+ +|| .+|.+++.+||+|++.|++++..|++.+.+.+..++.-.+++.||+.|.|...+. ..+.||.+|+
T Consensus 470 E~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELE 548 (777)
T KOG2285|consen 470 EMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELE 548 (777)
T ss_pred HHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHH
Confidence 99999998 577 4799999999999999999999999988766554556678999999999997643 3589999999
Q ss_pred HHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCCHHHHHH
Q 004939 514 KCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTS--DRLSYSEIMTQLNLTHDDLVR 591 (722)
Q Consensus 514 ~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~~s~~Q~~ILl~fn~~--~~~t~~ei~~~t~i~~~~l~~ 591 (722)
+.+-..++||+++|+||+|.|.|+++.++|++.-+-|.|++.|+|+||+||.+||+. +.+|++.+.-+|.+|..+|.+
T Consensus 549 D~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrR 628 (777)
T KOG2285|consen 549 DFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRR 628 (777)
T ss_pred HhCccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHH
Confidence 999999999999999999999999999999886666899999999999999999974 689999999999999999999
Q ss_pred HHhHhhh---cccceeecCCCC----CCCCCCCeEEecccCCC-C----CcceeccCCCh----hh--hhhHHHhHHHhh
Q 004939 592 LLHSLSC---AKYKILLKEPNT----KTISQSDHFEFNSKFTD-R----MRRIKIPLPPV----DE--RKKIVEDVDKDR 653 (722)
Q Consensus 592 ~L~~L~~---~k~kiL~~~~~~----~~i~~~~~~~~N~~f~~-~----~~~i~i~~~~~----~e--~~~~~~~v~~~r 653 (722)
.|-||+. .|..||..+|+. +++.++..|.+|.+|.- + .++-+++.+.- .| .++..+.+-+-|
T Consensus 629 TLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLR 708 (777)
T KOG2285|consen 629 TLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLR 708 (777)
T ss_pred HHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHH
Confidence 9999973 357888877642 34567889999999972 1 12333333221 11 122345677889
Q ss_pred hhhhhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 654 RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 654 ~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
-...+-+|++|||.||+++..+|-.+..+.|+..|-|+..+||+.||.|||..|++||++|-++|+|+|
T Consensus 709 iLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 709 ILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 999999999999999999999999999999999999999999999999999999999999999999997
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=1.3e-89 Score=794.16 Aligned_cols=581 Identities=42% Similarity=0.753 Sum_probs=508.0
Q ss_pred HHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccccCchHHH
Q 004939 12 WDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPSLSEKHDEYML 91 (722)
Q Consensus 12 W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~~~LY~~l~~~l~~~l~~~~~~~l~~~~~~~~L 91 (722)
|+.|++||..|+ .+ .++..+||.+|++||++|.++ +|+.||+++++.+.+|+.+. .+.+....++.+|
T Consensus 1 W~~l~~~i~~i~---~~----~~~~~~~~~lY~~vy~l~~~~----~~~~LY~~l~~~i~~~~~~~-~~~l~~~~~~~~l 68 (588)
T PF00888_consen 1 WEILEEAIDQIF---KK----SISKLSYMELYTCVYNLCDNK----YGEQLYDKLKEFISEYLKNI-IESLLSSSDEDLL 68 (588)
T ss_dssp HHHHHHHHHHHH---TT-----GCCSHHHHHHHHHHHHHHTT----THHHHHHHHHHHHHHHHHHH-HHHHCTTTTCHHH
T ss_pred ChHHHHHHHHHH---cC----CCChhHHHHHHHHHHhhcCCc----ccHHHHHHHHHHHHHHHHHH-HHHHHhcChhHHH
Confidence 999999999976 22 467788999999999999877 99999999999999999984 4555555778999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhchhhHhhhhcC-----CCCcHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhcc
Q 004939 92 RELVKRWANHKVMVRWLSRFFHYLDRYFIARR-----SLPALNEVGLTCFREQIDKEREGEQIDRALLKNVLDIFVEIGM 166 (722)
Q Consensus 92 ~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~-----~~~~i~~l~l~lf~~~I~~~R~g~~i~~~~i~~~i~~~~~l~~ 166 (722)
..|...|.+|+.++++|+++|+||||+|+.++ -..++.+-.....-.+|.++|.|+.+|+..++++++|++++|
T Consensus 69 ~~~~~~w~~~~~~~~~i~~if~yLdr~yv~~~~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~- 147 (588)
T PF00888_consen 69 EEYVQEWEKYKKAIKYISDIFSYLDRNYVKRNLFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELG- 147 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTTHHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccc-
Confidence 99999999999999999999999999999886 011233323333333799999999999999999999999998
Q ss_pred cchhchHHHHHHHHHHHHHHHHHHHHHhhHhcCChhHHHHHHHHHHHHHHHHHchhcCCCchHHHHHHHHHHHHHHHHHH
Q 004939 167 GQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATE 246 (722)
Q Consensus 167 ~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~ 246 (722)
...+|.+.||++||+.|.+||+.++ +.+.++.+|+.+|++++++|.+|+..|++++|..++.+.+.++||..|.+.
T Consensus 148 -~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~ 223 (588)
T PF00888_consen 148 -SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDE 223 (588)
T ss_dssp -HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHH
T ss_pred -hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999999 567799999999999999999999999999999999999999999999998
Q ss_pred HHHHhhhhHHHHhhcCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCCcchHHHHHHH
Q 004939 247 LLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKI 326 (722)
Q Consensus 247 ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~I~~l 326 (722)
| .+|+..|+++++.++|++||+|+++++++++.+++.|+++|...|..+++.... ...+..||+.+
T Consensus 224 l----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~----------~~~~~~~i~~l 289 (588)
T PF00888_consen 224 L----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK----------SSDPKEFIEDL 289 (588)
T ss_dssp H----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC----------GGGCHHHHHHH
T ss_pred H----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc----------ccchHHHHHHH
Confidence 8 469999999999999999999999999999999999999999999999986531 24578999999
Q ss_pred HHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhheec
Q 004939 327 IELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAY 406 (722)
Q Consensus 327 l~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~e~La~y~d~~lk~~~~~~~~~~e~~~~l~~i~~lf~~ 406 (722)
+++|++++.++.+||++++.|..++++||+.++|.+ ...++++||+|||.++++++ .+.++++++..++.++.||+|
T Consensus 290 l~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~--~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~~~~~i~~l~~~ 366 (588)
T PF00888_consen 290 LELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKN--NNKIPELLAKYCDSLLRKSN-KKLSEEEIEQKLDDIVKLFSY 366 (588)
T ss_dssp HHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCS--TSHHHHHHHHHHHHHHBSSC-CCS-HCCHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcC--CcchHHHHHHHhhHhhhhcc-cccchHHHHHHhhhhEEEeee
Confidence 999999999999999999999999999999999988 35899999999999999875 556788899999999999999
Q ss_pred ccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcchhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCC-CC
Q 004939 407 ISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAH-PG 485 (722)
Q Consensus 407 l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~-~~ 485 (722)
+++||+|+.+|+++||+|||..++.+.+.|..+|++|+.+||.+++++|++|++|+..|++++++|++...+.+... ++
T Consensus 367 l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~ 446 (588)
T PF00888_consen 367 LSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPP 446 (588)
T ss_dssp SSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--C
T ss_pred cchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999987654322 27
Q ss_pred cceEEEEeecCCCCCCCCCC-ccCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHH
Q 004939 486 IDLSVTVLTTGFWPSYKSSD-LNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATL 564 (722)
Q Consensus 486 ~~~~~~VLt~~~WP~~~~~~-~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~~s~~Q~~IL 564 (722)
++|+|.||++++||..+... +.+|++|+.+++.|++||+.+|+||+|+|.+++|+|+|+++++++++++.||++||+||
T Consensus 447 ~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iL 526 (588)
T PF00888_consen 447 FDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAIL 526 (588)
T ss_dssp CEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHH
T ss_pred CceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHH
Confidence 99999999999999988766 99999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccCC
Q 004939 565 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 626 (722)
Q Consensus 565 l~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~ 626 (722)
++||+.+++|++||++.||+++++++++|.+|+..+..++.+.+++..+++++.|.+|.+|+
T Consensus 527 l~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 527 LLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp HGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 99999999999999999999999999999999865433333677888999999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=1.6e-32 Score=255.85 Aligned_cols=141 Identities=48% Similarity=0.896 Sum_probs=132.5
Q ss_pred cccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcchhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCC
Q 004939 406 YISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPG 485 (722)
Q Consensus 406 ~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~ 485 (722)
|+++||+|+.+|+++||+|||..++++.+.|..+|++|+.+||.+++++|++|++|+..|++++++|++.+.+++ ...+
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 689999999999999999999999999999999999999999999999999999999999999999998876532 2346
Q ss_pred cceEEEEeecCCCCCCCC-CCccCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEe
Q 004939 486 IDLSVTVLTTGFWPSYKS-SDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKF 547 (722)
Q Consensus 486 ~~~~~~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~i~~~~ 547 (722)
++|+|.|||+++||..+. .++.||++|+.+++.|++||..+|+||+|+|++++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999999887 78999999999999999999999999999999999999999865
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=3.9e-26 Score=245.62 Aligned_cols=303 Identities=24% Similarity=0.322 Sum_probs=239.8
Q ss_pred HHhhheecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcchhhHhHHHHHHhHHHhHHHHHHHHHH--H
Q 004939 399 KVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY--L 476 (722)
Q Consensus 399 ~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~--~ 476 (722)
-+-.|+..+.+|+.|++.||.+||.||+....++.+.|..-++.||-++|....+.|++|++|+..|+++++.+++. .
T Consensus 441 i~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~ 520 (765)
T KOG2165|consen 441 IFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESEL 520 (765)
T ss_pred HHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhh
Confidence 34456677799999999999999999999999999999999999999999999999999999999999999999874 2
Q ss_pred hcCCCCCCCcceEEEEeecCCCCCCCCCCccCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEE
Q 004939 477 SNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIV 556 (722)
Q Consensus 477 ~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~~ 556 (722)
.......+.+.+++.+||+.+||......+.+|.+++..++.|.+-|.+..++|+|.|.+++|.|+|++.|++++.++.|
T Consensus 521 ~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tV 600 (765)
T KOG2165|consen 521 SRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTV 600 (765)
T ss_pred hcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEee
Confidence 22122345688999999999999888888999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccCCCCCcceeccC
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPL 636 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~ 636 (722)
|+.||+|+.+|.+.++||++++++.+|||...+++.|..|.. .++|..+|. ++++++|+++++=.+..+--.-+.
T Consensus 601 sp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~--~GvL~e~~~---~s~tgt~T~iEse~d~~q~~~~~~ 675 (765)
T KOG2165|consen 601 SPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQ--KGVLREEPI---ISDTGTLTVIESEMDFDQAEGTVL 675 (765)
T ss_pred CHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHH--cCeeecCCC---CCCCceeeeccccccccccCCCcc
Confidence 999999999999999999999999999999999999999974 588887642 367889999885443322111111
Q ss_pred CChhh-h--hhHHHhHHHhh--hhhhhhheeeccccCccCChhhHHHHHHHHhccCCCC-------ChhHHHHHHHhhhh
Q 004939 637 PPVDE-R--KKIVEDVDKDR--RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKP-------DIKAIKKRMEDLIT 704 (722)
Q Consensus 637 ~~~~e-~--~~~~~~v~~~r--~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~-------~~~~ik~~Ie~Lie 704 (722)
...++ . ......+++-+ -..-...||-.+-.-+.|..+.+++... .|.| +-++++.-+..++.
T Consensus 676 ~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLk-----mF~~~~~~~~~TlqeL~~fLq~kV~ 750 (765)
T KOG2165|consen 676 LEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLK-----MFVPPDGSAEITLQELQGFLQRKVR 750 (765)
T ss_pred cccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHe-----eeecCCCCCcccHHHHHHHHHHHhh
Confidence 11111 1 11222222211 1233457888777779999988888653 4544 34556666666665
Q ss_pred hhhhccc
Q 004939 705 RDYLERD 711 (722)
Q Consensus 705 reyl~r~ 711 (722)
-|-|+-.
T Consensus 751 e~kL~f~ 757 (765)
T KOG2165|consen 751 EGKLEFI 757 (765)
T ss_pred ccceEEe
Confidence 5555443
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.77 E-value=1.1e-19 Score=145.44 Aligned_cols=68 Identities=50% Similarity=0.963 Sum_probs=62.3
Q ss_pred HHHhhhhhhhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCC
Q 004939 649 VDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPN 716 (722)
Q Consensus 649 v~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~ 716 (722)
|+++|...|+|+||||||++|+++|++|+.+|.+.++++|.|+..+||++||.||++|||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 35789999999999999999999999999999999998999999999999999999999999999875
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=95.94 E-value=0.2 Score=47.05 Aligned_cols=126 Identities=18% Similarity=0.272 Sum_probs=88.1
Q ss_pred CCCHHHhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccc
Q 004939 5 TIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPSLSE 84 (722)
Q Consensus 5 ~~~fd~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~~~LY~~l~~~l~~~l~~~~~~~l~~ 84 (722)
++..++.|+.++.++-.++ +|+... .+-...-++-+.--+.|.++. ....+-+.+++.+..-+... ...+..
