Query 003676
Match_columns 804
No_of_seqs 256 out of 1031
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 03:55:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003676hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2167 Cullins [Cell cycle co 100.0 3E-137 6E-142 1114.5 49.4 654 147-804 2-661 (661)
2 KOG2166 Cullins [Cell cycle co 100.0 1E-118 3E-123 1037.2 63.8 692 100-802 13-725 (725)
3 COG5647 Cullin, a subunit of E 100.0 8E-116 2E-120 968.7 59.5 697 98-804 14-773 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 1E-101 2E-106 801.3 49.4 662 104-804 11-728 (728)
5 PF00888 Cullin: Cullin family 100.0 6.6E-93 1.4E-97 840.0 60.7 576 108-706 1-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 1.3E-86 2.7E-91 695.1 54.3 700 100-804 9-777 (777)
7 smart00182 CULLIN Cullin. 100.0 2E-33 4.3E-38 270.2 17.9 141 486-627 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 1.4E-26 3E-31 257.1 45.6 308 482-801 444-762 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 5.3E-19 1.1E-23 146.9 6.1 66 733-798 1-68 (68)
10 KOG2167 Cullins [Cell cycle co 97.6 0.00043 9.4E-09 78.0 11.8 313 103-440 109-458 (661)
11 PF08539 HbrB: HbrB-like; Int 97.4 0.0022 4.7E-08 62.4 11.8 124 104-229 5-149 (158)
12 TIGR01610 phage_O_Nterm phage 93.8 0.2 4.4E-06 44.5 6.9 66 633-706 20-93 (95)
13 PF09339 HTH_IclR: IclR helix- 92.7 0.17 3.8E-06 39.4 4.1 46 641-688 6-52 (52)
14 PF02082 Rrf2: Transcriptional 91.9 0.44 9.5E-06 41.2 6.1 59 639-704 11-70 (83)
15 PF13412 HTH_24: Winged helix- 91.4 0.41 8.8E-06 36.5 4.8 46 637-684 2-47 (48)
16 PF12802 MarR_2: MarR family; 91.1 0.29 6.3E-06 39.4 3.9 51 636-688 3-55 (62)
17 PF08220 HTH_DeoR: DeoR-like h 89.5 0.6 1.3E-05 37.3 4.3 47 640-688 2-48 (57)
18 PF13463 HTH_27: Winged helix 89.0 0.6 1.3E-05 38.2 4.2 51 636-688 1-52 (68)
19 PF01047 MarR: MarR family; I 88.1 0.4 8.7E-06 38.2 2.5 50 637-688 2-51 (59)
20 PF12840 HTH_20: Helix-turn-he 87.6 0.79 1.7E-05 37.0 4.0 50 637-688 9-58 (61)
21 TIGR02337 HpaR homoprotocatech 87.5 1.2 2.5E-05 41.2 5.6 52 635-688 25-76 (118)
22 PF09012 FeoC: FeoC like trans 87.3 0.64 1.4E-05 38.6 3.4 46 744-795 4-49 (69)
23 PF01022 HTH_5: Bacterial regu 86.3 1.7 3.7E-05 33.0 5.0 43 640-685 4-46 (47)
24 PRK11512 DNA-binding transcrip 84.8 2 4.3E-05 41.2 5.9 53 634-688 36-88 (144)
25 PF04492 Phage_rep_O: Bacterio 84.6 2.9 6.4E-05 37.5 6.4 62 635-706 29-98 (100)
26 smart00550 Zalpha Z-DNA-bindin 84.3 2 4.2E-05 35.7 4.8 47 639-687 7-55 (68)
27 smart00347 HTH_MARR helix_turn 82.6 2.5 5.5E-05 37.0 5.3 53 633-687 5-57 (101)
28 TIGR01889 Staph_reg_Sar staphy 82.5 3.3 7.2E-05 37.7 6.1 53 634-688 21-77 (109)
29 TIGR02698 CopY_TcrY copper tra 81.8 4.5 9.8E-05 38.2 6.8 60 742-804 6-65 (130)
30 PF01726 LexA_DNA_bind: LexA D 81.3 6.2 0.00013 32.4 6.6 59 735-797 5-63 (65)
31 smart00346 HTH_ICLR helix_turn 81.0 3.7 8E-05 35.6 5.6 45 642-688 9-54 (91)
32 smart00420 HTH_DEOR helix_turn 80.9 3.5 7.7E-05 31.4 4.9 45 641-687 3-47 (53)
33 PRK10857 DNA-binding transcrip 79.3 5.8 0.00013 39.1 6.9 58 640-704 12-70 (164)
34 PRK11920 rirA iron-responsive 78.8 6.1 0.00013 38.4 6.9 57 641-704 13-69 (153)
35 PF08318 COG4: COG4 transport 78.0 63 0.0014 35.7 15.3 160 343-509 7-213 (331)
36 PF13463 HTH_27: Winged helix 77.9 5.8 0.00012 32.3 5.5 54 741-800 4-60 (68)
37 PRK15090 DNA-binding transcrip 77.6 5.2 0.00011 42.4 6.5 143 641-794 17-197 (257)
38 PF01978 TrmB: Sugar-specific 77.6 2.3 5E-05 35.0 3.0 49 637-687 7-55 (68)
39 COG3682 Predicted transcriptio 77.3 5.8 0.00013 36.8 5.8 61 740-803 6-66 (123)
40 TIGR02010 IscR iron-sulfur clu 77.3 6.6 0.00014 37.2 6.5 45 640-686 12-57 (135)
41 smart00550 Zalpha Z-DNA-bindin 76.8 8.7 0.00019 31.8 6.2 54 741-800 7-62 (68)
42 PF03965 Penicillinase_R: Peni 76.7 2.4 5.1E-05 39.0 3.1 61 741-804 4-64 (115)
43 PF04703 FaeA: FaeA-like prote 76.2 5.5 0.00012 32.4 4.7 47 643-691 5-52 (62)
44 PF01978 TrmB: Sugar-specific 75.5 2.2 4.8E-05 35.1 2.3 57 741-803 9-65 (68)
45 PHA00738 putative HTH transcri 75.1 7.2 0.00016 35.3 5.5 68 633-706 7-74 (108)
46 PRK13777 transcriptional regul 75.1 6.6 0.00014 39.5 6.0 53 634-688 41-93 (185)
47 PRK03573 transcriptional regul 74.1 6.1 0.00013 37.7 5.4 53 634-688 27-80 (144)
48 cd00090 HTH_ARSR Arsenical Res 74.1 7.5 0.00016 31.6 5.3 48 637-687 6-53 (78)
49 smart00419 HTH_CRP helix_turn_ 73.0 8.4 0.00018 28.7 4.9 34 652-687 8-41 (48)
50 PF08279 HTH_11: HTH domain; 72.6 7.8 0.00017 30.2 4.8 36 643-678 5-41 (55)
51 COG3355 Predicted transcriptio 72.3 9.5 0.00021 35.6 5.9 37 649-687 39-75 (126)
52 PF08220 HTH_DeoR: DeoR-like h 72.0 6.7 0.00015 31.2 4.2 47 743-795 3-49 (57)
53 PF13601 HTH_34: Winged helix 71.9 3.2 7E-05 35.6 2.6 44 641-686 3-46 (80)
54 PF05732 RepL: Firmicute plasm 71.5 5.4 0.00012 39.3 4.4 49 652-709 75-123 (165)
55 smart00345 HTH_GNTR helix_turn 71.1 8 0.00017 30.2 4.6 40 647-688 14-54 (60)
56 TIGR03879 near_KaiC_dom probab 71.0 4.7 0.0001 33.9 3.2 42 643-686 23-64 (73)
57 PRK10141 DNA-binding transcrip 71.0 6.6 0.00014 36.4 4.5 57 642-704 20-76 (117)
58 TIGR01884 cas_HTH CRISPR locus 71.0 6.7 0.00015 39.9 5.2 52 635-688 140-191 (203)
59 TIGR00738 rrf2_super rrf2 fami 70.9 10 0.00022 35.5 6.0 47 639-687 11-58 (132)
60 PRK10870 transcriptional repre 69.9 11 0.00024 37.5 6.3 52 635-688 52-105 (176)
61 PF05584 Sulfolobus_pRN: Sulfo 69.4 13 0.00027 31.2 5.3 41 643-686 10-50 (72)
62 COG1959 Predicted transcriptio 68.1 13 0.00029 36.0 6.2 59 639-704 11-70 (150)
63 PF01047 MarR: MarR family; I 67.2 5.6 0.00012 31.5 2.9 46 742-793 5-50 (59)
64 PRK11569 transcriptional repre 66.6 12 0.00026 40.0 6.2 45 642-688 32-77 (274)
65 PRK10163 DNA-binding transcrip 66.1 14 0.0003 39.6 6.5 56 641-704 28-84 (271)
66 COG1414 IclR Transcriptional r 65.5 14 0.00031 38.8 6.4 46 641-688 7-53 (246)
67 PRK09834 DNA-binding transcrip 65.2 13 0.00028 39.5 6.1 45 642-688 15-60 (263)
68 smart00344 HTH_ASNC helix_turn 65.2 12 0.00025 33.7 5.0 46 639-686 4-49 (108)
69 PRK04172 pheS phenylalanyl-tRN 64.8 66 0.0014 37.6 12.2 50 635-686 3-52 (489)
70 TIGR02944 suf_reg_Xantho FeS a 64.7 16 0.00035 34.2 5.9 43 643-687 14-58 (130)
71 TIGR02431 pcaR_pcaU beta-ketoa 64.3 15 0.00033 38.6 6.4 43 642-686 13-56 (248)
72 KOG4552 Vitamin-D-receptor int 64.2 1.7E+02 0.0036 29.6 12.8 85 362-464 57-142 (272)
73 smart00418 HTH_ARSR helix_turn 64.0 15 0.00032 28.8 4.9 49 745-800 2-50 (66)
74 smart00418 HTH_ARSR helix_turn 63.0 15 0.00033 28.8 4.8 36 650-687 8-43 (66)
75 PF10771 DUF2582: Protein of u 62.4 13 0.00028 30.6 4.1 43 642-684 12-55 (65)