T Consensus 2 ~~~~~~~W~~~~~~vl~lF---~g~~l~-~~iEdlN~lv~~~i~~~~~~~---~~~~~~~dl~elL~tg~~~L-~~~l~~ 73 (158)
T PF08539_consen 2 NMSSDDAWNSLCAKVLPLF---QGERLR-LPIEDLNELVRFHIKLCIQSF---PPSYFLEDLEELLTTGMYIL-ENQLNE 73 (158)
T ss_pred CCchhhhHHHHHHHHHHHH---cCCCCC-cCHHHHHHHHHHHHHHhhccc---chHHHHHHHHHHHHHHHHHH-HHHHhh
Confidence 3567899999999998865 466553 665555556655566777662 23455566666666654432 334555
Q ss_pred cCchHHHHHHHHHHHHHHH-HHHHHHHhhchhhHhhhhc-----------------CCCCcHHHHHHHHHHH
Q 004939 85 KHDEYMLRELVKRWANHKV-MVRWLSRFFHYLDRYFIAR-----------------RSLPALNEVGLTCFRE 138 (722)
Q Consensus 85 ~~~~~~L~~~~~~W~~~~~-~~~~l~~if~YLdr~yv~~-----------------~~~~~i~~l~l~lf~~ 138 (722)
..++.+|..+...|.-|.. -+-++-.+|..|++.+-.. ....+|+.+++..||+
T Consensus 74 ~~~~~~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD 145 (158)
T PF08539_consen 74 VPDNRLLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRD 145 (158)
T ss_pred cchhHHHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHH
Confidence 6678899999999999664 4678899999999654322 2346899999999998
No 11
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=93.48 E-value=0.24 Score=42.48 Aligned_cols=65 Identities=17% Similarity=0.237 Sum_probs=52.4
Q ss_pred EEEcHHHHHHHHhhc--------CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccC
Q 004939 554 LIVSTYQAATLLLFN--------TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 625 (722)
Q Consensus 554 l~~s~~Q~~ILl~fn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f 625 (722)
..++.-|+.+|+... ....+|-.||++.+|++.+.+.+.|..|. +.+++.+.. ....|++|.++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~~ 92 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTPL 92 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCCc
Confidence 457888999888665 45689999999999999999999999996 457877542 24679999876
Q ss_pred C
Q 004939 626 T 626 (722)
Q Consensus 626 ~ 626 (722)
+
T Consensus 93 ~ 93 (95)
T TIGR01610 93 S 93 (95)
T ss_pred c
Confidence 5
No 12
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=91.60 E-value=0.3 Score=36.54 Aligned_cols=45 Identities=27% Similarity=0.294 Sum_probs=36.5
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 561 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 561 ~~ILl~fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
+.||..|.+.+ ++|+.||++.+|+|...+.+.|..|.. .+++.+.
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 589999999999999999999999973 5676654
No 13
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=91.59 E-value=0.39 Score=35.20 Aligned_cols=42 Identities=19% Similarity=0.299 Sum_probs=34.8
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
+..+..||..+.+++.+|..||++.+|++...+.+.|..|..
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 456778888888888999999999999999999999999963
No 14
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=91.54 E-value=0.57 Score=38.94 Aligned_cols=59 Identities=15% Similarity=0.225 Sum_probs=40.9
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEeccc
Q 004939 559 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 624 (722)
Q Consensus 559 ~Q~~ILl~fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~ 624 (722)
+++.+.+..+..+ .+|.++|++.+++|+..+.+.++.|. +.+++.... | .++.|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-G----~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-G----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-S----TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-C----CCCceeecCC
Confidence 3444444444443 49999999999999999999999997 567876442 1 3567887764
No 15
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=90.22 E-value=0.39 Score=37.22 Aligned_cols=51 Identities=20% Similarity=0.337 Sum_probs=42.2
Q ss_pred EcHHHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 556 VSTYQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+|+.|+.||..+...+. +|..||++.++++...+.+.+..|. +.+++.+.+
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 47789999988877766 9999999999999999999999997 457777653
No 16
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=89.49 E-value=0.92 Score=34.73 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=38.9
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 560 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 560 Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
|..|+..+++.+.+|++||++.+|+++..+++-|..|.. .+++.+.
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 456788888899999999999999999999999999973 4566554
No 17
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=88.02 E-value=29 Score=39.14 Aligned_cols=186 Identities=11% Similarity=0.074 Sum_probs=102.5
Q ss_pred HhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcc-------cccc
Q 004939 10 QGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMV-------LPSL 82 (722)
Q Consensus 10 ~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~~~LY~~l~~~l~~~l~~~~-------~~~l 82 (722)
-.|..|++++.-|.+.-.- ..++ ...|-.+++.+|+-|..+ .-+...+.+.++.....+..... .+.
T Consensus 112 vdrslLrsll~MLsd~~iY--~esF-~~~fls~f~~lY~aE~~d--~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st- 185 (661)
T KOG2167|consen 112 VDRSLLRSLLKMLSDLQIY--KESF-ELTFLSLFRELYAAEGQD--KRQELEVPEYLEHVEGRLEEENDRVIEYFDSST- 185 (661)
T ss_pred hhHHHHHHHHHHHHHHHhh--hhhh-HHHHHHHHHHHHHHHhcc--hhhhcccHHHHHhhhhcccchHHHHHHhccccc-
Confidence 4588899888876543110 0011 234677788899999876 22334444444443333332211 001
Q ss_pred cccCchHHHHHHHHHHHHHHHHHHHHHHhhchhhHhhhhcCCCCcHHHHHHH----------HHHH--------HHHHHh
Q 004939 83 SEKHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARRSLPALNEVGLT----------CFRE--------QIDKER 144 (722)
Q Consensus 83 ~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~~~~i~~l~l~----------lf~~--------~I~~~R 144 (722)
.......+.+.+...|-....... +++-+|-.=+. ....++.++-. .|.+ +|..++
T Consensus 186 ~k~l~atV~~~LL~~hL~~IL~kg----l~~lvDm~q~~--d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~ 259 (661)
T KOG2167|consen 186 KKPLIATVERCLLSRHLDLILTKG----LDSLVDMRQTS--DLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEE 259 (661)
T ss_pred ccchHHHHHHHHHHHHHHHHHhcc----hHHhhhhhhcc--chHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCch
Confidence 011224677778888877654443 33333322111 12233433332 2333 455555
Q ss_pred cCCccCHH--HHHHHHHHHHHhcccchhchHHHHHHHHHHHHHHHHHHHHHhhHhcCChhHHHHHHHHHHHHH
Q 004939 145 EGEQIDRA--LLKNVLDIFVEIGMGQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKE 215 (722)
Q Consensus 145 ~g~~i~~~--~i~~~i~~~~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~eE 215 (722)
.++....+ ..++-+++++.. .++...- .+|+..+++.|...++ .....+.+|+.+..+.+-.+
T Consensus 260 kDk~mVqELL~FK~k~Dii~~~-----sF~~~v~-e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~ 324 (661)
T KOG2167|consen 260 KDKDMVQELLDFKKKVDIIVDE-----SFLKYVA-EKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRA 324 (661)
T ss_pred hhHHHHHHHHHHHHHhhHHHHH-----HHHHhhH-HHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHh
Confidence 55433322 457777777663 3333333 8899999999999998 34667889998887765544
No 18
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=86.54 E-value=0.77 Score=35.15 Aligned_cols=50 Identities=18% Similarity=0.357 Sum_probs=42.6
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 556 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
+|..|+.+|....+.+++|..+|++.++++...+.+.+..|. +.+++.+.
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 367899999988888889999999999999999999999997 45777664
No 19
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=86.23 E-value=1.2 Score=35.08 Aligned_cols=50 Identities=16% Similarity=0.279 Sum_probs=38.3
Q ss_pred EcHHHHHHHHhhc-CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 556 VSTYQAATLLLFN-TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 556 ~s~~Q~~ILl~fn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
+|..|..||..+. ....++..+|++.++++...+-+.+..|.. .+++.+.
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 3677899999888 778999999999999999999999999973 4777654
No 20
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=86.01 E-value=1.9 Score=31.44 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=34.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
...-||.++-+ ++.++.||++.+|++...+-++|..|. +.+++.
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 34567777766 689999999999999999999999986 345553
No 21
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=85.94 E-value=1.1 Score=34.84 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=39.6
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
++.-..||.++...++.|+.||++.+|++...+..+|..|. +.+++...
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 45566788888667899999999999999999999999996 45777643
No 22
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=85.28 E-value=1.7 Score=38.77 Aligned_cols=52 Identities=12% Similarity=0.201 Sum_probs=45.0
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 555 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
.++..|+.||..+..++++|..+|++.+|++...+-+.+..|. +.+++.+.+
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le--~~GlI~r~~ 76 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLE--RDGLVTRLK 76 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHH--HCCCEEecc
Confidence 3578899999988888899999999999999999999999996 457777653
No 23
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=84.06 E-value=2.2 Score=34.01 Aligned_cols=47 Identities=21% Similarity=0.276 Sum_probs=38.0
Q ss_pred HHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 559 YQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
..-.||.++.+.+. +|..||++.+|++...+.++|..|. +.+++.+.
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 34567777777665 9999999999999999999999996 34666654
No 24
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=83.96 E-value=1 Score=40.01 Aligned_cols=62 Identities=21% Similarity=0.302 Sum_probs=53.2
Q ss_pred hhhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 656 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 656 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
..++-|+++|=.++..+.++++.++.. .+.++...|+.-|..|..||.|.+..+ ...|.|-|
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 457889999999999999999988765 478899999999999999999999975 46788854
No 25
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=83.15 E-value=2.4 Score=39.25 Aligned_cols=52 Identities=17% Similarity=0.161 Sum_probs=45.0
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 555 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
.++..|+.||......+++|..+|++.++++...+-+.+..|. +.+++.+.+
T Consensus 37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 4678899999887767789999999999999999999999996 567887754
No 26
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=81.59 E-value=2.9 Score=31.44 Aligned_cols=37 Identities=16% Similarity=0.315 Sum_probs=29.4
Q ss_pred HHHHhh-cCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 562 ATLLLF-NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 562 ~ILl~f-n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
.||.++ +..+.+|.++|++.+|++...+.+.|..|..
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 445444 6666799999999999999999999998853
No 27
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=81.26 E-value=1.7 Score=39.51 Aligned_cols=60 Identities=17% Similarity=0.201 Sum_probs=45.4
Q ss_pred hhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 658 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 658 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
+..|++++-..+.++..+++... .....+...-+...|..|.+||||+|..+ ...|.|-|
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 44567777677778777666554 33456788899999999999999999864 45788865
No 28
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=81.24 E-value=0.7 Score=36.92 Aligned_cols=45 Identities=18% Similarity=0.335 Sum_probs=34.6
Q ss_pred eeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCC
Q 004939 661 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 713 (722)
Q Consensus 661 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~ 713 (722)
|-.+|+.++.++..+|-. +|..+++.+...|+.|+.+|||++.+.
T Consensus 5 i~~~l~~~~~~S~~eLa~--------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAR--------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHHH--------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 334677888888877765 489999999999999999999998764
No 29
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=79.20 E-value=5.9 Score=37.19 Aligned_cols=56 Identities=11% Similarity=0.076 Sum_probs=41.0
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecc
Q 004939 561 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 623 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~ 623 (722)
+.+.|..+..+.+|..+|++..++|...|.+.|+.|. +.+++.... | .++.|.++.
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-G----~~GGy~La~ 68 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-G----RNGGVRLGR 68 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-C----CCCCeeecC
Confidence 3444445555678999999999999999999999996 567876542 1 245566654
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=78.91 E-value=5.2 Score=35.11 Aligned_cols=52 Identities=25% Similarity=0.367 Sum_probs=43.4
Q ss_pred EEcHHHHHHHHhhc----CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 555 IVSTYQAATLLLFN----TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn----~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
.+|..|..||..+. ..+++|..+|++.++++...+-+.+..|. +.+++.+.+
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 45788888887665 55789999999999999999999999997 567887754
No 31
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=78.28 E-value=6.6 Score=37.30 Aligned_cols=45 Identities=16% Similarity=0.216 Sum_probs=35.9
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 560 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 560 Q~~ILl~fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
.+.+.+.|+.. ..+|.++|++.+|+|...+.+.|+.|. +.+++..
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s 57 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSS 57 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 33444556643 589999999999999999999999997 5678874
No 32
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=77.79 E-value=2.1 Score=38.07 Aligned_cols=60 Identities=10% Similarity=0.197 Sum_probs=44.0
Q ss_pred hhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 658 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 658 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
+..|++++=..+.++..+++..+ .....+....|...+..|.+||||.|... ...|.|-|
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 44566666666777777766654 44467889999999999999999999875 46788865
No 33
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=77.66 E-value=4.4 Score=34.37 Aligned_cols=52 Identities=23% Similarity=0.299 Sum_probs=44.5
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 554 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 554 l~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
+.++..+..||.++...+.+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEec
Confidence 45688899999988877789999999999999999999999997 45677654
No 34
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=76.14 E-value=6.1 Score=33.09 Aligned_cols=45 Identities=22% Similarity=0.345 Sum_probs=37.3
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 561 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 561 ~~ILl~fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
..||..+... +++|+.||++.+|++...+.+.|..|. ..+++.+.
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 4566677665 689999999999999999999999996 45787764
No 35
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=75.82 E-value=2.3 Score=33.64 Aligned_cols=49 Identities=22% Similarity=0.274 Sum_probs=39.3
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
|-.++-|+..+-..+..|..||++.+|++...+.+.|..|.. .+++.+.
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 455666666555667899999999999999999999999974 4676654
No 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=75.74 E-value=5.8 Score=29.05 Aligned_cols=44 Identities=20% Similarity=0.263 Sum_probs=34.7
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 561 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
-.|+..+.+...+|..+|++.++++...+.+.|..|.. .+++.+
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~ 46 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTR 46 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 34566666667899999999999999999999999963 355544
No 37
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=74.57 E-value=7.5 Score=34.90 Aligned_cols=39 Identities=21% Similarity=0.260 Sum_probs=34.0
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 568 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 568 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+.+++.|+++|++.++.+...+.+.|++|.. .+++.+..
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Rek 76 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVEREK 76 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeeee
Confidence 3678999999999999999999999999974 57887753
No 38
>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=74.41 E-value=8.8 Score=35.13 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=34.5
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 561 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 561 ~~ILl~fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
+.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 3344445443 479999999999999999999999996 5677764
No 39
>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=74.24 E-value=11 Score=32.56 Aligned_cols=62 Identities=24% Similarity=0.393 Sum_probs=45.6
Q ss_pred EEcHHHHHHHHh-------hcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccCC
Q 004939 555 IVSTYQAATLLL-------FNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 626 (722)
Q Consensus 555 ~~s~~Q~~ILl~-------fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~ 626 (722)
.+|.-|..|++. ||. .+.+|..++++.||++...+.+++..|. +.++|... +..+-+|.+.+
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 345566666665 343 3589999999999999999999999997 56888654 34555665543
No 40
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=73.66 E-value=8.7 Score=35.92 Aligned_cols=59 Identities=15% Similarity=0.200 Sum_probs=42.9
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEeccc
Q 004939 559 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 624 (722)
Q Consensus 559 ~Q~~ILl~fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~ 624 (722)
+++.+.|.-+..+ ..|.++|++..|+|+..|.+.|..|. |.+++.... | .++.|.++.+
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~r-G----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVR-G----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeec-C----CCCCccCCCC
Confidence 3455555555554 68899999999999999999999996 678886442 1 2556766554
No 41
>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=73.65 E-value=5 Score=28.54 Aligned_cols=36 Identities=28% Similarity=0.451 Sum_probs=27.3
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 561 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
-.||-.+......++.+|++.+|+++..+.+-+..|
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 456767777788999999999999999998877654
No 42
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=72.17 E-value=8.3 Score=39.61 Aligned_cols=47 Identities=11% Similarity=0.244 Sum_probs=39.9
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 560 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 560 Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
-+.||.+|....++|+.||++.+|+|...+.+.|..|.. .+.|.+.+
T Consensus 16 ~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~ 62 (257)
T PRK15090 16 VFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG 62 (257)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 346888898877899999999999999999999999974 57787653
No 43
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=71.67 E-value=8.4 Score=37.38 Aligned_cols=53 Identities=13% Similarity=-0.011 Sum_probs=45.2
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 554 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 554 l~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+.++..|+.||......+++|..+|++.++++...+.+.+..|. +-+++.+.+
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE--~kGlI~R~~ 93 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE--ERGYLTFSK 93 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH--HCCCEEecC
Confidence 34678899999999888899999999999999999999999986 457777653
No 44
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=71.44 E-value=10 Score=30.35 Aligned_cols=42 Identities=17% Similarity=0.326 Sum_probs=33.5
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 562 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 562 ~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
.||+..... ..|++||.+.||++.+.|...|..|. +-+++.+
T Consensus 9 ~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 9 KILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred HHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 344445444 89999999999999999999999996 4567764
No 45
>PHA00738 putative HTH transcription regulator
Probab=71.37 E-value=10 Score=32.93 Aligned_cols=68 Identities=19% Similarity=0.094 Sum_probs=50.5
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccCC
Q 004939 553 ELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 626 (722)
Q Consensus 553 ~l~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~ 626 (722)
++...+.=-.||.++.+++.+++.+|++.++++...+-++|.-|. ..+|+.....|.. -.|++|.+..
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr~----vyY~Ln~~~~ 74 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGRT----LYAKIRENSK 74 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECCE----EEEEECCCcc
Confidence 345555556677777777789999999999999999999999996 4678876654432 3567776643
No 46
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=70.13 E-value=8.9 Score=35.38 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=44.0
Q ss_pred EEEcHHHHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 554 LIVSTYQAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 554 l~~s~~Q~~ILl~fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+.++..|..+|...... ++.|..+|++.+|++...+.+.+..|. +-+++.+.+
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 34678899998887654 568999999999999999999999997 567887654
No 47
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=69.39 E-value=9 Score=36.43 Aligned_cols=50 Identities=18% Similarity=0.258 Sum_probs=40.9
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccCCCCCc
Q 004939 572 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMR 630 (722)
Q Consensus 572 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~~~~~ 630 (722)
-+|..+|++.+|++...+.+.+..|. +.++|.+.. .+.|.+|++|--+-.
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~~-------~G~Y~iNP~~~~kG~ 124 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKIR-------NGAYMINPNFFFKGD 124 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEcc-------CCeEEECcHHheeCc
Confidence 47889999999999999999999997 457887653 468999999765433
No 48
>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=67.88 E-value=6.8 Score=30.10 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=30.0
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 560 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 560 Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
|.-+|-++-+.+.+|++||++.+|++...++.-+.-|-
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 55566555447799999999999999999998887774
No 49
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=66.55 E-value=9.4 Score=32.96 Aligned_cols=44 Identities=23% Similarity=0.306 Sum_probs=37.1
Q ss_pred EEcHHHHHHHHhhcC----CCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 555 IVSTYQAATLLLFNT----SDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~----~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
.++..|-.||-.+.. .+.+++++|++.++++.++++.+|..|+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSN 91 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 578899999998887 35899999999999999999999999975
No 50
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=66.50 E-value=14 Score=26.49 Aligned_cols=34 Identities=32% Similarity=0.436 Sum_probs=28.9
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 572 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 572 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
++|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 57899999999999999999999996 45777643
No 51
>PRK10870 transcriptional repressor MprA; Provisional
Probab=65.78 E-value=15 Score=35.40 Aligned_cols=51 Identities=14% Similarity=0.217 Sum_probs=42.4
Q ss_pred EcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 556 VSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+|..|..||..... ..++|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~ 105 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRE 105 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 56778888887764 4579999999999999999999999997 567887764
No 52
>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=65.36 E-value=17 Score=32.94 Aligned_cols=45 Identities=20% Similarity=0.278 Sum_probs=34.2
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 560 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 560 Q~~ILl~fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
++.+.+.-++. ..+|.++|++.+|+|...+.+.|..|. +.+++..
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~ 57 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVES 57 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 34444443433 389999999999999999999999997 4567764
No 53
>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=64.58 E-value=11 Score=37.18 Aligned_cols=52 Identities=17% Similarity=0.179 Sum_probs=45.0
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 555 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
.++..|..||..+.+++.++..+|++.+|++...+.++|..|. +.+++.+.+
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 4678899999999887889999999999999999999999996 457777653
No 54
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=63.83 E-value=15 Score=32.68 Aligned_cols=58 Identities=22% Similarity=0.359 Sum_probs=42.7
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecc
Q 004939 560 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 623 (722)
Q Consensus 560 Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~ 623 (722)
-..||.++-+.++.++.||++.+|++...+-++|.-|. ..+++.....|. .-.|.+|.
T Consensus 18 Rl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 18 RLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECc
Confidence 34566555455679999999999999999999999996 467887655442 22466665
No 55
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=63.29 E-value=9.7 Score=29.68 Aligned_cols=45 Identities=22% Similarity=0.189 Sum_probs=33.1
Q ss_pred HHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCC
Q 004939 563 TLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPN 609 (722)
Q Consensus 563 ILl~fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~ 609 (722)
||-.++. +.++|-.||++.+|++...+...|..|. +.+.+.+.|.
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~ 50 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPV 50 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecC
Confidence 4455555 6789999999999999999999999996 4455565543
No 56
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=62.90 E-value=17 Score=27.32 Aligned_cols=39 Identities=21% Similarity=0.339 Sum_probs=31.8
Q ss_pred hcCCCCc-CHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 567 FNTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 567 fn~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
+...+.+ |..+|++.+|++...+.++|..|. +.+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 4455567 899999999999999999999997 35677654
No 57
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=62.31 E-value=9.1 Score=30.86 Aligned_cols=28 Identities=21% Similarity=0.177 Sum_probs=24.6
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 570 SDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 570 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.+.+|+.||++.+|++...++..+..+.
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 3578999999999999999999887664
No 58
>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=61.32 E-value=4.9 Score=30.69 Aligned_cols=46 Identities=15% Similarity=0.374 Sum_probs=39.4
Q ss_pred hheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 659 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 659 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
..|+..++.++.++..+|.+. |..+...|.+=+..|-++|.|.|.-
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~--------~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEE--------FGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 356777888999998888773 8889999999999999999999864
No 59
>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=60.82 E-value=3.8 Score=32.41 Aligned_cols=55 Identities=13% Similarity=0.262 Sum_probs=38.8
Q ss_pred hheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeec
Q 004939 659 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYL 721 (722)
Q Consensus 659 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yi 721 (722)
+.|-..|-..+.++..+|...+ ..+...+-+.++.|.++|+++|.+.++..|..+
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 3333334366667776665543 457888999999999999999998765555544
No 60
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=60.67 E-value=9.8 Score=30.21 Aligned_cols=53 Identities=9% Similarity=0.201 Sum_probs=40.7
Q ss_pred hhheeeccccCcc--CChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCce
Q 004939 658 DAALVRIMKSRKV--LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 718 (722)
Q Consensus 658 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y 718 (722)
+..|...|+.++. ++..+|-.+ ...+...+.+.+..|.++|||.+++..+..|
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~--------lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKN--------LGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 4557778888876 887776664 3456778999999999999999988664554
No 61
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=60.64 E-value=19 Score=28.17 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=37.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
+..+..|+..+.+.. ++..||++.+|++...+.+.|..|.. .+++..
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 346777887777665 99999999999999999999999863 356654
No 62
>PRK11569 transcriptional repressor IclR; Provisional
Probab=60.58 E-value=17 Score=37.65 Aligned_cols=47 Identities=17% Similarity=0.173 Sum_probs=39.1
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 560 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 560 Q~~ILl~fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
-..||.+|.+. ..+|+.||++.+|++...+.+.|.+|.. .+.|.+.+
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG 77 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 34678889864 5799999999999999999999999974 57887653
No 63
>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=60.02 E-value=10 Score=29.63 Aligned_cols=53 Identities=9% Similarity=0.201 Sum_probs=33.3
Q ss_pred hhheeeccc-cCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccc--CCCCCce
Q 004939 658 DAALVRIMK-SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD--KENPNMF 718 (722)
Q Consensus 658 ~A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~--~~d~~~y 718 (722)
+..|.+.+. ..+.++..+|... +..+.+.+-+.|+.|+++|||++. +.|+...
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~--------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~ 60 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAER--------LGISKSTVSRIIKKLEEKGLVEKERDPHDKRSK 60 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHH--------TT--HHHHHHHHHHHHHTTSEEEEEESSCTTSE
T ss_pred HHHHHHHHHccCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCCee
Confidence 344555555 5666666655553 556788899999999999999664 4455533
No 64
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=59.78 E-value=16 Score=31.67 Aligned_cols=45 Identities=13% Similarity=0.198 Sum_probs=37.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
..-.||..+..+...|+.+|++.+|++...+.+.+..|.. .+++.