76 PF13412 HTH_24: Winged helix- 61.5 17 0.00037 27.4 4.5 45 741-791 4-48 (48)
77 PF08784 RPA_C: Replication pr 59.8 15 0.00033 32.8 4.6 44 635-678 44-91 (102)
78 PF13730 HTH_36: Helix-turn-he 59.3 20 0.00044 27.8 4.7 28 654-683 27-54 (55)
79 COG1846 MarR Transcriptional r 58.9 20 0.00044 32.3 5.5 51 636-688 20-70 (126)
80 PF13404 HTH_AsnC-type: AsnC-t 58.9 17 0.00036 27.1 3.9 35 642-676 7-41 (42)
81 PF09756 DDRGK: DDRGK domain; 58.7 8.4 0.00018 38.7 3.0 58 741-804 100-157 (188)
82 PF08221 HTH_9: RNA polymerase 57.9 14 0.0003 30.0 3.6 35 649-685 24-58 (62)
83 PRK11014 transcriptional repre 57.2 31 0.00067 32.9 6.5 40 647-688 20-59 (141)
84 PF01325 Fe_dep_repress: Iron 55.8 27 0.00058 28.2 4.9 44 643-688 13-56 (60)
85 cd00092 HTH_CRP helix_turn_hel 55.5 21 0.00047 28.6 4.5 36 651-688 24-59 (67)
86 smart00420 HTH_DEOR helix_turn 54.7 27 0.00058 26.3 4.7 46 744-795 4-49 (53)
87 PF12395 DUF3658: Protein of u 54.5 40 0.00086 30.8 6.5 62 740-802 48-109 (111)
88 PF09763 Sec3_C: Exocyst compl 54.2 4.9E+02 0.011 31.9 21.2 65 362-426 630-701 (701)
89 PF02186 TFIIE_beta: TFIIE bet 53.9 22 0.00048 29.2 4.2 55 741-804 6-61 (65)
90 cd07153 Fur_like Ferric uptake 53.4 42 0.00092 30.4 6.6 58 744-802 5-63 (116)
91 COG2345 Predicted transcriptio 53.4 20 0.00044 36.8 4.8 44 641-686 14-57 (218)
92 PF08280 HTH_Mga: M protein tr 52.9 20 0.00042 28.7 3.7 38 640-677 7-44 (59)
93 PF12802 MarR_2: MarR family; 52.1 18 0.00039 28.7 3.4 49 741-795 6-56 (62)
94 PF02002 TFIIE_alpha: TFIIE al 52.1 11 0.00023 34.0 2.3 44 640-685 15-58 (105)
95 PF14394 DUF4423: Domain of un 52.1 37 0.0008 33.7 6.3 54 633-688 19-75 (171)
96 smart00344 HTH_ASNC helix_turn 51.4 27 0.00059 31.3 4.9 46 741-792 4-49 (108)
97 cd07377 WHTH_GntR Winged helix 51.2 31 0.00067 27.4 4.8 38 648-687 20-58 (66)
98 PF09012 FeoC: FeoC like trans 50.3 23 0.00049 29.2 3.8 40 645-686 7-46 (69)
99 PRK10434 srlR DNA-bindng trans 50.1 22 0.00048 37.7 4.7 47 640-688 7-53 (256)
100 PF04545 Sigma70_r4: Sigma-70, 46.7 47 0.001 25.3 4.9 33 640-674 10-42 (50)
101 PRK00135 scpB segregation and 46.6 2.3E+02 0.005 28.6 11.0 34 644-677 11-45 (188)
102 TIGR00373 conserved hypothetic 46.3 33 0.00072 33.5 4.9 43 641-685 17-59 (158)
103 PRK06266 transcription initiat 45.7 31 0.00067 34.4 4.6 44 640-685 24-67 (178)
104 PF08281 Sigma70_r4_2: Sigma-7 45.4 39 0.00085 26.0 4.3 24 651-674 25-48 (54)
105 TIGR02702 SufR_cyano iron-sulf 44.7 52 0.0011 33.4 6.3 44 642-687 5-48 (203)
106 PF01726 LexA_DNA_bind: LexA D 44.3 30 0.00064 28.4 3.5 51 636-688 4-60 (65)
107 COG4189 Predicted transcriptio 44.1 37 0.0008 35.0 4.8 49 637-687 22-70 (308)
108 PRK13509 transcriptional repre 44.1 38 0.00082 35.8 5.3 50 639-690 6-55 (251)
109 COG4190 Predicted transcriptio 43.9 64 0.0014 30.3 5.9 65 640-706 66-133 (144)
110 COG1349 GlpR Transcriptional r 43.4 33 0.00071 36.3 4.7 49 640-690 7-55 (253)
111 PRK00215 LexA repressor; Valid 43.1 52 0.0011 33.4 6.0 52 636-689 2-59 (205)
112 PF01853 MOZ_SAS: MOZ/SAS fami 42.0 25 0.00054 35.3 3.2 26 652-677 150-175 (188)
113 PRK11179 DNA-binding transcrip 41.4 47 0.001 32.1 5.1 49 636-686 7-55 (153)
114 PRK11169 leucine-responsive tr 40.4 44 0.00095 32.7 4.8 49 636-686 12-60 (164)
115 PF01638 HxlR: HxlR-like helix 39.4 47 0.001 28.9 4.3 45 640-687 7-52 (90)
116 PRK10906 DNA-binding transcrip 39.0 44 0.00096 35.3 4.9 49 640-690 7-55 (252)
117 PF07516 SecA_SW: SecA Wing an 38.5 4.5E+02 0.0097 26.8 12.8 131 103-242 56-210 (214)
118 PRK09802 DNA-binding transcrip 38.2 45 0.00098 35.6 4.8 49 638-688 17-65 (269)
119 PF00325 Crp: Bacterial regula 37.4 38 0.00082 23.7 2.6 25 653-677 3-27 (32)
120 PF09904 HTH_43: Winged helix- 36.5 78 0.0017 27.7 5.0 40 643-685 13-52 (90)
121 COG1522 Lrp Transcriptional re 36.0 51 0.0011 31.5 4.4 48 637-686 7-54 (154)
122 smart00347 HTH_MARR helix_turn 35.9 82 0.0018 27.1 5.5 49 741-795 11-59 (101)
123 PRK04424 fatty acid biosynthes 35.9 35 0.00077 34.2 3.4 46 639-686 8-53 (185)
124 PRK10411 DNA-binding transcrip 35.5 61 0.0013 34.0 5.2 46 640-687 6-51 (240)
125 PF09339 HTH_IclR: IclR helix- 35.4 41 0.00089 25.9 2.9 44 745-794 8-52 (52)
126 TIGR00498 lexA SOS regulatory 35.3 44 0.00095 33.7 4.0 51 636-688 4-60 (199)
127 PHA02943 hypothetical protein; 35.2 70 0.0015 30.9 4.9 54 643-703 16-69 (165)
128 PF08784 RPA_C: Replication pr 34.9 53 0.0011 29.3 4.0 46 740-791 47-96 (102)
129 COG1522 Lrp Transcriptional re 34.7 87 0.0019 29.9 5.8 50 739-794 7-56 (154)
130 PF10007 DUF2250: Uncharacteri 34.6 79 0.0017 28.0 4.8 53 634-688 3-55 (92)
131 PRK09334 30S ribosomal protein 34.2 75 0.0016 27.7 4.5 57 742-804 26-85 (86)
132 KOG2747 Histone acetyltransfer 34.0 49 0.0011 37.0 4.2 64 612-677 282-354 (396)
133 TIGR02337 HpaR homoprotocatech 33.8 1.1E+02 0.0023 27.9 6.0 47 742-794 30-76 (118)
134 cd06170 LuxR_C_like C-terminal 33.2 91 0.002 23.6 4.7 38 638-677 3-40 (57)
135 smart00421 HTH_LUXR helix_turn 32.8 93 0.002 23.5 4.7 39 637-677 5-43 (58)
136 TIGR00281 segregation and cond 32.7 5.3E+02 0.011 26.0 13.7 33 645-677 9-43 (186)
137 PF10163 EnY2: Transcription f 32.4 1.7E+02 0.0036 25.4 6.6 56 104-159 28-85 (86)
138 PF08461 HTH_12: Ribonuclease 32.2 1.1E+02 0.0024 25.2 5.1 50 744-794 2-52 (66)
139 PRK11512 DNA-binding transcrip 32.1 91 0.002 29.6 5.4 45 744-794 44-88 (144)
140 PF10408 Ufd2P_core: Ubiquitin 31.9 3.4E+02 0.0075 32.7 11.5 59 212-270 321-392 (629)
141 PF06163 DUF977: Bacterial pro 31.9 1.3E+02 0.0029 28.1 6.0 52 738-795 10-61 (127)
142 COG4742 Predicted transcriptio 31.7 78 0.0017 33.6 5.1 42 643-687 18-59 (260)
143 TIGR01889 Staph_reg_Sar staphy 31.4 1.1E+02 0.0023 27.7 5.4 41 751-797 40-82 (109)
144 PF05158 RNA_pol_Rpc34: RNA po 31.4 36 0.00078 37.5 2.7 50 634-685 80-131 (327)
145 PF03444 HrcA_DNA-bdg: Winged 31.3 1.3E+02 0.0027 25.8 5.3 48 639-688 10-57 (78)
146 PF06784 UPF0240: Uncharacteri 31.2 77 0.0017 31.7 4.8 64 609-677 96-161 (179)
147 PF02796 HTH_7: Helix-turn-hel 31.2 63 0.0014 24.2 3.3 30 643-674 14-43 (45)
148 PLN03238 probable histone acet 31.0 76 0.0016 34.0 4.9 39 639-677 209-248 (290)
149 PF02270 TFIIF_beta: Transcrip 30.8 73 0.0016 34.2 4.9 58 638-705 216-273 (275)
150 PF11994 DUF3489: Protein of u 30.8 98 0.0021 26.0 4.5 47 637-683 9-55 (72)
151 PRK10434 srlR DNA-bindng trans 30.6 64 0.0014 34.1 4.5 45 743-793 8-52 (256)
152 smart00346 HTH_ICLR helix_turn 30.4 1.4E+02 0.0031 25.4 6.0 45 745-795 10-55 (91)
153 TIGR01610 phage_O_Nterm phage 30.0 96 0.0021 27.4 4.8 38 751-794 44-81 (95)
154 PF00538 Linker_histone: linke 29.8 2E+02 0.0043 24.2 6.5 54 740-794 8-65 (77)
155 KOG3054 Uncharacterized conser 29.8 86 0.0019 32.5 4.8 58 741-804 201-258 (299)
156 PRK11050 manganese transport r 29.3 1.1E+02 0.0024 29.5 5.5 44 642-687 41-84 (152)
157 PF07393 Sec10: Exocyst comple 29.1 1.1E+03 0.025 28.7 28.3 98 127-227 192-302 (710)
158 PF03037 KMP11: Kinetoplastid 29.1 2.8E+02 0.006 23.1 6.7 64 376-442 11-74 (90)
159 PF04182 B-block_TFIIIC: B-blo 28.7 89 0.0019 26.3 4.1 49 638-688 2-52 (75)
160 PF00392 GntR: Bacterial regul 28.6 67 0.0015 25.8 3.3 38 649-688 20-58 (64)
161 TIGR02844 spore_III_D sporulat 28.3 99 0.0021 26.6 4.3 33 640-673 8-40 (80)
162 PRK10906 DNA-binding transcrip 28.3 78 0.0017 33.4 4.6 46 742-793 7-52 (252)
163 smart00762 Cog4 COG4 transport 28.2 3.5E+02 0.0076 29.7 9.8 53 343-395 7-63 (324)
164 COG2512 Predicted membrane-ass 28.1 79 0.0017 33.6 4.5 50 639-690 197-246 (258)
165 PRK06474 hypothetical protein; 27.9 1.6E+02 0.0035 29.3 6.6 52 635-688 8-61 (178)
166 PF12324 HTH_15: Helix-turn-he 27.7 1.5E+02 0.0032 25.3 5.1 38 640-677 26-63 (77)
167 COG1349 GlpR Transcriptional r 27.0 71 0.0015 33.8 4.0 45 743-793 8-52 (253)
168 PF09681 Phage_rep_org_N: N-te 26.5 1E+02 0.0022 28.8 4.4 51 635-687 26-86 (121)
169 smart00526 H15 Domain in histo 26.4 3E+02 0.0065 22.2 6.8 53 740-793 10-64 (66)
170 PRK03902 manganese transport t 25.8 1.2E+02 0.0026 28.8 5.0 42 643-686 13-54 (142)
171 PRK11179 DNA-binding transcrip 25.8 1.3E+02 0.0027 29.1 5.2 47 740-792 9-55 (153)
172 PRK11169 leucine-responsive tr 25.5 1.3E+02 0.0028 29.4 5.3 48 739-792 13-60 (164)
173 PF01316 Arg_repressor: Argini 25.5 3.1E+02 0.0067 22.9 6.6 60 739-803 4-63 (70)
174 cd00090 HTH_ARSR Arsenical Res 25.4 1.6E+02 0.0035 23.3 5.2 46 744-796 11-56 (78)
175 smart00345 HTH_GNTR helix_turn 25.1 1.7E+02 0.0036 22.4 5.0 39 751-795 16-55 (60)
176 smart00753 PAM PCI/PINT associ 24.8 1E+02 0.0022 26.3 4.0 34 649-684 21-54 (88)
177 smart00088 PINT motif in prote 24.8 1E+02 0.0022 26.3 4.0 34 649-684 21-54 (88)
178 PRK04214 rbn ribonuclease BN/u 24.8 1.8E+02 0.004 33.1 7.1 39 647-687 305-343 (412)
179 PF13545 HTH_Crp_2: Crp-like h 24.7 1.3E+02 0.0028 24.7 4.5 33 652-686 28-60 (76)
180 PRK09462 fur ferric uptake reg 24.6 2.3E+02 0.0051 27.0 6.8 51 743-794 20-72 (148)
181 cd07153 Fur_like Ferric uptake 24.5 1.7E+02 0.0036 26.4 5.6 57 642-703 5-67 (116)
182 PLN00104 MYST -like histone ac 24.4 1.1E+02 0.0023 35.1 4.9 37 641-677 362-399 (450)
183 PRK03573 transcriptional regul 24.1 1.5E+02 0.0032 28.0 5.4 25 770-794 56-80 (144)
184 PF13542 HTH_Tnp_ISL3: Helix-t 24.1 1.8E+02 0.0039 22.0 4.9 35 639-675 16-50 (52)
185 PF01399 PCI: PCI domain; Int 24.0 1.1E+02 0.0024 26.6 4.2 39 640-678 48-86 (105)
186 PRK10681 DNA-binding transcrip 24.0 1.1E+02 0.0024 32.2 4.8 39 639-677 8-46 (252)
187 smart00531 TFIIE Transcription 23.8 95 0.0021 29.9 3.9 30 649-678 12-41 (147)
188 PF11372 DUF3173: Domain of un 23.7 1E+02 0.0022 24.9 3.2 34 753-791 2-37 (59)
189 cd06171 Sigma70_r4 Sigma70, re 23.1 1.8E+02 0.0039 21.3 4.7 39 637-676 12-50 (55)
190 COG1321 TroR Mn-dependent tran 23.0 1.5E+02 0.0033 28.8 5.1 44 643-688 15-58 (154)
191 TIGR02698 CopY_TcrY copper tra 22.6 2.2E+02 0.0048 26.7 6.1 50 636-687 2-55 (130)
192 PRK00135 scpB segregation and 22.5 2.4E+02 0.0052 28.4 6.6 111 589-706 34-153 (188)
193 COG1654 BirA Biotin operon rep 22.5 2.6E+02 0.0055 24.0 5.7 42 644-685 11-52 (79)
194 TIGR01714 phage_rep_org_N phag 22.3 1.2E+02 0.0026 28.2 3.9 49 636-686 27-83 (119)
195 PLN03239 histone acetyltransfe 22.2 1.2E+02 0.0027 33.3 4.7 39 639-677 267-309 (351)
196 PF13601 HTH_34: Winged helix 22.1 1E+02 0.0022 26.4 3.3 47 742-794 2-48 (80)
197 PF05186 Dpy-30: Dpy-30 motif; 22.0 1.2E+02 0.0026 22.6 3.2 30 430-459 10-39 (42)
198 PF14947 HTH_45: Winged helix- 22.0 1.5E+02 0.0033 24.9 4.4 43 641-686 9-51 (77)
199 KOG1488 Translational represso 21.8 7.6E+02 0.016 28.9 11.1 30 305-337 468-497 (503)
200 PF00165 HTH_AraC: Bacterial r 21.7 1.4E+02 0.003 21.7 3.6 28 650-677 6-33 (42)
201 KOG2905 Transcription initiati 21.7 1.2E+02 0.0026 31.5 4.2 55 641-705 189-243 (254)
202 PRK10430 DNA-binding transcrip 21.6 1.7E+02 0.0036 30.1 5.6 36 649-686 175-210 (239)
203 cd07977 TFIIE_beta_winged_heli 21.6 1.9E+02 0.004 24.5 4.7 58 739-804 8-70 (75)
204 PF00196 GerE: Bacterial regul 21.2 1.8E+02 0.0038 22.8 4.3 39 637-677 5-43 (58)
205 PF13384 HTH_23: Homeodomain-l 21.1 1.2E+02 0.0026 22.8 3.2 33 643-677 10-42 (50)
206 PF07393 Sec10: Exocyst comple 21.0 1.6E+03 0.034 27.5 19.2 136 232-374 106-264 (710)
207 PRK14999 histidine utilization 20.5 1.7E+02 0.0037 30.4 5.4 47 748-801 29-76 (241)
208 COG3355 Predicted transcriptio 20.2 1.8E+02 0.0038 27.4 4.6 41 748-794 36-76 (126)
No 1
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3e-137 Score=1114.54 Aligned_cols=654 Identities=65% Similarity=1.010 Sum_probs=637.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccceecc-ccccccHHHHHHHHHHH
Q 003676 147 LYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQ-TPNVRSLWDMGLQLFRK 225 (804)
Q Consensus 147 LY~~L~~~~~~~l~~~~~~l~~~~~d~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDr~yv~~-~~~~~sI~~lgl~lFr~ 225 (804)
||++|++.|++|+++.+.++.....|.+.||..+.++|+.|+.+|.+|++||.||||+|+.+ ++.++|||+||+.+||.
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 89999999999999998888877777789999999999999999999999999999999999 78899999999999999
Q ss_pred Hhcc--ccchHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHhhhhcchHhhHHhHHHHHHHHHHHHHHHhhhcCChhh
Q 003676 226 YLSS--YSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPD 303 (804)
Q Consensus 226 ~v~~--~~~i~~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~~L~iY~~~FE~~fL~~t~~yY~~~s~~~i~~~~~~e 303 (804)
+++. .+.+..++.++++..|+++|.|+++|+++|++++.|+.++++|.+.|++.|++.+.++|++++...+++..+++
T Consensus 82 ~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~e 161 (661)
T KOG2167|consen 82 HFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPE 161 (661)
T ss_pred HhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHH
Confidence 9998 67889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhcCcCchHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHhccc-ccHHHHHH
Q 003676 304 YLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQ 382 (804)
Q Consensus 304 YL~~ve~~l~eE~~r~~~yl~~~t~~~l~~~l~~~Li~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~ 382 (804)
||++|+.++.+|.+|+..|++.++.+++..+++++|+..|++.|+..|+..+++.+++.++.+||.|++++ ++...++.