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 4456788888778899999999999999999999999963 46665
No 65
>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=59.70 E-value=23 Score=32.06 Aligned_cols=44 Identities=25% Similarity=0.258 Sum_probs=34.6
Q ss_pred HHHHHhhc--CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 561 AATLLLFN--TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 561 ~~ILl~fn--~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
..+|..+. ..+.+|+.||++.+|+|...+.+.|..|. +.+++..
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~ 57 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTS 57 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 34455554 33579999999999999999999999997 4677764
No 66
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=59.50 E-value=20 Score=36.54 Aligned_cols=46 Identities=28% Similarity=0.416 Sum_probs=38.9
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 561 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 561 ~~ILl~fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+.||.+|.... .+++.||++.+|+|...+.+.|..|. ..+++...+
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 46788888754 37899999999999999999999997 468888765
No 67
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=59.08 E-value=13 Score=36.91 Aligned_cols=43 Identities=21% Similarity=0.253 Sum_probs=35.7
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 561 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
..||.+.+..+++|.+||++.+|++..-++++|+.|.. -+++.
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~--~Glv~ 56 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA--EGLVE 56 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh--Cccee
Confidence 35677777888999999999999999999999999973 34444
No 68
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=58.76 E-value=21 Score=36.98 Aligned_cols=47 Identities=26% Similarity=0.312 Sum_probs=39.1
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 560 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 560 Q~~ILl~fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
-..||.+|... ..+|+.||++.+|+|...+.+.|.+|.. .+.|.+.+
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~~ 74 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQDS 74 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 34688889765 4799999999999999999999999974 57777653
No 69
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=57.86 E-value=9.5 Score=31.42 Aligned_cols=43 Identities=26% Similarity=0.351 Sum_probs=33.0
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 561 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
..|+...+..+.+++.+|.+.+|++...+-++|..|.. .+.+.
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 45666666677899999999999999999999999963 45554
No 70
>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=57.68 E-value=5.1 Score=38.81 Aligned_cols=58 Identities=17% Similarity=0.332 Sum_probs=40.5
Q ss_pred hhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 657 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 657 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
+-...|...|.+|.+..++|-. .|..+.+++-.+|..|...|-|.---+|++.|+||.
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 3344557889999999888765 488899999999999999999998888999999984
No 71
>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=57.49 E-value=23 Score=36.12 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=37.2
Q ss_pred HHHHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 561 AATLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 561 ~~ILl~fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
..||.+|.. ..++|+.||++.+|+|...+.+.|..|.. .+.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 467888986 45899999999999999999999999974 567764
No 72
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=56.43 E-value=2.8e+02 Score=29.64 Aligned_cols=163 Identities=11% Similarity=0.210 Sum_probs=87.9
Q ss_pred hHHHHhhcCcHHHHHHHHHhhccC---CCChHHHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCCcchHHHHHHHHHHH
Q 004939 254 GCRALLREDKVEDLSRMYRLYHKI---PKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELH 330 (722)
Q Consensus 254 gl~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~I~~ll~l~ 330 (722)
.|..-.+.++.+.+.|.++||--+ +.|++...+.+.+.|.....+.+......... +..+.-|...|..++
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 466677788899999988888554 45777777777777766666665543221100 123344555555555
Q ss_pred HHH-------HHHHHHhcCCChHHH--H----HHHH----HHHHHhhCCCCCCCcHHHHHHHHHHHhhc-----------
Q 004939 331 DKY-------MEYVTNCFINHTLFH--K----ALKE----AFEIFCNKAVGGSSSSELLATFCDNILKK----------- 382 (722)
Q Consensus 331 ~~~-------~~l~~~~F~~~~~f~--~----~l~~----af~~~~N~~~~~~~~~e~La~y~d~~lk~----------- 382 (722)
+.. ..++..+|+...... . ..+. -+..|..... -.+....+..|-...+.+
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 544 446777888654321 1 1111 1111111110 001112222333322221
Q ss_pred ------CCCCCCChHHHHHHHHHHhhheecccChhHHHHHHHHHHHHHhcCCCC
Q 004939 383 ------GGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRS 430 (722)
Q Consensus 383 ------~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~ 430 (722)
+.....+.-+++..|+.+..+...- ..|.++++.|.-....
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 0012234557888888888887654 4899999999887443
No 73
>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=56.30 E-value=25 Score=27.10 Aligned_cols=44 Identities=16% Similarity=0.265 Sum_probs=34.1
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 563 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 563 ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
|..+-.+...++..+|++.+|+++..+...+..|. +.+++...+
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 44444577899999999999999999999999996 356766543
No 74
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=55.86 E-value=35 Score=31.41 Aligned_cols=40 Identities=15% Similarity=0.262 Sum_probs=33.0
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 567 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 567 fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+..+..++..+|++.+|+|...+.+.|..|. +.+++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEec
Confidence 4444578999999999999999999999996 567886543
No 75
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=55.68 E-value=23 Score=36.49 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=38.4
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 561 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 561 ~~ILl~fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+.||.+|.+.. .+|..||++.+|++...+.+.|..|. ..++|.+.+
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~ 60 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSA 60 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 45778887654 59999999999999999999999997 457887654
No 76
>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=55.35 E-value=24 Score=27.81 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=32.8
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 561 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
..|-.++++...+|+.+|++.||++..++..++--|..
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar 48 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR 48 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 45667788888999999999999999999999998874
No 77
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=54.86 E-value=25 Score=26.58 Aligned_cols=35 Identities=17% Similarity=0.218 Sum_probs=29.7
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 570 SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 570 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
.++.|..+|++.+|++...+.+.|..|.. .+++..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeee
Confidence 56789999999999999999999999973 466654
No 78
>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=54.01 E-value=31 Score=25.21 Aligned_cols=33 Identities=21% Similarity=0.391 Sum_probs=24.3
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhH
Q 004939 561 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 595 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 595 (722)
..|-+.| ..+.|++||++.+|++...+.+....
T Consensus 11 ~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 11 EVIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 3444556 45789999999999999988776543
No 79
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=53.94 E-value=25 Score=30.73 Aligned_cols=51 Identities=20% Similarity=0.303 Sum_probs=43.0
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 556 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+++.|+.+|.......+.+..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le--~~glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLE--DKGLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 678899999888877766669999999999999999999996 457777653
No 80
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=51.92 E-value=20 Score=27.88 Aligned_cols=34 Identities=21% Similarity=0.319 Sum_probs=26.1
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccee
Q 004939 569 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKIL 604 (722)
Q Consensus 569 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL 604 (722)
..+..|+.+|.+.|++|.+.++..|-.|.. .+++
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 346899999999999999999999999873 4554
No 81
>PF13730 HTH_36: Helix-turn-helix domain
Probab=51.74 E-value=35 Score=25.37 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=22.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 574 SYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 574 t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
|.+.|++.+|++...+.+++..|.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 899999999999999999999986
No 82
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=50.81 E-value=37 Score=26.22 Aligned_cols=35 Identities=26% Similarity=0.340 Sum_probs=30.3
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 571 DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 571 ~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
..+|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE--EEGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 479999999999999999999999997 35777654
No 83
>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=49.57 E-value=41 Score=27.38 Aligned_cols=39 Identities=10% Similarity=0.208 Sum_probs=28.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
+.-.+|-++-...++|..+|+..+|.+.+++...|..+.
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 345567778888999999999999999999999998774
No 84
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=48.03 E-value=15 Score=31.87 Aligned_cols=45 Identities=13% Similarity=0.143 Sum_probs=31.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
-.+.|+..+..++.++-++|++.+|++..++.+.|..|.. .+++.
T Consensus 14 ~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv~ 58 (105)
T PF02002_consen 14 EAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLVS 58 (105)
T ss_dssp TTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-E
T ss_pred hHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeE
Confidence 3456666666667899999999999999999999999974 35553
No 85
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=47.64 E-value=20 Score=27.05 Aligned_cols=44 Identities=11% Similarity=0.191 Sum_probs=31.4
Q ss_pred eccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCC
Q 004939 663 RIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENP 715 (722)
Q Consensus 663 RimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~ 715 (722)
+.+. .+.++..++... +..+...+.+.|+.|.++|++.+..+.+
T Consensus 4 ~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 4 KLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 3444 556666665443 3457788999999999999999876443
No 86
>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=47.46 E-value=14 Score=39.40 Aligned_cols=143 Identities=12% Similarity=0.144 Sum_probs=39.3
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccCCCCCcce
Q 004939 555 IVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRI 632 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~~~~~~i 632 (722)
.++..+..|.-+..+ ..++-..+|...||++...+.++|.+|.. | +++.... +.+.+++|+
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 456677777777654 45889999999999999999999999974 2 4444221 122333333
Q ss_pred eccCCChhhhhh------HHHhHHHhhhhhhhhheeeccccCcc-----------------------------CChhhHH
Q 004939 633 KIPLPPVDERKK------IVEDVDKDRRYAIDAALVRIMKSRKV-----------------------------LGHQQLV 677 (722)
Q Consensus 633 ~i~~~~~~e~~~------~~~~v~~~r~~~i~A~IVRimK~~k~-----------------------------l~~~~L~ 677 (722)
.+-..-....+- +..+.+.+=...+...|.+.+.++.. .+.+++.
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 322110000000 01122223333444444444444443 4555555
Q ss_pred HHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCC
Q 004939 678 SECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 714 (722)
Q Consensus 678 ~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d 714 (722)
..+.+.=-..-..+.++|...|+-||=-|-|++-...
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 87
>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=46.37 E-value=33 Score=28.30 Aligned_cols=35 Identities=3% Similarity=-0.031 Sum_probs=30.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHh
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 594 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 594 (722)
-++.|+-.... +.+|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 46778888888 899999999999999999988664
No 88
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=46.21 E-value=26 Score=35.98 Aligned_cols=47 Identities=19% Similarity=0.200 Sum_probs=40.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
-|..|+-+.++.+.+++.||++.+|++...+++-|..|- +.++|.+.
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 467889999999999999999999999999999999996 45666654
No 89
>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=45.84 E-value=47 Score=26.69 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=39.3
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccce
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKI 603 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~ki 603 (722)
++=|+.++-++...+..|+++|++.||-....+.-.|..+...|.++
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 45689999999988899999999999999999998888885434444
No 90
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=44.64 E-value=58 Score=31.14 Aligned_cols=54 Identities=20% Similarity=0.174 Sum_probs=40.5
Q ss_pred EEEEcHHHHHHHHhhcCCCC-cCHHHHHHHh--CCCHHHHHHHHhHhhhcccceeecCC
Q 004939 553 ELIVSTYQAATLLLFNTSDR-LSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 553 ~l~~s~~Q~~ILl~fn~~~~-~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
++--+.+..+|.-+..-.+. -+..+|++.+ +++.++++..|..|. +.++|.+..
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 33345556666665554433 3899999999 999999999999997 678998864
No 91
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=44.58 E-value=24 Score=28.02 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=27.3
Q ss_pred HHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 564 LLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 564 Ll~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
.-...+++.+|+.||+..++++++.|...|.-|..
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33445677899999999999999999999999974
No 92
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.28 E-value=46 Score=24.35 Aligned_cols=39 Identities=18% Similarity=0.312 Sum_probs=29.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
|.-+..|+.++. .+++..+|++.+|++...+...+..+.
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 357999999999999999998887663
No 93
>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=43.94 E-value=40 Score=31.76 Aligned_cols=44 Identities=14% Similarity=0.148 Sum_probs=34.9
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 560 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 560 Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
...|+..+-.++.+|-+||++.+|++...+++.|..|.. .+++.
T Consensus 16 ~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e--~~Lv~ 59 (158)
T TIGR00373 16 VGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYD--AGLAD 59 (158)
T ss_pred HHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCce
Confidence 345565554566899999999999999999999999974 45664
No 94
>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=43.74 E-value=38 Score=24.28 Aligned_cols=31 Identities=23% Similarity=0.389 Sum_probs=21.5
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHh
Q 004939 562 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 594 (722)
Q Consensus 562 ~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 594 (722)
.|+-++.++ +|+.+||+.+|++...+.+.|.
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 8999999999999999988764
No 95
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.83 E-value=35 Score=32.86 Aligned_cols=45 Identities=13% Similarity=0.086 Sum_probs=36.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
....||.++-.++.+|-++|++.+|++...++++|..|.. .+++.
T Consensus 23 ~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e--~gLv~ 67 (178)
T PRK06266 23 EGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYD--ARLAD 67 (178)
T ss_pred cHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeE
Confidence 3455666666767899999999999999999999999974 45665
No 96
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=42.75 E-value=38 Score=32.08 Aligned_cols=48 Identities=13% Similarity=0.171 Sum_probs=40.7
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 556 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
+.-.-..||..+.++...|+.+|++.+|++...+.+.++.|.. .+++.
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 3556778888899999999999999999999999999999963 45654
No 97
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=42.70 E-value=51 Score=24.18 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=28.5
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
+..|..++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344555554443 468999999999999999988877653
No 98
>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=42.65 E-value=26 Score=30.77 Aligned_cols=57 Identities=9% Similarity=0.108 Sum_probs=42.3
Q ss_pred eeecccc-CccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceee
Q 004939 661 LVRIMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 720 (722)
Q Consensus 661 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Y 720 (722)
|..+|.. .+.++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4444544 55799999999887642 457889999999999999999997644343444
No 99
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=42.64 E-value=33 Score=35.10 Aligned_cols=47 Identities=19% Similarity=0.287 Sum_probs=40.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
-|-.|+-+.++.+.++++||++.+|+++..++|=|..|. +.++|.+.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEE
Confidence 366788899999999999999999999999999999996 45677664
No 100
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=41.86 E-value=46 Score=24.62 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=17.5
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHh
Q 004939 571 DRLSYSEIMTQLNLTHDDLVRLLH 594 (722)
Q Consensus 571 ~~~t~~ei~~~t~i~~~~l~~~L~ 594 (722)
.++|+.||++.+|++...++..+.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 468999999999999999887765
No 101
>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=40.67 E-value=27 Score=33.74 Aligned_cols=26 Identities=19% Similarity=0.429 Sum_probs=22.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 572 RLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 572 ~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.+|+++|++.||+..+++..+|+.|-
T Consensus 150 ~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 150 SISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp -EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred eEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 69999999999999999999999883
No 102
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=40.17 E-value=66 Score=25.29 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=35.2
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-HHHHHHHHhHhhhcccceeecCC
Q 004939 556 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
++.-|.-||..+-+ +-+-|+.||++.+|+. ...+..+|..|. +.+.|.+.+
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 35567777765432 2367999999999997 899999999996 457777654
No 103
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=40.09 E-value=42 Score=31.72 Aligned_cols=50 Identities=30% Similarity=0.343 Sum_probs=37.2
Q ss_pred cCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 526 KTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 526 ~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
+++.+.|+|.+++- -|+-.+.- +...+|+++|++.+|.++..++++|..=
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 56899999987532 22222223 4457999999999999999999998754
No 104
>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=39.52 E-value=18 Score=26.13 Aligned_cols=44 Identities=7% Similarity=0.274 Sum_probs=33.0
Q ss_pred hhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhc
Q 004939 658 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLE 709 (722)
Q Consensus 658 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~ 709 (722)
+-.|+..+.....++..+|-.. ...+.+.+.+.|..|.++|||+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~--------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEK--------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHH--------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH--------hCCCHHHHHHHHHHHHHCcCcC
Confidence 4456667777788888777665 3468889999999999999985
No 105
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=39.11 E-value=47 Score=32.94 Aligned_cols=49 Identities=24% Similarity=0.318 Sum_probs=41.2
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 557 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 557 s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
|..-..||.++...+++.+.||++.+|+|...+..+++.|. +.+++..+
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 44455688889988999999999999999999999999996 56787644
No 106
>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=38.84 E-value=53 Score=25.84 Aligned_cols=56 Identities=13% Similarity=0.296 Sum_probs=34.4
Q ss_pred hhhhhhhheeeccccCc-cCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCC
Q 004939 653 RRYAIDAALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENP 715 (722)
Q Consensus 653 r~~~i~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~ 715 (722)
|+..|=.+|...+...+ .-+..||-.. +. +. +..-+...|+.|.++|||+|++.-+
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~----~g--~~-S~~tv~~~L~~Le~kG~I~r~~~~~ 63 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREIAEA----LG--LK-STSTVQRHLKALERKGYIRRDPGKA 63 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHHHHH----HT--SS-SHHHHHHHHHHHHHTTSEEEGCCSC
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHH----hC--CC-ChHHHHHHHHHHHHCcCccCCCCCC
Confidence 44445555555555544 3444444432 21 22 5788999999999999999998543
No 107
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=38.71 E-value=68 Score=31.51 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=35.3
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 562 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 562 ~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
.||......+++|..+|++.+|++...+.++|..|. +.+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le--~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLE--TEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEe
Confidence 455555555679999999999999999999999997 35777654
No 108
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=38.63 E-value=48 Score=30.97 Aligned_cols=48 Identities=13% Similarity=0.225 Sum_probs=40.7
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 556 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
++..--.||..+..+...|+.+|++.+|+++..+.+.++.|.. .+++.
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 4566778888888888999999999999999999999999974 35554
No 109
>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=38.47 E-value=45 Score=22.22 Aligned_cols=26 Identities=27% Similarity=0.482 Sum_probs=20.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 572 RLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 572 ~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
++|-+||++.+|++.+.+-+.|..|.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36789999999999999999998874
No 110
>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=38.41 E-value=74 Score=24.20 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=29.4
Q ss_pred cCCCCc-CHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 568 NTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 568 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
.....+ |..+|++.+|++...+.++|..|.. .++|...
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 333334 5999999999999999999999974 5676543
No 111
>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=38.23 E-value=2.5e+02 Score=26.63 Aligned_cols=59 Identities=22% Similarity=0.241 Sum_probs=42.3
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHh--CCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEeccc
Q 004939 560 QAATLLLFNTS-DRLSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 624 (722)
Q Consensus 560 Q~~ILl~fn~~-~~~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~ 624 (722)
...|+-.+... .++|..+|...+ +++...+.++|..|+. +-+|..+. +...-+|..|.+
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~-~g~i~~K~-----~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVE-EGKIVEKE-----YGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHh-CCCeeeee-----ecceEEEeeCcc
Confidence 35677777654 599999999988 6889999999999985 33555543 222456777754
No 112
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=37.55 E-value=52 Score=24.86 Aligned_cols=40 Identities=15% Similarity=0.233 Sum_probs=31.8
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 556 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.|.-+..||.++.. +.+..+|++.+|+++..+..++..+.
T Consensus 4 LT~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 4 LTERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp S-HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 35567778877765 57899999999999999999998885
No 113
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=37.45 E-value=52 Score=33.60 Aligned_cols=47 Identities=15% Similarity=0.159 Sum_probs=40.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
-|..|+..+++++.+++.||++.+|++...+++-|..|. +.+++.+.
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 466788899999999999999999999999999999985 34566654
No 114
>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=36.59 E-value=22 Score=27.96 Aligned_cols=54 Identities=24% Similarity=0.233 Sum_probs=32.6
Q ss_pred hhheeeccccCc-cCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 658 DAALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 658 ~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
=|.||..||++. .++.+||..++. +..+ ++.++.|-+.+=|+-+++ .++|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l~------~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYLS------LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHHT------SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHc------CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 467888999875 588888877653 3333 345566668889999974 47999976
No 115
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=36.43 E-value=48 Score=33.87 Aligned_cols=39 Identities=21% Similarity=0.224 Sum_probs=36.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
-|..|+.+.+.++.+++.||++.+|+++..++|-|..|-
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 578899999999999999999999999999999999875
No 116
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=36.15 E-value=63 Score=29.88 Aligned_cols=49 Identities=16% Similarity=0.318 Sum_probs=41.0
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 556 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
++-.-.-||..+.+....++.+|++.+|++...+.+.+..|. +.+++..
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~--~~GiI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLE--EEGVIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCceee
Confidence 345667788888888889999999999999999999999996 4567654
No 117
>PRK00215 LexA repressor; Validated
Probab=36.10 E-value=75 Score=31.18 Aligned_cols=51 Identities=20% Similarity=0.259 Sum_probs=39.8
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCC-CHHHHHHHHhHhhhcccceeecCC
Q 004939 556 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNL-THDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~-----~~~~t~~ei~~~t~i-~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
++.-|..||..+.+ ..+.|+.||++.+|+ +...+.+.|..|. +.+.+.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCC
Confidence 35678888876642 346899999999999 9999999999996 346776654
No 118
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=35.88 E-value=1.1e+02 Score=25.21 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=32.1
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 565 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 565 l~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
+..++.+.+|=++|++.+|++...+-++++.|-...+.|..
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEe
Confidence 34456678999999999999999999999999643344443
No 119
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=35.02 E-value=26 Score=30.31 Aligned_cols=46 Identities=11% Similarity=0.223 Sum_probs=38.3
Q ss_pred hhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcc
Q 004939 657 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 710 (722)
Q Consensus 657 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r 710 (722)
+|-.|++.+.....++..+|-.. +..+...+.++|..|.++|+|+|
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 45677888888888888877764 46788999999999999999995
No 120
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.55 E-value=1.2e+02 Score=32.92 Aligned_cols=92 Identities=12% Similarity=0.279 Sum_probs=63.5
Q ss_pred HHHhHHHHHHHHHHHHHHhhCCCC-------CCCCHHHHHHHHH-HHhhhhccCCCCCchHHHHHHHHHHHHHHHHhccc
Q 004939 8 LDQGWDYMQKGITKLKRILEGLPE-------SPFSSEEYMMLYT-TIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVL 79 (722)
Q Consensus 8 fd~~W~~l~~ai~~i~~~l~~~~~-------~~~s~~~y~~lY~-~vy~lc~~~~~~~~~~~LY~~l~~~l~~~l~~~~~ 79 (722)
=++.|+.|.-.+++|.+-.+|-.. +--|+.+|+.+|. +|-.+|... -|++.++.+..+ .||.+.+.
T Consensus 22 ~eedw~ai~~fceqinkdp~gp~lAv~LlaHKiqSPqe~EAl~altvLe~cmkn----cGekfH~evgkf--rFLNELIk 95 (594)
T KOG1086|consen 22 DEEDWKAIDGFCEQINKDPEGPLLAVRLLAHKIQSPQEWEALQALTVLEYCMKN----CGEKFHEEVGKF--RFLNELIK 95 (594)
T ss_pred hHHHHHHHHHHHHHHhcCCCCchhHHHHHHhhcCChhHHHHHHHHHHHHHHHHh----hhHHHHHHHHHH--HHHHHHHH
Confidence 478899999999998665444211 1236789999998 678888765 688888887764 44554331
Q ss_pred ccccccCchHHHHHHHHHHHHHHHHHHHHHHhhch
Q 004939 80 PSLSEKHDEYMLRELVKRWANHKVMVRWLSRFFHY 114 (722)
Q Consensus 80 ~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~Y 114 (722)
.+ -..|...|..=+...++|.-+|++
T Consensus 96 -vv--------sPKYlG~~tSekvKtkiIelLfsW 121 (594)
T KOG1086|consen 96 -VV--------SPKYLGSRTSEKVKTKIIELLFSW 121 (594)
T ss_pred -Hh--------CchhcchhhhHHHHHHHHHHHhhh
Confidence 11 124666777778888888887774
No 121
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=33.53 E-value=21 Score=27.24 Aligned_cols=45 Identities=11% Similarity=0.272 Sum_probs=29.6
Q ss_pred eeeccccCcc--CChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCC
Q 004939 661 LVRIMKSRKV--LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 713 (722)
Q Consensus 661 IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~ 713 (722)
|...+..... ++..+|... +..+.+.+.+.|..|+++|||+|..+
T Consensus 10 vL~~l~~~~~~~~t~~~la~~--------l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 10 VLMALARHPGEELTQSELAER--------LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHSTTSGEEHHHHHHH--------HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHCCCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 3333444443 555555543 34577889999999999999999764
No 122
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=33.50 E-value=1.3e+02 Score=27.15 Aligned_cols=67 Identities=15% Similarity=0.210 Sum_probs=48.0
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCC---CCeEEecccCC
Q 004939 558 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQ---SDHFEFNSKFT 626 (722)
Q Consensus 558 ~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~---~~~~~~N~~f~ 626 (722)
.--..+|-+..+.+..|+.|+++.+|-+.+.|.+.|..|. .++++..+.+|+.-.+ =+.+.++-.|.
T Consensus 64 p~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 64 PRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred hhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 3344556677888899999999999999999999999996 5788877654443222 13344555554
No 123
>PRK13239 alkylmercury lyase; Provisional
Probab=33.15 E-value=75 Score=31.32 Aligned_cols=40 Identities=15% Similarity=0.257 Sum_probs=35.2
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 558 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 558 ~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.+...||.++-++..+|+.+|+..+|.+.+.+.+.|+.|.