T Consensus 162 Yl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~kgl~~lvDm~q~~d~~rly~L~~r~~~g~l~l~q 241 (661)
T KOG2167|consen 162 YLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTKGLDSLVDMRQTSDLTRLYMLFSRVQGGQLSLLQ 241 (661)
T ss_pred HHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhcchHHhhhhhhccchHhHHHHHHHHhcchHHHHH
Confidence 99999999999999999999999988899999999999999999999999999999999999999999999 89999999
Q ss_pred HHHHHHHHHhhhhhcCchhhHHHHHHHHHHHHHHHHHHHHhcCCc--HHhHHHHHHHHHHHhhcCCCcchHHHHHHHHHH
Q 003676 383 ALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKN--EAFCNTIKDAFEYLINLRQNRPAELIAKFLDEK 460 (804)
Q Consensus 383 ~~~~yi~~~g~~iv~~~~~~~~~V~~Ll~l~~~~~~li~~~F~~~--~~f~~~l~~af~~~lN~~~~~~~e~La~y~D~~ 460 (804)
.|.+|+++.|.++|.+++.++++|++++.|++++|-++..||-.+ ..|.+++++||+.|+|.++++|||+||+|+|.+
T Consensus 242 q~sdylk~~G~KlV~de~kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fink~~~rpAelIak~~dt~ 321 (661)
T KOG2167|consen 242 QWSDYLKKPGFKLVIDEEKDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFINKRRNRPAELIAKYVDTK 321 (661)
T ss_pred HHHHHHhcccceeccCchhhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999988 999999999999999999999999999999999
Q ss_pred HhcCCCCCCHHHHHhcccccceeeeeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHHHHHHHH
Q 003676 461 LRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFK 540 (804)
Q Consensus 461 lr~~~k~~~~~e~e~~l~~i~~lf~~i~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~i~~Lk~~~G~~~t~kle~M~~ 540 (804)
||.|+++.++++++..+++++.|||||.+||+||++|++.||+|||.++|+|.|+|+.|+.+||.+||..||+||||||+
T Consensus 322 Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfk 401 (661)
T KOG2167|consen 322 LRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFK 401 (661)
T ss_pred HHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHhcCCCceeEeecCCce
Q 003676 541 DIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGH 620 (804)
Q Consensus 541 D~~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~lg~ 620 (804)
||+.|++++..|+++...+...+.++ +.|.|||.|+||+|++.++.||++|..+++.|..||..+|.||+|+|+++||+
T Consensus 402 dme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~ 480 (661)
T KOG2167|consen 402 DMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGH 480 (661)
T ss_pred hHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHHHHHHHhccccccCcceeeecCCcc
Confidence 99999999999999865545555556 99999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEecCceEEEEEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEE
Q 003676 621 CVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFV 700 (804)
Q Consensus 621 ~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~ 700 (804)
|+|++.|+.|++||+||++|++|||+||+.+.+|++||.++|+|.+.+|+|+|+||+||+.++|.++|+|+++.++|.|.
T Consensus 481 ~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~ 560 (661)
T KOG2167|consen 481 CVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFI 560 (661)
T ss_pred hhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCCCcceEeeccccccccchhhhhhhHhHHHhhHHHHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHH
Q 003676 701 FNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKR 780 (804)
Q Consensus 701 ~N~~F~~~~~~iki~~i~~k~t~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~ 780 (804)
+|..|+++.+|||||+|++|+|.+|+++|+|+|.+||+++||||||||||+||+|+|+.|+.|+++|++||+.+ ++|+|
T Consensus 561 ~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlkfpv~~-d~kkr 639 (661)
T KOG2167|consen 561 VNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLKFPVKP-DLKKR 639 (661)
T ss_pred echhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcCCCCCh-hHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999 99999
Q ss_pred HHHHhhcCceeecCCCCCceeeCC
Q 003676 781 IESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 781 Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
||+||+|||++|| +| +.|+|||
T Consensus 640 iesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 640 IESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred HHHHHhHHHhccc-cc-ccccccC
Confidence 9999999999999 44 8999998
No 2
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.4e-118 Score=1037.20 Aligned_cols=692 Identities=38% Similarity=0.645 Sum_probs=646.3
Q ss_pred CCchHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhhhccCch----hHHHHHHHHHHHHHHHHHHHhhhcCCCcHHH
Q 003676 100 PTNFEEDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMG----GNLYQRIEKECEEHISAAIRSLVGQSPDLVV 175 (804)
Q Consensus 100 ~~~~~e~~W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~----e~LY~~L~~~~~~~l~~~~~~l~~~~~d~~~ 175 (804)
...+.+++|.+|..+++.+..+....++|+++|+++|++|.+++| ++||++|++.+.+|+.+.+......+++ ..
T Consensus 13 ~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~~~~~~-~~ 91 (725)
T KOG2166|consen 13 GWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPALREKHD-EY 91 (725)
T ss_pred cHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhcCc-HH
Confidence 347779999999999986664556678999999999999999999 9999999999999999999887776665 78
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcccceeccccccccHHHHH-HHHHHHHhccccchHHHHHHHHHHHHHHHhcCCcC
Q 003676 176 FLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMG-LQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAV 254 (804)
Q Consensus 176 ~L~~~~~~W~~~~~~~~~i~~iF~YLDr~yv~~~~~~~sI~~lg-l~lFr~~v~~~~~i~~~l~~~ll~lI~~eR~g~~i 254 (804)
+|..+...|.+|+.++.+++++|+||||+||.+..+..++.+++ +.+|+..+... ++..+++++++.+|..+|.|+.|
T Consensus 92 ~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~-~~~~~~~~all~lI~~eR~ge~i 170 (725)
T KOG2166|consen 92 MLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKF-EMQSEAIDALLALIHKEREGEQI 170 (725)
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHH-HHHHHHHHHHHHHHHhhcccccc
Confidence 99999999999999999999999999999999873356677766 99999998865 69999999999999999999999
Q ss_pred ChHHHHHHHHHHhhhh-----cchHhhHHhHHHHHHHHHHHHHHHhhhcCChhhHHHHHHHHHHHHHHHHhhhcCcCchH
Q 003676 255 DRTLLNHLLKMFTALG-----IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRK 329 (804)
Q Consensus 255 d~~llk~ii~ml~~L~-----iY~~~FE~~fL~~t~~yY~~~s~~~i~~~~~~eYL~~ve~~l~eE~~r~~~yl~~~t~~ 329 (804)
|+..|++++.|+..|| +|...||++|++.|++||..++.+|+...++++|+.+++.++.+|.+|+..|++..+..
T Consensus 171 n~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~ 250 (725)
T KOG2166|consen 171 DRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEP 250 (725)
T ss_pred cHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccc
Confidence 9999999999999986 99999999999999999999999999988999999999999999999999998887777
Q ss_pred HHHHHHHHHHHHHHHHHHH---HHHHHHhhccCCHHHHHHHHHHhccc-ccHHHHHHHHHHHHHHHhhhhhcCc-----h
Q 003676 330 PLIATAERQLLERHISAIL---DKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE-----E 400 (804)
Q Consensus 330 ~l~~~l~~~Li~~~~~~ll---~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yi~~~g~~iv~~~-----~ 400 (804)
++...++..++..+++.++ .+|+..|+.+++.++|.+||+|++++ +|++.++..|..|++.+|..++... .
T Consensus 251 ~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~~~ 330 (725)
T KOG2166|consen 251 KLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETAAT 330 (725)
T ss_pred hhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhccc
Confidence 8888888888888877766 58999999999999999999999999 9999999999999999998777542 4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhcCCcHHhHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHhcCCCCCCHHHHHhccccc
Q 003676 401 KDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKV 480 (804)
Q Consensus 401 ~~~~~V~~Ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~lN~~~~~~~e~La~y~D~~lr~~~k~~~~~e~e~~l~~i 480 (804)
.++.+|+.++++++++..++..||+++..|.++++.||+.|+|.+...++|+||+|||.++|+|.++.++++++..++++
T Consensus 331 ~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v 410 (725)
T KOG2166|consen 331 NPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKV 410 (725)
T ss_pred chHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhcc
Confidence 56899999999999999999999999999999999999999999885556999999999999999999999999999999
Q ss_pred ceeeeeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 003676 481 LVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQART 560 (804)
Q Consensus 481 ~~lf~~i~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~i~~Lk~~~G~~~t~kle~M~~D~~~S~~l~~~f~~~~~~~~ 560 (804)
+.+|+|+.+||+|+.+|+++||||||+++|.|+|+|+.||++|+++||.+||+||++||+|+..|++++..|.++ .+ .
T Consensus 411 ~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~-~~-~ 488 (725)
T KOG2166|consen 411 VKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADY-AN-Y 488 (725)
T ss_pred eeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhh-hc-h
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999976 21 2
Q ss_pred CCCCCccEEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHhcCCCceeEeecCCceEEEEEEecCceEEEEEcHHH
Q 003676 561 KLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQ 640 (804)
Q Consensus 561 ~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Q 640 (804)
....+++|.|.|||+|+||.++..++.||++|..+++.|..||.++|+||+|.|+++||.|+|.++|.+++++|+||++|
T Consensus 489 ~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Q 568 (725)
T KOG2166|consen 489 SANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQ 568 (725)
T ss_pred hccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHH
Confidence 22357999999999999999999899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCcceEeecccccc
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMK 720 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~~~iki~~i~~k 720 (804)
|+|||+||+.+.+|+++|.+.|+++.+++.+.|+||+|.|.+++.+ |.+++ ++++.|.+|.+|+++.+|++++.+..+
T Consensus 569 m~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~ 646 (725)
T KOG2166|consen 569 MAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMD 646 (725)
T ss_pred HHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCch
Confidence 9999999999999999999999999999999999999988777777 88888 899999999999999999999987655
Q ss_pred ccchhhhhhhHhHHHhhHHHHHHHHHHHhhcCCCCChHHHHHHHHHhc--CCCCChHHHHHHHHHHhhcCceeecCCCCC
Q 003676 721 ETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQ 798 (804)
Q Consensus 721 ~t~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l--~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~ 798 (804)
|.+.+.+.+.+||+++|+||||||||+||.|.|++|+.||++|+ +|.|++.+||+|||.|||||||+|| +|++
T Consensus 647 ----e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~ 721 (725)
T KOG2166|consen 647 ----ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPN 721 (725)
T ss_pred ----hHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 66778899999999999999999999999999999999999999 6999999999999999999999999 8999
Q ss_pred ceee
Q 003676 799 IYNY 802 (804)
Q Consensus 799 ~y~Y 802 (804)
+|+|
T Consensus 722 ~Y~Y 725 (725)
T KOG2166|consen 722 IYRY 725 (725)
T ss_pred cccC
Confidence 9998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.4e-116 Score=968.71 Aligned_cols=697 Identities=36% Similarity=0.579 Sum_probs=632.1
Q ss_pred CCCCchHHHHHHHHHHHHHHHH---hcCCCCccHHHHHHHHHhhhccC----------------chhHHHHHHHHHHHHH
Q 003676 98 TLPTNFEEDTWAKLKLAIKAIF---LKQPTSCDLEKLYQAVNDLCLHK----------------MGGNLYQRIEKECEEH 158 (804)
Q Consensus 98 ~~~~~~~e~~W~~L~~aI~~I~---~~~~~~~s~e~LY~~Vy~lC~~k----------------~~e~LY~~L~~~~~~~ 158 (804)
+++++.++.+|..++.||+.|+ ......++|+++|+.+|+.|.++ +|+.||++|....+.+
T Consensus 14 ~~~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k~~ 93 (773)
T COG5647 14 TLSEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAKNY 93 (773)
T ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHHHH
Confidence 4566666999999999999999 44556789999999999999987 4778899999988888
Q ss_pred HHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccceec--ccc--ccccHHHHHHHHHHHHhccccchH
Q 003676 159 ISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVK--QTP--NVRSLWDMGLQLFRKYLSSYSEVE 234 (804)
Q Consensus 159 l~~~~~~l~~~~~d~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDr~yv~--~~~--~~~sI~~lgl~lFr~~v~~~~~i~ 234 (804)
+...-..... .....||..+++.|.+|+.++.++.++|.||||+|++ +.+ ....+..+++..|+..+|. .+.
T Consensus 94 i~~~~~~~s~--~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~--~i~ 169 (773)
T COG5647 94 IEEYNRGRSQ--ENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFR--LIV 169 (773)
T ss_pred HHHhcccccc--hhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHH--hhh
Confidence 8876544211 2237899999999999999999999999999999999 222 1456778888899888876 899
Q ss_pred HHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHhhh-----------hcchHhhHHhHHHHHHHHHHHHHHHhhhcCChhh
Q 003676 235 HKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTAL-----------GIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPD 303 (804)
Q Consensus 235 ~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~~L-----------~iY~~~FE~~fL~~t~~yY~~~s~~~i~~~~~~e 303 (804)
+.+++.+|..+++.|.|+.+|+..+..++.|+..+ .+|...|||.||+.|.+||..++.+.+..+++.+
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 99999999999999999999999999999999998 5899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhcCcCchHHHHHHHHHHHHHHHHHHHHHH--HHHHhhccCCHHHHHHHHHHhccc-ccHHHH
Q 003676 304 YLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDK--GFTMLMDGHRTEDLQRMYSLFSRV-NALESL 380 (804)
Q Consensus 304 YL~~ve~~l~eE~~r~~~yl~~~t~~~l~~~l~~~Li~~~~~~ll~~--gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l 380 (804)
||.+++.++++|..++..|++.++.++|..+++++||.+|.+.+..+ |+..+++..+.+.|..||+++++. .++..|
T Consensus 250 yL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl 329 (773)
T COG5647 250 YLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQVLYRLLSETKYGVQPL 329 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhchHHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhH
Confidence 99999999999999999999999999999999999999999999863 899999999999999999999999 779999
Q ss_pred HHHHHHHHHHHhh--hh-----hc----------CchhhHHHHHHHHHHHHHHHHHHHHhcCCcHHhHHHHHHHHHHHhh
Q 003676 381 RQALAMYIRRTGH--GI-----VM----------DEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLIN 443 (804)
Q Consensus 381 ~~~~~~yi~~~g~--~i-----v~----------~~~~~~~~V~~Ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~lN 443 (804)
++.|..||+..|. .+ +. ++..+..+|+.++++++.+..++.++|.+|..+..++++||+.|+|
T Consensus 330 ~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin 409 (773)
T COG5647 330 QEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFIN 409 (773)
T ss_pred HHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhc
Confidence 9999999999991 11 11 1223579999999999999999999999999999999999999999
Q ss_pred cCC---CcchHHHHHHHHHHHhcCCCCCCHHHHHhcccccceeeeeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHH
Q 003676 444 LRQ---NRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMI 520 (804)
Q Consensus 444 ~~~---~~~~e~La~y~D~~lr~~~k~~~~~e~e~~l~~i~~lf~~i~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~i 520 (804)
.+. ..++|+||+|+|.+||++.+......++..+..++.||+|+.+||+|+++|+++||||||+++|+|.++|..||
T Consensus 410 ~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mi 489 (773)
T COG5647 410 GNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMI 489 (773)
T ss_pred cccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHH
Confidence 843 36899999999999999887655667888889999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCC-CCccCChHHHHHHHHH
Q 003676 521 SKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIF 599 (804)
Q Consensus 521 ~~Lk~~~G~~~t~kle~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F 599 (804)
++||+.||.+||+|+|+||+||..|.++...|++...+ ....+|+.|.||+..+||..|+ ..+.||++|.+..+.|
T Consensus 490 s~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s---~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~f 566 (773)
T COG5647 490 SMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQS---YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEGF 566 (773)
T ss_pred HHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchh---hccccchhHHHHHHhcCCCCccccccCCChHHHHHHHHH
Confidence 99999999999999999999999999999999875432 1246899999999999996665 5799999999999999
Q ss_pred HHHHHhcCCCceeEeecCCceEEEEEEecCceEEEE---EcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHh
Q 003676 600 KEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELA---VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (804)
Q Consensus 600 ~~~Y~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~---vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL 676 (804)
++||.+||+||+|.|.++||+|+|+++|+.|++.+. ++++|+.|+++||+++++|+++|.+.|+|+.++++++|+||
T Consensus 567 ~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl 646 (773)
T COG5647 567 KKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSL 646 (773)
T ss_pred HHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHH
Confidence 999999999999999999999999999998865554 56789999999999999999999999999999999999999
Q ss_pred hcCCcceeeeCCCCCCCCCCCeEEEecCCCCCcceEeeccccccccchhhhhhhHhHHHhhHHHHHHHHHHHhhcCCCCC
Q 003676 677 ACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLS 756 (804)
Q Consensus 677 ~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~~~iki~~i~~k~t~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~K~l~ 756 (804)
+|.|..+|.+ +++.+++++.|.+|.+|+++..||+++.+..++..+++..+++.+.+||+..+|||||||||+||+|.
T Consensus 647 ~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~ 724 (773)
T COG5647 647 SCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLK 724 (773)
T ss_pred Hhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 9766655554 48889999999999999999999999998777666778888999999999999999999999999999
Q ss_pred hHHHHHHHHHhc--CCCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 757 HTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 757 ~~~Li~ev~~~l--~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
|++|+.||+.|. ||.|++.+||++|+.|||||||+|.++| .+|+|+|
T Consensus 725 H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 725 HGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred HHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999999 7999999999999999999999999888 8999997
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-101 Score=801.28 Aligned_cols=662 Identities=27% Similarity=0.492 Sum_probs=612.3
Q ss_pred HHHHHHHHHHHHHHHHhcCCCC-ccHHHHHHHHHhhhccC---chhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHH
Q 003676 104 EEDTWAKLKLAIKAIFLKQPTS-CDLEKLYQAVNDLCLHK---MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSL 179 (804)
Q Consensus 104 ~e~~W~~L~~aI~~I~~~~~~~-~s~e~LY~~Vy~lC~~k---~~e~LY~~L~~~~~~~l~~~~~~l~~~~~d~~~~L~~ 179 (804)
++++|.+|...|.+|.+-++.. ..|..-|+.||.+|..- .||+||...+..+++|++..+..+...+ ++.+|..
T Consensus 11 fd~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v~~~--p~~~l~~ 88 (728)
T KOG2284|consen 11 FDKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIVDVD--PDLLLQE 88 (728)
T ss_pred HHHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhhcCC--HHHHHHH
Confidence 4899999999999999888764 58999999999999974 6999999999999999998877766443 3579999
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcccceecccc-----------------ccccHHHHHHHHHHHHhccccchHHHHHHHHH
Q 003676 180 VERCWQDLCDQMLMIRGIALYLDRTYVKQTP-----------------NVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLL 242 (804)
Q Consensus 180 ~~~~W~~~~~~~~~i~~iF~YLDr~yv~~~~-----------------~~~sI~~lgl~lFr~~v~~~~~i~~~l~~~ll 242 (804)
|.+.|+.|.....++..+|.||+..|+++++ .+..|..+|+++||+.++. .+...++.-+|
T Consensus 89 yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~--~i~~~lv~~ll 166 (728)
T KOG2284|consen 89 YHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVK--TILPQLVKLLL 166 (728)
T ss_pred HHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHH--HHHHHHHHHHH
Confidence 9999999999999999999999999999864 3456888999999999875 89999999999
Q ss_pred HHHHHHhcCCcCC-hHHHHHHHHHHhhhh----------------------cchHhhHHhHHHHHHHHHHHHHHHhhhcC
Q 003676 243 RMIERERLGEAVD-RTLLNHLLKMFTALG----------------------IYSESFEKPFLECTSEFYAAEGMKYMQQS 299 (804)
Q Consensus 243 ~lI~~eR~g~~id-~~llk~ii~ml~~L~----------------------iY~~~FE~~fL~~t~~yY~~~s~~~i~~~ 299 (804)
..|.++|.|+..+ ...+..+|..|+.+. +|++.||.|||.+|.+||+++++.++++.
T Consensus 167 ~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~~l~~~ 246 (728)
T KOG2284|consen 167 IAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALAQKMLTDL 246 (728)
T ss_pred HHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHHHHHHhhc
Confidence 9999999999877 567888888886542 79999999999999999999999999999
Q ss_pred ChhhHHHHHHHHHHHHHHHHhhhcCcCchHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHhccc-ccHH
Q 003676 300 DVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALE 378 (804)
Q Consensus 300 ~~~eYL~~ve~~l~eE~~r~~~yl~~~t~~~l~~~l~~~Li~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~ 378 (804)
+|++|+.+|..++++|+-||..||++++..+++..|.+.+|..|.+.+ +-.+..++.+.+..||+.||.|+..+ -|+.