T Consensus 22 ~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 22 TLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 3566777778888999999999999999999999999884
No 124
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=33.11 E-value=6.2e+02 Score=26.89 Aligned_cols=160 Identities=14% Similarity=0.262 Sum_probs=81.6
Q ss_pred hHHHHhhcCcHHHHHHHHHhhccC---CCChHHHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCCcchHHHHHHHHHHH
Q 004939 254 GCRALLREDKVEDLSRMYRLYHKI---PKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELH 330 (722)
Q Consensus 254 gl~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~I~~ll~l~ 330 (722)
.|..-+++++...+.+.++||--+ +.|++.....+.+.|....+.+.+.... ... ++..+..|+..+..++
T Consensus 15 ~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~---~~~---~~~~~~~~a~~lt~Lf 88 (324)
T smart00762 15 RFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAG---ASD---DTRAAVFYADTLTHLF 88 (324)
T ss_pred HHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhcccc---ccc---cccccchHHHHHHHHH
Confidence 367777888999999999998655 3566666665655555554444332211 000 1122334544444444
Q ss_pred HHH-------HHHHHHhcCCChHHH------HHHHHH----HHHHhhCCCCCCCcHHHHHHHHHHHhhc-----------
Q 004939 331 DKY-------MEYVTNCFINHTLFH------KALKEA----FEIFCNKAVGGSSSSELLATFCDNILKK----------- 382 (722)
Q Consensus 331 ~~~-------~~l~~~~F~~~~~f~------~~l~~a----f~~~~N~~~~~~~~~e~La~y~d~~lk~----------- 382 (722)
+.. ..++..+|+.+.... ...+.- +..|..... -.+....+..|....+..
T Consensus 89 e~ia~ii~~h~~~I~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~-l~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 167 (324)
T smart00762 89 ENVATIIEQHQPVIEKYYGPDGMLYVITKLQKEADLQGGIILDTFMDERR-IDRLISDINSYNHAQLHAGASNDARASSN 167 (324)
T ss_pred HHHHHHHHhccHHHHHHcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhh-HHHHHHHHHHhhccccccccccccccccc
Confidence 443 456777887543221 111111 111111110 001111122232221111
Q ss_pred CCCCCCChHHHHHHHHHHhhheecccChhHHHHHHHHHHHHHhcC
Q 004939 383 GGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLF 427 (722)
Q Consensus 383 ~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~ 427 (722)
+.....+..+++..|+.+..+..... .|.++++.|.-.
T Consensus 168 ~~~~~~d~revd~lL~Eis~i~~~~~-------lY~rFi~~k~~~ 205 (324)
T smart00762 168 GEDEGLDPRELDAILEEISQILSRWE-------LYCRFISRKINE 205 (324)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHhHH-------HHHHHHHHHHhh
Confidence 01123455688888998888876544 899999998774
No 125
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=32.98 E-value=54 Score=35.47 Aligned_cols=64 Identities=22% Similarity=0.316 Sum_probs=41.1
Q ss_pred EEeccCCceEEEEeEecCeeEEEEE-------cHHHHHHHHhhcC-C-CCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 532 LTWIYSLGQCNINGKFEQKNIELIV-------STYQAATLLLFNT-S-DRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 532 L~w~~~lg~~~i~~~~~~~~~~l~~-------s~~Q~~ILl~fn~-~-~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
+.+.|.||..|=++ ++...-|+= +-+-..||-++-+ . ..+|+++|++.|||..+++...|++|-
T Consensus 282 IdFSYeLSr~E~~~--GsPEKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 282 IDFSYELSRREGKI--GSPEKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhcccCcC--CCCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 56778888766554 322222221 2233344433333 2 239999999999999999999999983
No 126
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=32.85 E-value=27 Score=35.11 Aligned_cols=35 Identities=11% Similarity=0.246 Sum_probs=29.6
Q ss_pred hccCCCCChhHHHHHHHhhhhhhhhcccCCCCCcee
Q 004939 684 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 719 (722)
Q Consensus 684 l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~ 719 (722)
|..+|..+...++++|+.|++.|+|.|... +++|+
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 56665
No 127
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=32.22 E-value=17 Score=27.57 Aligned_cols=44 Identities=14% Similarity=0.323 Sum_probs=30.6
Q ss_pred eeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 661 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 661 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
+..++-..+.++..+|-. .+..+...+-+.+..|..+|||+|..
T Consensus 8 iL~~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 8 ILRILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 334444555566655544 34568899999999999999999864
No 128
>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=32.14 E-value=90 Score=23.50 Aligned_cols=31 Identities=16% Similarity=0.411 Sum_probs=25.4
Q ss_pred hhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 566 LFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 566 ~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
.|+.-...|++||++.+|++...+-.+|..-
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3565568999999999999999888877643
No 129
>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=32.07 E-value=95 Score=22.04 Aligned_cols=40 Identities=25% Similarity=0.373 Sum_probs=28.6
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 556 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
++..+..++.++- ..++|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445555554443 246899999999999999998877654
No 130
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=31.86 E-value=79 Score=30.47 Aligned_cols=64 Identities=16% Similarity=0.168 Sum_probs=48.0
Q ss_pred CceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 529 HRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 529 ~R~L~w~~~lg~~~i~~~~~~~~~~l~~s~~Q~~ILl~fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.|.-.|.+.+|..+++-- ..| .||+.||.-|+.-.. -..||.+-||+..+++.+++...|..+.
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 344457888888887642 334 467799988875443 3489999999999999999998888774
No 131
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=31.74 E-value=65 Score=22.46 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=20.3
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 570 SDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 570 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.+.+|+++||+..|++...+.+..+...
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4579999999999999998888776553
No 132
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=31.49 E-value=63 Score=33.41 Aligned_cols=48 Identities=6% Similarity=0.065 Sum_probs=40.7
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 558 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 558 ~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
--|..|+.+++..+.+++.||++.+|++...++|-|..|-. .+++.+.
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 45788999999998999999999999999999999999853 4566554
No 133
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=31.48 E-value=33 Score=24.84 Aligned_cols=43 Identities=12% Similarity=0.234 Sum_probs=32.2
Q ss_pred eeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 662 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 662 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
.+.+.+++.++..+|... |..+...+.+.|..|.++|+|.+..
T Consensus 6 l~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 6 LELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEee
Confidence 334444556776666654 4668899999999999999999865
No 134
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=31.35 E-value=67 Score=32.87 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=39.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
-+..|+-++++.+.+++.||++.++++...++|-|..|.. .++|.+.
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 4667888888889999999999999999999999999963 4666654
No 135
>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=31.14 E-value=27 Score=27.07 Aligned_cols=34 Identities=15% Similarity=0.313 Sum_probs=26.7
Q ss_pred hccCCCCChhHHHHHHHhhhhhhhhcccCCCCCce
Q 004939 684 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 718 (722)
Q Consensus 684 l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y 718 (722)
+.++|..+...+.+++..|.+.|+|.+.+. ++++
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 334688999999999999999999999874 3443
No 136
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=30.84 E-value=1.1e+02 Score=22.21 Aligned_cols=35 Identities=17% Similarity=0.360 Sum_probs=26.1
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhH
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 595 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 595 (722)
+.+.|+.+.-+. .|+.+++..+|++...+.+.+..
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 444555444332 69999999999999999887754
No 137
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=30.82 E-value=35 Score=28.51 Aligned_cols=37 Identities=22% Similarity=0.216 Sum_probs=33.1
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 686 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 686 ~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
.++..+.+.-+++|..|.++|.|..-..+...-+|.|
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 3678899999999999999999998888888999986
No 138
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.76 E-value=44 Score=33.27 Aligned_cols=54 Identities=22% Similarity=0.379 Sum_probs=43.7
Q ss_pred eeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceeecC
Q 004939 661 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 722 (722)
Q Consensus 661 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Yia 722 (722)
-|-..|+.|.+..++|-. .|....++.-.+|..|+..|.|.-.-+|++.|+||.
T Consensus 205 Fv~YIk~nKvV~ledLas--------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLAS--------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHH--------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 345667777777777765 366777777789999999999999999999999984
No 139
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=30.62 E-value=63 Score=31.34 Aligned_cols=40 Identities=13% Similarity=0.076 Sum_probs=36.4
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 558 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 558 ~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.-+..|+.+.+.++.+++.+|++.+|++...+++-|..|.
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~ 46 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELG 46 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHh
Confidence 3567888899999999999999999999999999999886
No 140
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=30.51 E-value=47 Score=29.77 Aligned_cols=52 Identities=21% Similarity=0.366 Sum_probs=45.3
Q ss_pred hhhhhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCC
Q 004939 654 RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 713 (722)
Q Consensus 654 ~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~ 713 (722)
...|.+.||-..++++.++..+|... +..+...+++.+..|+++|.|-+.+.
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 46789999999999999999999885 45688899999999999999988763
No 141
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.51 E-value=79 Score=32.68 Aligned_cols=38 Identities=18% Similarity=0.299 Sum_probs=30.5
Q ss_pred HHHHHHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 559 YQAATLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 559 ~Q~~ILl~fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
+...|+-.+.+ ...+|+++|++.|||..+++..+|+.|
T Consensus 209 W~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 209 WTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 44455554433 568999999999999999999999987
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=30.36 E-value=1e+02 Score=30.13 Aligned_cols=50 Identities=18% Similarity=0.184 Sum_probs=40.1
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-HHHHHHHHhHhhhcccceeecC
Q 004939 556 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
++..|..||....+ .-+.|+.||++.+|++ ...+.++|..|. +.++|.+.
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 46788888877653 2358899999999998 999999999996 45777765
No 143
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=30.10 E-value=32 Score=34.82 Aligned_cols=35 Identities=23% Similarity=0.310 Sum_probs=29.2
Q ss_pred hccCCCCChhHHHHHHHhhhhhhhhcccCCCCCcee
Q 004939 684 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 719 (722)
Q Consensus 684 l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~ 719 (722)
|...|..+...++++|+.|++.|+|.|... +++|+
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 56665
No 144
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=29.79 E-value=1.1e+02 Score=29.55 Aligned_cols=45 Identities=13% Similarity=0.221 Sum_probs=36.0
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 562 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 562 ~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
-++.-++.++..|..+|+..+|++..++.++|-.|. +.+.+...+
T Consensus 17 ~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~--~~~~v~~~~ 61 (183)
T PHA03103 17 KEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQ--REGMVYMSD 61 (183)
T ss_pred HHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHH--hcCceecCC
Confidence 355666778899999999999999999999999996 345555443
No 145
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=29.64 E-value=62 Score=30.05 Aligned_cols=30 Identities=13% Similarity=0.207 Sum_probs=27.0
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 569 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 569 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
.++.+|-++|++.+|++...|++.|..|..
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 445799999999999999999999999974
No 146
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.47 E-value=59 Score=23.53 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=21.2
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 563 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 563 ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
++.++.+ +.|..+|++.+|++...+.+-+..+
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 7899999999999999988776654
No 147
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=29.15 E-value=77 Score=35.92 Aligned_cols=50 Identities=12% Similarity=0.133 Sum_probs=43.3
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 555 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
.+|..|..||..+...+.+|..+|++.+|++...+.+.+.+|.. .+++..
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 46789999999998888999999999999999999999999963 356554
No 148
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=28.84 E-value=38 Score=25.26 Aligned_cols=28 Identities=7% Similarity=0.172 Sum_probs=24.4
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhcccCC
Q 004939 686 RMFKPDIKAIKKRMEDLITRDYLERDKE 713 (722)
Q Consensus 686 ~~F~~~~~~ik~~Ie~Liereyl~r~~~ 713 (722)
..|..+...+.+.+..|.+.|+|.+...
T Consensus 28 ~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 28 AQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3577899999999999999999988763
No 149
>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=28.57 E-value=95 Score=25.95 Aligned_cols=45 Identities=16% Similarity=0.236 Sum_probs=36.0
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHh-CCCHHHHHHHHhHhhhcccceeecC
Q 004939 560 QAATLLLFNTSDRLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 560 Q~~ILl~fn~~~~~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
-+.||..... +...+.||.+.+ |++...|.+.|..|. ..+++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~--~~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELE--EAGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHH--Hcchhhcc
Confidence 4567766666 688999999999 999999999999997 45788764
No 150
>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=27.95 E-value=91 Score=27.85 Aligned_cols=48 Identities=19% Similarity=0.221 Sum_probs=36.8
Q ss_pred HHHHHHHHhhcCC--------CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 558 TYQAATLLLFNTS--------DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 558 ~~Q~~ILl~fn~~--------~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
.+.-..|+..|.. -++|.++||..++-+.+.++.+|..|. +.+++...
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 3455555555543 489999999999999999999999986 67777653
No 151
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=27.94 E-value=74 Score=28.51 Aligned_cols=38 Identities=8% Similarity=0.065 Sum_probs=31.9
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 568 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 568 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
++.-++|.++||..++-+.+.++.+|..|. +.+++...