T Consensus 247 ~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l-ha~ch~~i~~e~~~d~~nmy~ll~~i~~gl~ 325 (728)
T KOG2284|consen 247 SCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL-HAVCHDLITNEENKDLRNMYRLLKPIQAGLS 325 (728)
T ss_pred cHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhhhhhhHHHHHHHHHHHhcCch
Confidence 999999999999999999999999999999999999999999999875 56799999999999999999999999 8999
Q ss_pred HHHHHHHHHHHHHhhhhhcCc---hhhHHHHHHHHHHHHHHHHHHHHhcCCcHHhHHHHHHHHHHHhhcCC-----Ccch
Q 003676 379 SLRQALAMYIRRTGHGIVMDE---EKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQ-----NRPA 450 (804)
Q Consensus 379 ~l~~~~~~yi~~~g~~iv~~~---~~~~~~V~~Ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~lN~~~-----~~~~ 450 (804)
.+.+.|.+||++.|...++.- .-+..||+.+|.+|.++..++...|.+|..|..+++.|+..++|.+. .+.+
T Consensus 326 ~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv~ka~ 405 (728)
T KOG2284|consen 326 VMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSVPKAS 405 (728)
T ss_pred HHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccccchH
Confidence 999999999999999888653 23679999999999999999999999999999999999999999754 3678
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHhcccccceeeeeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCc
Q 003676 451 ELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQ 530 (804)
Q Consensus 451 e~La~y~D~~lr~~~k~~~~~e~e~~l~~i~~lf~~i~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~i~~Lk~~~G~~ 530 (804)
|.||+|||.+|+++.|++++.++|.+|+..+.+|+||.|||+|.+||.+.||+||+.+.|.|.|.|..||++||+.||.+
T Consensus 406 e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqacgye 485 (728)
T KOG2284|consen 406 ERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQACGYE 485 (728)
T ss_pred HHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHhCce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHhcCCCc
Q 003676 531 FTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGR 610 (804)
Q Consensus 531 ~t~kle~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~R 610 (804)
||+++- +.|+..|.+++++|.+.+.+ +.+|.+|+..++.|+.||..+|+||
T Consensus 486 fts~~~--~td~~~s~~lnn~f~~~i~n---------------------------f~~pq~l~~~iq~fe~fyt~~~~gr 536 (728)
T KOG2284|consen 486 FTSSWP--LTDPQLSTNLNNQFAQDIAN---------------------------FHLPQILQPVIQEFEKFYTGKHNGR 536 (728)
T ss_pred ecccCC--CCChhhccccchhHHHHHHh---------------------------ccchHHHHHHHHHHHHHhccccCCc
Confidence 999998 99999999999999876542 7899999999999999999999999
Q ss_pred eeEeecCCceEEEEEEecCceEEEEEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003676 611 RLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (804)
Q Consensus 611 kL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (804)
||+|.+.+++++++.++-++.|.-.|.+|||++||+||..+.+++.+|.+.+|+++++|.+++.++. ..++|....
T Consensus 537 kltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~til--dv~~~~~d~-- 612 (728)
T KOG2284|consen 537 KLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTIL--DVTLLTCDD-- 612 (728)
T ss_pred eehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHH--hceeecccc--
Confidence 9999999999999999998899999999999999999999999999999999999999999999999 788887643
Q ss_pred CCCCCCCeEEEecCCCCCcceEeeccccc-cccchhhhhhhHhHHHhhHHHHHHHHHHHhhcCCCCChHHHHHHHHHhc-
Q 003676 691 RDVEDDDSFVFNEGFTAPLYRIKVNAIQM-KETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL- 768 (804)
Q Consensus 691 ~~i~~~d~f~~N~~F~~~~~~iki~~i~~-k~t~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l- 768 (804)
.++..+..|++|.+|+++..+.++...++ |.+++|.+.+...|.+||++.++||||||||+||.+.|+.|+.||+.|.
T Consensus 613 ~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~ 692 (728)
T KOG2284|consen 613 QNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTK 692 (728)
T ss_pred cccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhc
Confidence 46777888999999999999999876443 4567788888899999999999999999999999999999999999999
Q ss_pred -CCCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 769 -KFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 769 -~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
||.|++.+||++||.||++-||+|...+ +.|.|+|
T Consensus 693 ~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 693 GRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred ccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 6999999999999999999999998765 7899997
No 5
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=6.6e-93 Score=839.99 Aligned_cols=576 Identities=43% Similarity=0.716 Sum_probs=525.2
Q ss_pred HHHHHHHHHHHHhcCCCCccHHHHHHHHHhhhccCchhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHH
Q 003676 108 WAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDL 187 (804)
Q Consensus 108 W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~e~LY~~L~~~~~~~l~~~~~~l~~~~~d~~~~L~~~~~~W~~~ 187 (804)
|+.|++||+.|+.+.+...+|+++|+.||++|.+++|+.||+++++.+..|+..++..+.+..+ ..+|..+..+|.+|
T Consensus 1 W~~l~~~i~~i~~~~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~--~~~l~~~~~~w~~~ 78 (588)
T PF00888_consen 1 WEILEEAIDQIFKKSISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNIIESLLSSSD--EDLLEEYVQEWEKY 78 (588)
T ss_dssp HHHHHHHHHHHHTT-GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTT--CHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHcCCCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHhcCh--hHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999998888776533 68999999999999
Q ss_pred HHHHHHHHHhhhhcccceeccccccccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHh
Q 003676 188 CDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFT 267 (804)
Q Consensus 188 ~~~~~~i~~iF~YLDr~yv~~~~~~~sI~~lgl~lFr~~v~~~~~i~~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~ 267 (804)
+.++.+|+++|+||||.|+.++ +|++.|+. .+.++++++++++|.++|.|+.+|+.+++.+++|+.
T Consensus 79 ~~~~~~i~~if~yLdr~yv~~~------------~f~~~v~~--~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~ 144 (588)
T PF00888_consen 79 KKAIKYISDIFSYLDRNYVKRN------------LFREQVFK--PLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFV 144 (588)
T ss_dssp HHHHHHHHHHTHHHHHTSTTTT------------HHHHHTTT--SHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHhhhhhh------------hHHHHHHH--HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Confidence 9999999999999999999885 99999987 599999999999999999999999999999999999
Q ss_pred hhh---cchHhhHHhHHHHHHHHHHHHHHHhhhcCChhhHHHHHHHHHHHHHHHHhhhcCcCchHHHHHHHHHHHHHHHH
Q 003676 268 ALG---IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHI 344 (804)
Q Consensus 268 ~L~---iY~~~FE~~fL~~t~~yY~~~s~~~i~~~~~~eYL~~ve~~l~eE~~r~~~yl~~~t~~~l~~~l~~~Li~~~~ 344 (804)
++| +|.+.||++|++.|.+||+.++ +++.++.+||.+|+.++.+|.+||..|++++|..++.+++.++||..|.
T Consensus 145 ~l~~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~ 221 (588)
T PF00888_consen 145 ELGSLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHL 221 (588)
T ss_dssp HTTHTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGH
T ss_pred ccchHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHH
Confidence 765 8999999999999999999999 6777999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCHHHHHHHHHHhccc-ccHHHHHHHHHHHHHHHhhhhhcCc---hhhHHHHHHHHHHHHHHHHHH
Q 003676 345 SAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE---EKDKDMVSSLLEFKASLDTIW 420 (804)
Q Consensus 345 ~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yi~~~g~~iv~~~---~~~~~~V~~Ll~l~~~~~~li 420 (804)
+.| .+|+..|+++++.++|++||+|++++ ++++.+++.|++||.+.|..++... ..+..+|+.+++++++++.++
T Consensus 222 ~~l-~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~ 300 (588)
T PF00888_consen 222 DEL-SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLI 300 (588)
T ss_dssp HHH-HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHH
T ss_pred HHH-HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHH
Confidence 988 78999999999999999999999998 9999999999999999999998763 467899999999999999999
Q ss_pred HHhcCCcHHhHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHhcCCCCCCHHHHHhcccccceeeeeccChhHHHHHHHHH
Q 003676 421 EQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKD 500 (804)
Q Consensus 421 ~~~F~~~~~f~~~l~~af~~~lN~~~~~~~e~La~y~D~~lr~~~k~~~~~e~e~~l~~i~~lf~~i~~KD~F~~~Y~~~ 500 (804)
.+||+++..|..++++||+.++|....+++++||+|||.+++++.++.++++++..++.++.||+|+++||+|+.+|+++
T Consensus 301 ~~~F~~~~~f~~~l~~af~~~~n~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~ 380 (588)
T PF00888_consen 301 QECFDNDSEFKKALDEAFEEFLNKNNNKIPELLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKL 380 (588)
T ss_dssp HHTTTT-HHHHHHHHHHHHHHHHCSTSHHHHHHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHH
T ss_pred HHhccccHHHHHHHHHhHHHHHHcCCcchHHHHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHH
Confidence 99999999999999999999999997789999999999999999888888999999999999999999999999999999
Q ss_pred HHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCC--CccEEEEEeecCCC
Q 003676 501 LAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPS--GIEMSVHVLTTGYW 578 (804)
Q Consensus 501 LakRLL~~~s~s~d~E~~~i~~Lk~~~G~~~t~kle~M~~D~~~S~~l~~~f~~~~~~~~~~~~--~~~~~v~VLt~~~W 578 (804)
||+|||.+++.+.+.|+.||++|+.+||.+||++|++|++|++.|++++++|++.... .+... +++|++.||++|+|
T Consensus 381 L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~-~~~~~~~~~~~~~~vls~~~W 459 (588)
T PF00888_consen 381 LAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQ-NNIQLIPPFDFNVKVLSKGYW 459 (588)
T ss_dssp HHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TT-SS--CCEEEEEEEETTTS
T ss_pred HHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhh-ccccccCCCceEEEEecCCCC
Confidence 9999999999999999999999999999999999999999999999999999988764 22222 79999999999999
Q ss_pred CCCCCCC-ccCChHHHHHHHHHHHHHHhcCCCceeEeecCCceEEEEEEecCceEEEEEcHHHHHHHHhHhCCCCCCHHH
Q 003676 579 PTYPPMD-VRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQD 657 (804)
Q Consensus 579 P~~~~~~-~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~~~lt~~e 657 (804)
|.++..+ +.||++|+.+++.|++||+.+|+||+|+|++.+|+|+|+++|+++++++.||++||+||++||+.+++|++|
T Consensus 460 p~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~e 539 (588)
T PF00888_consen 460 PKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEE 539 (588)
T ss_dssp -S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHH
T ss_pred CCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHH
Confidence 9999877 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCHHHHHHHHhHhhcCCcceee--eCCCCCCCCCCCeEEEecCCC
Q 003676 658 IKDATGIEDKELRRTLQSLACGKVRVLQ--KLPKGRDVEDDDSFVFNEGFT 706 (804)
Q Consensus 658 i~~~t~i~~~~l~~~L~sL~~~k~~iL~--k~~~~~~i~~~d~f~~N~~F~ 706 (804)
|++.||+++++++++|.+|+ +.++|. +.+++++++++|.|.+|.+||
T Consensus 540 i~~~~~~~~~~l~~~L~~l~--~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 540 ISEKTGISEEELKRALKSLV--KSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp HHHHC---HHHHHHHHHCCC--TTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHHHHCcCHHHHHHHHHHHH--hCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 99999999999999999999 555554 788999999999999999996
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-86 Score=695.12 Aligned_cols=700 Identities=27% Similarity=0.448 Sum_probs=621.6
Q ss_pred CCchHHHHHHHHHHHHHHHHhcCCC-CccHHHHHHHHHhhhccC--chhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHH
Q 003676 100 PTNFEEDTWAKLKLAIKAIFLKQPT-SCDLEKLYQAVNDLCLHK--MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVF 176 (804)
Q Consensus 100 ~~~~~e~~W~~L~~aI~~I~~~~~~-~~s~e~LY~~Vy~lC~~k--~~e~LY~~L~~~~~~~l~~~~~~l~~~~~d~~~~ 176 (804)
+.+-+++.|...++.+.+++..... ...|+.||.+|+.+|.+. ...++|+.|+..+.+++.+.........+| ..+
T Consensus 9 ~r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d-~aL 87 (777)
T KOG2285|consen 9 DRDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTD-GAL 87 (777)
T ss_pred chhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccc-cHH
Confidence 3345689999999999998876654 568999999999999986 678999999999999999887777766555 789
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcccceecccc-------ccccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHh
Q 003676 177 LSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP-------NVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERER 249 (804)
Q Consensus 177 L~~~~~~W~~~~~~~~~i~~iF~YLDr~yv~~~~-------~~~sI~~lgl~lFr~~v~~~~~i~~~l~~~ll~lI~~eR 249 (804)
|..|..+|.+|..+..++.--|.-||.+-....+ +..+|..+-+.-|.++||. .++.++....+.++..+|
T Consensus 88 L~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~--nIk~rLq~sAmklVhaER 165 (777)
T KOG2285|consen 88 LIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFM--NIKERLQVSAMKLVHAER 165 (777)
T ss_pred HHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999987543322 2357999999999999997 799999999999999999
Q ss_pred cCCcCChHHHHHHHHHHhhhh--------cchHhhHHhHHHHHHHHHHHHHHHhhhcCChhhHHHHHHHHHHHHHHHHhh
Q 003676 250 LGEAVDRTLLNHLLKMFTALG--------IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLL 321 (804)
Q Consensus 250 ~g~~id~~llk~ii~ml~~L~--------iY~~~FE~~fL~~t~~yY~~~s~~~i~~~~~~eYL~~ve~~l~eE~~r~~~ 321 (804)
.|+.+|.+++-.+-..++.|. +|++.||..||++|.+||+..+..++++.++-+|+++++..++||..|..+
T Consensus 166 ~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkR 245 (777)
T KOG2285|consen 166 DGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKR 245 (777)
T ss_pred ccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHH
Confidence 999999999989989998874 999999999999999999999999999999999999999999999999999
Q ss_pred hcCc--CchHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHhccc-ccHHHHHHHHHHHHHHHhhhhhcC
Q 003676 322 YLDV--STRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMD 398 (804)
Q Consensus 322 yl~~--~t~~~l~~~l~~~Li~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yi~~~g~~iv~~ 398 (804)
||.. .+..+++.++.+.|+..+.+.|+. .+..|+...+++-|.+||+|+.++ .|++.+...+..||...|..-+..
T Consensus 246 YLE~~~~s~~~lme~~VnaLv~sf~~tIlA-EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~ 324 (777)
T KOG2285|consen 246 YLEMNSPSSGKLMEKAVNALVESFEDTILA-ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRN 324 (777)
T ss_pred hhccCCCcHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHh
Confidence 9865 888999999999999999999985 589999999999999999999999 999999999999999999654322
Q ss_pred -c----hhhHHHHHHHHHHHHHHHHHHHHhcCCcHHhHHHHHHHHHHHhhcCC--------------------CcchHHH
Q 003676 399 -E----EKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQ--------------------NRPAELI 453 (804)
Q Consensus 399 -~----~~~~~~V~~Ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~lN~~~--------------------~~~~e~L 453 (804)
. .....+|+.||.++++|..++.++|..|+.|..+-+.||..++|... ++.||+|
T Consensus 325 aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELL 404 (777)
T KOG2285|consen 325 AAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELL 404 (777)
T ss_pred hhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHH
Confidence 1 23458999999999999999999999999999999999999999631 4789999
Q ss_pred HHHHHHHHhcCC--CCCCHHHHHhcccccceeeeeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhC--C
Q 003676 454 AKFLDEKLRAGN--KGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECG--S 529 (804)
Q Consensus 454 a~y~D~~lr~~~--k~~~~~e~e~~l~~i~~lf~~i~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~i~~Lk~~~G--~ 529 (804)
|.|||.+||+.. |..+.+|++.+|.+++-+++|+.+||+|..|++.+|++||+.+.|++.+.|..|++.|+ ||| .
T Consensus 405 ANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPa 483 (777)
T KOG2285|consen 405 ANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPA 483 (777)
T ss_pred HHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcH
Confidence 999999999863 67889999999999999999999999999999999999999999999999999999998 688 5
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCC-CCccCChHHHHHHHHHHHHHHhcCC
Q 003676 530 QFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYS 608 (804)
Q Consensus 530 ~~t~kle~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~~Y~~k~~ 608 (804)
+|.+||..||+|++.|++++++|+..+...+.....-.+++.||+.|.|..... ..+.||.+|+..+-.-++||+.+|+
T Consensus 484 DyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hs 563 (777)
T KOG2285|consen 484 DYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHS 563 (777)
T ss_pred HHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccC
Confidence 799999999999999999999999877653222223467899999999987754 5799999999999999999999999
Q ss_pred CceeEeecCCceEEEEEEecCceEEEEEcHHHHHHHHhHhCC--CCCCHHHHHHHhCCCHHHHHHHHhHhhc-CC--cce
Q 003676 609 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLAC-GK--VRV 683 (804)
Q Consensus 609 ~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~--~~lt~~ei~~~t~i~~~~l~~~L~sL~~-~k--~~i 683 (804)
||+|+|.|+++.++|++.-.-|.|+|.|+++||+||.+||+. +.+|++.+.-+|.+|+.+|+|+|-||+. || ..|
T Consensus 564 grkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~Qi 643 (777)
T KOG2285|consen 564 GRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQI 643 (777)
T ss_pred ccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhhe
Confidence 999999999999999877556899999999999999999974 7899999999999999999999999987 65 568
Q ss_pred eeeCCC----CCCCCCCCeEEEecCCCC-----CcceEeecccccc--ccchhhhhhhHhHHHhhHHHHHHHHHHHhhcC
Q 003676 684 LQKLPK----GRDVEDDDSFVFNEGFTA-----PLYRIKVNAIQMK--ETVEENTSTTERVFQDRQYQVDAAIVRIMKTR 752 (804)
Q Consensus 684 L~k~~~----~~~i~~~d~f~~N~~F~~-----~~~~iki~~i~~k--~t~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~ 752 (804)
|..+|+ .+++.++..|.+|.+|.- ...|-|+|.|..- .+....++.++.+.+-|-...|-+||+|||.|
T Consensus 644 LL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~R 723 (777)
T KOG2285|consen 644 LLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTR 723 (777)
T ss_pred eeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHH
Confidence 877774 377888999999999963 2346666654211 12222334457788999999999999999999
Q ss_pred CCCChHHHHHHHHHhcC--CCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 753 KVLSHTLLITELFQQLK--FPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 753 K~l~~~~Li~ev~~~l~--F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
|+++..+|-.|+++-|+ |-|+..+||..||.|||..|++||++|-++|.|+|
T Consensus 724 K~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 724 KTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 99999999999999995 99999999999999999999999999999999997
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=2e-33 Score=270.18 Aligned_cols=141 Identities=55% Similarity=0.904 Sum_probs=132.7
Q ss_pred eccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCC
Q 003676 486 FIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSG 565 (804)
Q Consensus 486 ~i~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~i~~Lk~~~G~~~t~kle~M~~D~~~S~~l~~~f~~~~~~~~~~~~~ 565 (804)
|+++||+|+.+|+++||+|||..++++.+.|..||++||.+||.+||++|++||+|++.|++++++|++.+.+ .....+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~-~~~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLEN-NSNKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999987654 223356
Q ss_pred ccEEEEEeecCCCCCCCC-CCccCChHHHHHHHHHHHHHHhcCCCceeEeecCCceEEEEEEe
Q 003676 566 IEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEF 627 (804)
Q Consensus 566 ~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~lg~~~l~~~f 627 (804)
++|+|.|||.++||.++. .++.||++|+.+++.|++||..+|+||+|+|+|+||+|+|+++|
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 899999999999999988 78999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.4e-26 Score=257.07 Aligned_cols=308 Identities=22% Similarity=0.295 Sum_probs=247.0
Q ss_pred eeeeeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHHHHHHHHHHHHh--hhc
Q 003676 482 VLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSS--QAR 559 (804)
Q Consensus 482 ~lf~~i~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~i~~Lk~~~G~~~t~kle~M~~D~~~S~~l~~~f~~~~--~~~ 559 (804)
.|...+.+|+.|.+.||.+||.|||....++.+.|..-++.||-.+|.+-.+.|++|++|+..|+++++.++... ..+
T Consensus 444 mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~r~ 523 (765)
T KOG2165|consen 444 MLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELSRG 523 (765)
T ss_pred HHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhhcc
Confidence 455566999999999999999999999999999999999999999999999999999999999999999998742 110
Q ss_pred cCCCCCccEEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHhcCCCceeEeecCCceEEEEEEecCceEEEEEcHH
Q 003676 560 TKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLF 639 (804)
Q Consensus 560 ~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~ 639 (804)
....+.+.+++.||++.+||......+.||..++..++.|.+-|.+...+|+|.|.+++|.|+|+++|.+++.+++||+.