T Consensus 49 ~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 49 SGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred CCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 344589999999999999999999999996 67777653
No 152
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=27.90 E-value=36 Score=34.22 Aligned_cols=34 Identities=15% Similarity=0.373 Sum_probs=28.9
Q ss_pred ccCCCCChhHHHHHHHhhhhhhhhcccCCCCCcee
Q 004939 685 SRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 719 (722)
Q Consensus 685 ~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~ 719 (722)
..+|..+...+.++|+.|.+.|+|.|... +++|+
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 34699999999999999999999999864 56665
No 153
>PHA02591 hypothetical protein; Provisional
Probab=27.85 E-value=73 Score=25.88 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=22.1
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHhH
Q 004939 571 DRLSYSEIMTQLNLTHDDLVRLLHS 595 (722)
Q Consensus 571 ~~~t~~ei~~~t~i~~~~l~~~L~~ 595 (722)
.++|.++||+.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3799999999999999999887765
No 154
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=27.71 E-value=37 Score=34.35 Aligned_cols=51 Identities=12% Similarity=0.359 Sum_probs=37.0
Q ss_pred eeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCcee
Q 004939 661 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 719 (722)
Q Consensus 661 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~ 719 (722)
|...++....|.-+ .+|...|..+...++++|+.|++.|+|.|... +++|+
T Consensus 25 I~~~~~~G~~LPsE-------~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 25 LRQHYRCGDYLPAE-------QQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred HhcccCCCCcCCCH-------HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 33345665555532 23444699999999999999999999999874 56664
No 155
>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=27.67 E-value=1e+02 Score=25.90 Aligned_cols=38 Identities=11% Similarity=0.252 Sum_probs=24.4
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccce
Q 004939 565 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKI 603 (722)
Q Consensus 565 l~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~ki 603 (722)
.+..+... ++..|.+.||||...++.+|.+|......+
T Consensus 15 ~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~ 52 (90)
T PF09904_consen 15 YLIDSGER-NVPALMEATGMPRRTIQDTIKALPELGIEC 52 (90)
T ss_dssp HHHHHS-B--HHHHHHHH---HHHHHHHHHGGGGGT-EE
T ss_pred HHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcCCeEE
Confidence 34444555 999999999999999999999997433333
No 156
>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=27.56 E-value=2.1e+02 Score=23.50 Aligned_cols=48 Identities=15% Similarity=0.240 Sum_probs=37.5
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+++.|=+.-....++.-++|++.++++...++..+..|- ..++|.+.|
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le--~lGlve~~p 57 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE--ELGLVESQP 57 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH--HCCCccCCC
Confidence 444555555667799999999999999999999999985 467886543
No 157
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=26.48 E-value=89 Score=31.68 Aligned_cols=40 Identities=25% Similarity=0.309 Sum_probs=35.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
-|..|+..+++++.++.+||++.+|++...+++-|..|..
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3567888888888999999999999999999999999853
No 158
>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=26.44 E-value=48 Score=26.94 Aligned_cols=58 Identities=16% Similarity=0.255 Sum_probs=34.5
Q ss_pred hhhhhheeeccccCc--cCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhh---cccCCCCCceeecC
Q 004939 655 YAIDAALVRIMKSRK--VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYL---ERDKENPNMFRYLA 722 (722)
Q Consensus 655 ~~i~A~IVRimK~~k--~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl---~r~~~d~~~y~Yia 722 (722)
...=|.||..||++. .++.+||..++.. +... ..++.-+. +-.-+ +-+.. .++|.|.|
T Consensus 8 ~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~-----~d~~-~~~~~~L~---~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 8 FTQLAKIVDYMKKRHQHPLTLDEILDYLSL-----LDIG-PKLKEWLK---SEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhhHHHHHHHHHhcCCCCccHHHHHHHHhc-----cCcc-HHHHHHHH---hhhhccCceeccC-CCEEEecc
Confidence 345578999999987 6898888887642 2222 22333332 22233 44443 46899875
No 159
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=26.33 E-value=1e+02 Score=26.47 Aligned_cols=53 Identities=8% Similarity=0.156 Sum_probs=42.6
Q ss_pred hhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcc
Q 004939 657 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 710 (722)
Q Consensus 657 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r 710 (722)
++-+|..++. .+.++=-+|.+++.+...+.+.++...+=..+..|-++|+|++
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 3445556665 4677888999998877655568889999999999999999998
No 160
>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=26.29 E-value=1.2e+03 Score=27.87 Aligned_cols=132 Identities=17% Similarity=0.320 Sum_probs=74.4
Q ss_pred HHHHHHHHHHHHHHHhhHhcCChhHHHHHHHHHHHHHHHHHchhcCCCchHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Q 004939 179 HMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRAL 258 (722)
Q Consensus 179 ~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~ll~~~~sgl~~l 258 (722)
-+++...-||..++.--. ...+..+.+.|...++++.+..-..+-.....+|..-+ .|+..+
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 344555556666555433 35567888888888888887554333333333443322 233334
Q ss_pred hhcC-----------cHHHHHHHHHhh--ccCCCChHHHHHHHHHHHHHHH------HHHHHhhHHHhhhcCCCCCCcch
Q 004939 259 LRED-----------KVEDLSRMYRLY--HKIPKGLEPVANVFKQHITAEG------TVLVQQAEDAATNQGGSSGAVQE 319 (722)
Q Consensus 259 l~~~-----------~~~~L~~ly~L~--~~~~~~l~~l~~~~~~~i~~~g------~~i~~~~~~~~~~~~~~~~~~~~ 319 (722)
+... ....|+.+-.-+ +.+..+++.+.+.+.+|+...+ ..++.. -.
T Consensus 613 ~~~~~~~ei~~~~~ySk~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~---------------vW 677 (701)
T PF09763_consen 613 LQTVSPEEISYQAAYSKQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQV---------------VW 677 (701)
T ss_pred HhccCchhcccchhccHHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHH---------------HH
Confidence 3321 245555555543 2234566777777777761111 112211 23
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC
Q 004939 320 QVLIRKIIELHDKYMEYVTNCFIN 343 (722)
Q Consensus 320 ~~~I~~ll~l~~~~~~l~~~~F~~ 343 (722)
..+-...++.|.++..++..|+.|
T Consensus 678 ~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 678 SAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCC
Confidence 445677889999999999999874
No 161
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.39 E-value=1.3e+02 Score=27.08 Aligned_cols=48 Identities=15% Similarity=0.266 Sum_probs=39.4
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 558 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 558 ~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
.+.+-|+-+.-+++.+|+.++...||.+-..+++++.-|+. .+-|..+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~ 59 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeC
Confidence 35677888888899999999999999999999999999873 2344443
No 162
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=25.37 E-value=42 Score=33.95 Aligned_cols=36 Identities=17% Similarity=0.389 Sum_probs=30.2
Q ss_pred HhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCcee
Q 004939 683 QLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 719 (722)
Q Consensus 683 ~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~ 719 (722)
+|...|.++...++++|..|.+.|+|.|... +++|+
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 3445799999999999999999999999864 56665
No 163
>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=25.31 E-value=1.1e+02 Score=24.77 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=39.0
Q ss_pred HHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 558 TYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 558 ~~Q~~ILl~fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
..|.++|..... ..+++-.+|+..+|++...+-..++.|. +.+++.+.
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 467888887764 3588999999999999999999999996 45677764
No 164
>PRK14999 histidine utilization repressor; Provisional
Probab=25.27 E-value=41 Score=33.99 Aligned_cols=47 Identities=15% Similarity=0.289 Sum_probs=35.6
Q ss_pred ccccCccC-ChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCcee
Q 004939 664 IMKSRKVL-GHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 719 (722)
Q Consensus 664 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~ 719 (722)
.++....| +-.+|.+ .|..+...|+++|+.|.+.|+|.|... +++|+
T Consensus 29 ~~~~G~~LPsE~eLa~--------~~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSEAELVA--------QYGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 45555555 4444444 588999999999999999999999874 56765
No 165
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=25.20 E-value=1.2e+02 Score=30.98 Aligned_cols=42 Identities=21% Similarity=0.394 Sum_probs=34.0
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 563 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 563 ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
||++.-+ ++-|++||...++++...+..+|..|. +.+++.+.
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 5555555 688999999999999999999999986 45677654
No 166
>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=25.09 E-value=48 Score=24.75 Aligned_cols=23 Identities=17% Similarity=0.528 Sum_probs=19.1
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHH
Q 004939 571 DRLSYSEIMTQLNLTHDDLVRLL 593 (722)
Q Consensus 571 ~~~t~~ei~~~t~i~~~~l~~~L 593 (722)
+.+++.|||+.+|++..++.+.|
T Consensus 2 ~~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 2 EKIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH
T ss_pred CceEHHHHHHHHCcCHHHHHHHH
Confidence 35789999999999999998877
No 167
>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=24.69 E-value=61 Score=25.08 Aligned_cols=52 Identities=12% Similarity=0.133 Sum_probs=33.9
Q ss_pred eeeccccCccCChhhHHHHHHHH--hccCCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 661 LVRIMKSRKVLGHQQLVSECVEQ--LSRMFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 661 IVRimK~~k~l~~~~L~~~v~~~--l~~~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
|+..+..-..++.+.+.+...-. -...++++.++++..++.+++.|-|+-++
T Consensus 2 I~gMLtN~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~~ 55 (60)
T PF08672_consen 2 IVGMLTNLGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECSG 55 (60)
T ss_dssp HHHHHHHH-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--T
T ss_pred HhHHhhcCCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEecC
Confidence 34445555667777777766544 23568899999999999999999998874
No 168
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=24.43 E-value=92 Score=28.07 Aligned_cols=40 Identities=15% Similarity=0.304 Sum_probs=31.8
Q ss_pred cccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 665 MKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 665 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
|..++.++.++|-+.+ .-+.+.+-+++.+|++.|.+.|..
T Consensus 37 L~~~~~~tvdelae~l--------nr~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 37 LEENGPLTVDELAEIL--------NRSRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HhhcCCcCHHHHHHHH--------CccHHHHHHHHHHHHHcCCeeeee
Confidence 3467788887776654 347888999999999999999965
No 169
>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=24.31 E-value=56 Score=28.50 Aligned_cols=42 Identities=17% Similarity=0.335 Sum_probs=30.8
Q ss_pred cCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcc--cCCCCC
Q 004939 667 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER--DKENPN 716 (722)
Q Consensus 667 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r--~~~d~~ 716 (722)
..+.++..+|... ...+.+.+-+.|..|.++|||.| ++.|+.
T Consensus 40 ~~~~~t~~eL~~~--------l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R 83 (109)
T TIGR01889 40 NEGKLTLKEIIKE--------ILIKQSALVKIIKKLSKKGYLSKERSEDDER 83 (109)
T ss_pred cCCcCcHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEeccCCcccCC
Confidence 4456777666654 34577889999999999999997 555543
No 170
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.28 E-value=48 Score=24.61 Aligned_cols=21 Identities=5% Similarity=0.325 Sum_probs=18.3
Q ss_pred CCCChhHHHHHHHhhhhhhhh
Q 004939 688 FKPDIKAIKKRMEDLITRDYL 708 (722)
Q Consensus 688 F~~~~~~ik~~Ie~Liereyl 708 (722)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 456788999999999999986
No 171
>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=24.28 E-value=99 Score=32.10 Aligned_cols=57 Identities=14% Similarity=0.274 Sum_probs=32.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccC
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 625 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f 625 (722)
+--.|.-+|.++.-|++.+|.+.|+-|+..|+.+|..++ ++.+.+. -...|.|=..|
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 445677789999999999999999999999999998774 5665532 12456655444
No 172
>PRK11050 manganese transport regulator MntR; Provisional
Probab=23.77 E-value=1.3e+02 Score=28.02 Aligned_cols=43 Identities=12% Similarity=0.161 Sum_probs=34.6
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 562 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 562 ~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
.|+.++...+.++..+|++.++++...+.+.|..|.. .+++.+
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 4455666777899999999999999999999999964 356654
No 173
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=23.71 E-value=5.6e+02 Score=24.60 Aligned_cols=62 Identities=10% Similarity=0.068 Sum_probs=37.2
Q ss_pred HHHHHhhhhccCCCCCc--hHHHHHHHHHHHHHHHHhcccccccccCchHHHHHHHHHHHHHHHHHHHHHHhhchh
Q 004939 42 LYTTIYNMCTQKPPHDY--SQQLYDKYKQAFEEYISSMVLPSLSEKHDEYMLRELVKRWANHKVMVRWLSRFFHYL 115 (722)
Q Consensus 42 lY~~vy~lc~~~~~~~~--~~~LY~~l~~~l~~~l~~~~~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YL 115 (722)
|+-.+|++...+|.... -..||+++-+.+++- .. -.=.+..-+.|.-|..-++-|++|+.+|
T Consensus 126 LryDL~tiIsskP~~eK~~L~~LankLFdnvt~L-Dy-----------AAR~K~~~eae~yY~~Tv~slddVl~~l 189 (190)
T PLN02999 126 LSQDLTNAMNILPESRRNDYVQAANELVENMSEL-DY-----------YVRTPKVYESYLYYEKTLKSIDNVVELL 189 (190)
T ss_pred HHHHHHHHHhcCCHhhhHHHHHHHHHHhhhHHHH-HH-----------HHhcCChHHHHHHHHHHHHHHHHHHHHh
Confidence 67788888887742211 222444444433321 10 0112235678999999999999999887
No 174
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=23.66 E-value=1.7e+02 Score=23.73 Aligned_cols=43 Identities=21% Similarity=0.220 Sum_probs=30.3
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceee
Q 004939 560 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 605 (722)
Q Consensus 560 Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 605 (722)
-+-||.... .++.+..+|+..+|++...+.+.|..|.. .+++.
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 56788999999999999999999999973 46664
No 175
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=23.31 E-value=1.4e+02 Score=27.43 Aligned_cols=43 Identities=16% Similarity=0.262 Sum_probs=34.1
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeec
Q 004939 562 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 606 (722)
Q Consensus 562 ~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 606 (722)
.|..+.+..+..++.+|++.++++...+.+.|..|.. .+++..
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~--~Gli~~ 54 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDK--DEYLIY 54 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHH--CCCEEE
Confidence 3444556677889999999999999999999999963 466653
No 176
>PLN03239 histone acetyltransferase; Provisional
Probab=23.11 E-value=1.2e+02 Score=32.45 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=29.6
Q ss_pred HHHHHHHhhcCC----CCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 559 YQAATLLLFNTS----DRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 559 ~Q~~ILl~fn~~----~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
+...|+-.+-+. ..+|+++|+..|||..+++..+|+.|
T Consensus 267 W~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 267 WGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred HHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 444555544222 46999999999999999999999988
No 177
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=22.96 E-value=1.1e+02 Score=26.85 Aligned_cols=48 Identities=17% Similarity=0.201 Sum_probs=37.1
Q ss_pred CChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCceee
Q 004939 671 LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 720 (722)
Q Consensus 671 l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~Y 720 (722)
.....++.+|+.... .+ ++...+--||+.||..|.|+-.++-.++-.|
T Consensus 62 ~~~arvIg~vl~~~~-~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 62 QKAARVIGEVLGHSD-QG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred cHHHHHHHHHHHhcC-cC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 455678899988864 34 6778899999999999999998865554443
No 178
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.72 E-value=1.6e+02 Score=24.99 Aligned_cols=53 Identities=15% Similarity=0.207 Sum_probs=43.6
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 554 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 554 l~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+..+.....||..+...++=...-|+..+++|.+++...|..|. ..++|.+..
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEec
Confidence 34567788899988877777778899999999999999999996 468887653
No 179
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=22.68 E-value=1.5e+02 Score=27.24 Aligned_cols=39 Identities=23% Similarity=0.222 Sum_probs=31.4
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 556 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 556 ~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
+|.-|..|+.++ ..++|.+||++.+|++...+...+...
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 577888888886 367999999999999998887655543
No 180
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=22.43 E-value=1.5e+02 Score=29.52 Aligned_cols=41 Identities=22% Similarity=0.288 Sum_probs=36.4
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 555 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.+|.-+..||.+... ++|.+|||+.+++++..++.++..+.
T Consensus 143 ~LS~RE~eVL~Lia~--G~SnkEIA~~L~IS~~TVk~hvs~I~ 183 (217)
T PRK13719 143 KVTKYQNDVFILYSF--GFSHEYIAQLLNITVGSSKNKISEIL 183 (217)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 468899999998876 58999999999999999999988875
No 181
>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=22.36 E-value=1.1e+02 Score=22.29 Aligned_cols=21 Identities=14% Similarity=0.390 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHh
Q 004939 574 SYSEIMTQLNLTHDDLVRLLH 594 (722)
Q Consensus 574 t~~ei~~~t~i~~~~l~~~L~ 594 (722)
|+.||++..|++...+-+.|+
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 689999999999999877775
No 182
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=22.14 E-value=65 Score=29.79 Aligned_cols=50 Identities=12% Similarity=0.247 Sum_probs=42.4
Q ss_pred hhhhhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 655 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 655 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
..+|..|.+++....+++..+|-..+ ..+++.+.++|+.|.+.|.|++-.
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 45678889999999999998888765 368889999999999999999854
No 183
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=21.99 E-value=93 Score=25.91 Aligned_cols=47 Identities=13% Similarity=0.224 Sum_probs=34.7
Q ss_pred hhheeeccccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 658 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 658 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
+..|...+...+.++..+|... +.++...+.+.|..|.++|+|.+..
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~--------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKR--------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH--------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 4455566666667777776554 3457778999999999999998764
No 184
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=21.98 E-value=1.9e+02 Score=27.80 Aligned_cols=45 Identities=22% Similarity=0.286 Sum_probs=34.1
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 561 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 561 ~~ILl~fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
..||.++...+ .+|..+|+..+||+...+.++|-.|. +.+.+..+
T Consensus 7 ~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~--~~~~v~~~ 52 (183)
T PHA02701 7 SLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLL--ESDAVSCE 52 (183)
T ss_pred HHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHh--hcCcEecC
Confidence 44665555554 69999999999999999999999986 33455443
No 185
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=21.82 E-value=54 Score=32.87 Aligned_cols=33 Identities=15% Similarity=0.275 Sum_probs=28.5
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhcccCCCCCcee
Q 004939 686 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 719 (722)
Q Consensus 686 ~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~ 719 (722)
..|..+...|.++|+.|++.|+|.|... +++|+
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 3599999999999999999999999874 56664
No 186
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=21.71 E-value=62 Score=29.66 Aligned_cols=26 Identities=8% Similarity=0.266 Sum_probs=22.2
Q ss_pred CCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 687 MFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 687 ~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 45567788999999999999999964
No 187
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=21.63 E-value=1.2e+02 Score=30.37 Aligned_cols=56 Identities=11% Similarity=0.236 Sum_probs=41.5
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEecccCC
Q 004939 561 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 626 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~f~ 626 (722)
..+.-+|.++..||+.+|.+.|+-|...|+.+|..++ ++.+.+. ...+|.+-..|.
T Consensus 189 d~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-----v~NkKg~-----~k~tyeLKPEYK 244 (254)
T KOG2905|consen 189 DMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-----VLNKKGP-----YKNTYELKPEYK 244 (254)
T ss_pred HHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-----HHhccCc-----ccCceecCHHHh
Confidence 3455678899999999999999999999999999885 4443321 135676665554
No 188
>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=21.61 E-value=1.3e+02 Score=23.12 Aligned_cols=39 Identities=21% Similarity=0.356 Sum_probs=29.9
Q ss_pred cCCCCc-CHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 568 NTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 568 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
..++.+ |..+|++..|++...+.++|..|.. .+++...+
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~--~g~i~~~~ 58 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEA--EGLIERRP 58 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEET
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHH--CCcEEEEC
Confidence 345678 9999999999999999999999974 56776543
No 189
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=21.58 E-value=1.1e+02 Score=24.49 Aligned_cols=45 Identities=13% Similarity=0.359 Sum_probs=25.6
Q ss_pred cccCccCChhhHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcccCCCCCce
Q 004939 665 MKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 718 (722)
Q Consensus 665 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y 718 (722)
....+..+-.++-. ++.. +..+...+. ..||+-|||+|+++. +.|
T Consensus 24 f~~g~~y~E~EVN~-~L~~----~~~D~a~LR---R~LVd~g~L~R~~dg-~~Y 68 (71)
T PF09860_consen 24 FEPGREYSEKEVNE-ILKR----FFDDYATLR---RYLVDYGLLERTRDG-SRY 68 (71)
T ss_pred CCCCCccCHHHHHH-HHHH----HcccHHHHH---HHHHHcCCeeecCCC-Cee
Confidence 34445555544333 2222 233544444 478999999999754 555
No 190
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=21.41 E-value=1.7e+02 Score=23.07 Aligned_cols=34 Identities=24% Similarity=0.364 Sum_probs=28.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 572 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 572 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
.+|-++||+.+|++...+.+.|..|. +-+++...
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~--~~g~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLK--DEGIIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHH--HTTSEEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEc
Confidence 58899999999999999999999996 34666543
No 191
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=21.31 E-value=1.4e+02 Score=29.42 Aligned_cols=42 Identities=21% Similarity=0.302 Sum_probs=37.1
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 555 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
..|.-|..||.++.+ ++|.+||++.+++++..++.++..+..
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 468899999999975 589999999999999999999988863
No 192
>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=21.06 E-value=68 Score=24.41 Aligned_cols=28 Identities=11% Similarity=0.255 Sum_probs=24.0
Q ss_pred ccCCCCChhHHHHHHHhhhhhhhhcccC
Q 004939 685 SRMFKPDIKAIKKRMEDLITRDYLERDK 712 (722)
Q Consensus 685 ~~~F~~~~~~ik~~Ie~Liereyl~r~~ 712 (722)
...|..+...+.+.|..|.++|+|.+.+
T Consensus 32 a~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 32 AEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 3356778999999999999999998875
No 193
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=21.03 E-value=1.5e+02 Score=24.82 Aligned_cols=47 Identities=17% Similarity=0.211 Sum_probs=34.5
Q ss_pred HHHHHhhcCCCCcCHHHHHHHh--CCCHHHHHHHHhHhhhcccceeecCCC
Q 004939 561 AATLLLFNTSDRLSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEPN 609 (722)
Q Consensus 561 ~~ILl~fn~~~~~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~kiL~~~~~ 609 (722)
+.|+...-+++-+|..++++.+ .++...+...+.-|. |.+++.++++
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLI--KkglIEKSGD 67 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLI--KKGLIEKSGD 67 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHH--HTTSEEEETT
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHH--HcCcccccCC
Confidence 4556666677788999999977 888899999898886 6688888753
No 194
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=20.99 E-value=1.6e+02 Score=24.74 Aligned_cols=40 Identities=23% Similarity=0.257 Sum_probs=31.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004939 559 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 598 (722)
Q Consensus 559 ~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 598 (722)
....+..++.....+++++|++.++++.+++...+..++.
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 4445555556778999999999999999999998888863
No 195
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=20.96 E-value=1.7e+02 Score=27.39 Aligned_cols=45 Identities=16% Similarity=0.284 Sum_probs=35.5
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecCC
Q 004939 562 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 608 (722)
Q Consensus 562 ~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 608 (722)
+|..++.+.......+|++.+++++..+...++-|. +.+++...+
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~~ 58 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYEP 58 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEec
Confidence 344555567789999999999999999999999986 456776543
No 196
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=20.93 E-value=61 Score=32.74 Aligned_cols=33 Identities=12% Similarity=0.264 Sum_probs=28.3
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhcccCCCCCcee
Q 004939 686 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 719 (722)
Q Consensus 686 ~~F~~~~~~ik~~Ie~Liereyl~r~~~d~~~y~ 719 (722)
..|..+...|+++|+.|...|+|.|... +++|+
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 3588999999999999999999999874 56664
No 197
>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=20.61 E-value=1e+02 Score=24.77 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=20.3
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004939 571 DRLSYSEIMTQLNLTHDDLVRLLHSL 596 (722)
Q Consensus 571 ~~~t~~ei~~~t~i~~~~l~~~L~~L 596 (722)
..-|.+|||+.+|++.+.+...+...
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 36799999999999999999888754
No 198
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=20.45 E-value=2.4e+02 Score=21.18 Aligned_cols=41 Identities=17% Similarity=0.198 Sum_probs=35.0
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004939 555 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 597 (722)
Q Consensus 555 ~~s~~Q~~ILl~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 597 (722)
.++.-+..++.++..+ .+..||+...+++...+..++....
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 4577788888888765 7999999999999999998888774
No 199
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=20.38 E-value=1.3e+02 Score=27.63 Aligned_cols=38 Identities=21% Similarity=0.288 Sum_probs=29.0
Q ss_pred EcHHHHHHHHh-hcCCCCcCHHHHHHHhCCCHHHHHHHHhH
Q 004939 556 VSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHS 595 (722)
Q Consensus 556 ~s~~Q~~ILl~-fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 595 (722)
+|+-|..|+.+ +- .+++.+||++.+|+|...+...+.-
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 45666666655 43 4689999999999999988876654
No 200
>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=20.36 E-value=2.1e+02 Score=21.26 Aligned_cols=41 Identities=20% Similarity=0.257 Sum_probs=32.0
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccceeecC
Q 004939 565 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 607 (722)
Q Consensus 565 l~fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 607 (722)
-+|.+++.+|+.++.+.+|++-+.....|.-|= +.++..+.
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 457788899999999999999998888887773 45666554
No 201
>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=20.10 E-value=1.4e+02 Score=23.18 Aligned_cols=22 Identities=9% Similarity=0.380 Sum_probs=19.0
Q ss_pred CCCCcCHHHHHHHhCCCHHHHH
Q 004939 569 TSDRLSYSEIMTQLNLTHDDLV 590 (722)
Q Consensus 569 ~~~~~t~~ei~~~t~i~~~~l~ 590 (722)
.++.+++.+||+.+|+++..+.
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHH
Confidence 4568999999999999998764
Done!