T Consensus 524 ~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp~ 603 (765)
T KOG2165|consen 524 AEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSPE 603 (765)
T ss_pred cccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCHH
Confidence 11113578899999999999998888999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCcceEeeccccc
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQM 719 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~~~iki~~i~~ 719 (804)
||+|+++|.+.++||++|+++.+|||...++|.|..|+ +.++|..+|. ++++.+|++++.=.+.-+- .+.+.+
T Consensus 604 qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~d~~q~--~~~~~~ 676 (765)
T KOG2165|consen 604 QAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEMDFDQA--EGTVLL 676 (765)
T ss_pred HHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeecccccccccc--CCCccc
Confidence 99999999999999999999999999999999999999 8999998864 3778899999854432211 111211
Q ss_pred cccchhhhhhh--HhHHHhh--HHHHHHHHHHHhhcCCCCChHHHHHHHHHhc-----CCCCChHHHHHHHHHHhhcCce
Q 003676 720 KETVEENTSTT--ERVFQDR--QYQVDAAIVRIMKTRKVLSHTLLITELFQQL-----KFPIKPADLKKRIESLIDREYL 790 (804)
Q Consensus 720 k~t~~e~~~~~--~~v~~dR--~~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l-----~F~~~~~~iK~~Ie~LIereyi 790 (804)
+..+++.+.. ..+.+-+ -..-...||..+-.-..|..+.+.+ +.+.. ...++-++++.-+..++..|-+
T Consensus 677 -e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHn-mLkmF~~~~~~~~~TlqeL~~fLq~kV~e~kL 754 (765)
T KOG2165|consen 677 -EAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHN-MLKMFVPPDGSAEITLQELQGFLQRKVREGKL 754 (765)
T ss_pred -ccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHH-HHeeeecCCCCCcccHHHHHHHHHHHhhccce
Confidence 1222221111 1222211 1234458888777778998877664 22322 1235678999999999999988
Q ss_pred eecCCCCCcee
Q 003676 791 ERDKNNPQIYN 801 (804)
Q Consensus 791 ~Rd~~d~~~y~ 801 (804)
+--+ +.|.
T Consensus 755 ~f~~---G~Y~ 762 (765)
T KOG2165|consen 755 EFIA---GSYR 762 (765)
T ss_pred EEec---ceee
Confidence 8765 3564
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=99.76 E-value=5.3e-19 Score=146.94 Aligned_cols=66 Identities=59% Similarity=0.959 Sum_probs=60.3
Q ss_pred HHHhhHHHHHHHHHHHhhcCCCCChHHHHHHHHHhc--CCCCChHHHHHHHHHHhhcCceeecCCCCC
Q 003676 733 VFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQ 798 (804)
Q Consensus 733 v~~dR~~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l--~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~ 798 (804)
|.++|.+.|+||||||||++|+|+|++|+.+|.+++ +|+|+..+||++||+||++|||+||++|+|
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 468999999999999999999999999999999999 599999999999999999999999999875
No 10
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.61 E-value=0.00043 Score=78.01 Aligned_cols=313 Identities=12% Similarity=0.026 Sum_probs=187.3
Q ss_pred hHHHHHHHHHHHHHHHHhcCCC----CccHHHHHHHHHhhhccCc--hhHHHHHHHHHHHHHHHHHHHhhhc---CC--C
Q 003676 103 FEEDTWAKLKLAIKAIFLKQPT----SCDLEKLYQAVNDLCLHKM--GGNLYQRIEKECEEHISAAIRSLVG---QS--P 171 (804)
Q Consensus 103 ~~e~~W~~L~~aI~~I~~~~~~----~~s~e~LY~~Vy~lC~~k~--~e~LY~~L~~~~~~~l~~~~~~l~~---~~--~ 171 (804)
++...|..|++++.-|..-... ...|-++.+.+|+-|..+. ...+.+-++..+..+..+...-+.. .+ .
T Consensus 109 geAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~ 188 (661)
T KOG2167|consen 109 GEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKP 188 (661)
T ss_pred cchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccc
Confidence 3456788888888877765433 3456678999999999873 4556666776666666653322221 11 1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccceeccccccccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHhcC
Q 003676 172 DLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLG 251 (804)
Q Consensus 172 d~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDr~yv~~~~~~~sI~~lgl~lFr~~v~~~~~i~~~l~~~ll~lI~~eR~g 251 (804)
....+.+.+...|-+....... ++-+|-. +.++...+|+++-..+....-.-+...+-+++....+|..++.+
T Consensus 189 l~atV~~~LL~~hL~~IL~kgl----~~lvDm~---q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~kD 261 (661)
T KOG2167|consen 189 LIATVERCLLSRHLDLILTKGL----DSLVDMR---QTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEKD 261 (661)
T ss_pred hHHHHHHHHHHHHHHHHHhcch----HHhhhhh---hccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchhh
Confidence 3467888888888877555544 4444543 22335667777666663332222356677777778888888877
Q ss_pred CcCC--hHHHHHHHHHHhhhhcchHhhHHhHHHHHHHHHHHHHHHhhhcCChhhHHHHHHHHHHHHHHHHhhhcCcCchH
Q 003676 252 EAVD--RTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRK 329 (804)
Q Consensus 252 ~~id--~~llk~ii~ml~~L~iY~~~FE~~fL~~t~~yY~~~s~~~i~~~~~~eYL~~ve~~l~eE~~r~~~yl~~~t~~ 329 (804)
+... ....|..++|......+...- .+|+..++++|..+.+. ....+.+||.+....+-.+-+ ...+-+
T Consensus 262 k~mVqELL~FK~k~Dii~~~sF~~~v~-e~f~~~~~~afe~fink--~~~rpAelIak~~dt~Lr~gn------k~~~d~ 332 (661)
T KOG2167|consen 262 KDMVQELLDFKKKVDIIVDESFLKYVA-EKFLNSMSKAFETFINK--RRNRPAELIAKYVDTKLRAGN------KETSDE 332 (661)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHhhH-HHHHHHHHHHHHHHHhc--ccCCHHHHHHHHHHHHHHhcc------ccccch
Confidence 7633 345778888888777666544 89999999999999994 666799999988765444311 011122
Q ss_pred HHHHHHHHH------------------------HHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHhcccccHHHHHHHHH
Q 003676 330 PLIATAERQ------------------------LLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRVNALESLRQALA 385 (804)
Q Consensus 330 ~l~~~l~~~------------------------Li~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~~~l~~l~~~~~ 385 (804)
.|-.++.++ |+..|... ++.|+.-|..-......+.+|+|.+..+..+...+..+
T Consensus 333 ~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAs-vdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~ 411 (661)
T KOG2167|consen 333 ELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSAS-VDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINR 411 (661)
T ss_pred hHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchh-hcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHH
Confidence 222333333 33322221 23444444444556778889999888765655555555
Q ss_pred HHHHHHhhhhhcCchhhHHHHHHHHHHHHHHHHHHHHhcCCcHHhHHHHHHHHHH
Q 003676 386 MYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEY 440 (804)
Q Consensus 386 ~yi~~~g~~iv~~~~~~~~~V~~Ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~ 440 (804)
.|....|..-- . ...|+.++--...+|-.||+.+..+-..+++.++.
T Consensus 412 ~f~~~~~~~~~-~-------~~~l~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~ 458 (661)
T KOG2167|consen 412 AFKQSKGANNR-L-------EGNLLTVNVLTMGYWPTYPPMEVLLPKEMRDCQEI 458 (661)
T ss_pred HHHHHHHhhcc-C-------cCCceEEEeecccccCCCCchhccCCHHHHHHHHH
Confidence 55554333210 0 11122233334556777777766666666544433
No 11
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.36 E-value=0.0022 Score=62.39 Aligned_cols=124 Identities=15% Similarity=0.212 Sum_probs=89.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhh---hccCch-hHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHH
Q 003676 104 EEDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVNDL---CLHKMG-GNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSL 179 (804)
Q Consensus 104 ~e~~W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~l---C~~k~~-e~LY~~L~~~~~~~l~~~~~~l~~~~~d~~~~L~~ 179 (804)
.++.|..+..++-.+|+++....+.|.|-+.|.-. |.++.. ..+-+.+++.+..-+......+.... ...+|..
T Consensus 5 ~~~~W~~~~~~vl~lF~g~~l~~~iEdlN~lv~~~i~~~~~~~~~~~~~~dl~elL~tg~~~L~~~l~~~~--~~~~l~r 82 (158)
T PF08539_consen 5 SDDAWNSLCAKVLPLFQGERLRLPIEDLNELVRFHIKLCIQSFPPSYFLEDLEELLTTGMYILENQLNEVP--DNRLLKR 82 (158)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHhhcc--hhHHHHH
Confidence 47899999999999999999889999988888654 444432 23444445544444443333343222 2689999
Q ss_pred HHHHHHHHHHH-HHHHHHhhhhcccceeccc----------------cccccHHHHHHHHHHHHhcc
Q 003676 180 VERCWQDLCDQ-MLMIRGIALYLDRTYVKQT----------------PNVRSLWDMGLQLFRKYLSS 229 (804)
Q Consensus 180 ~~~~W~~~~~~-~~~i~~iF~YLDr~yv~~~----------------~~~~sI~~lgl~lFr~~v~~ 229 (804)
+...|.-|... +=++..||..|++.+-... ....+|..++|..||+.|+-
T Consensus 83 L~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvL 149 (158)
T PF08539_consen 83 LVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVL 149 (158)
T ss_pred HHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhh
Confidence 99999996665 5579999999995432211 23579999999999999985
No 12
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=93.80 E-value=0.2 Score=44.50 Aligned_cols=66 Identities=17% Similarity=0.184 Sum_probs=54.4
Q ss_pred EEEEcHHHHHHHHhHh--------CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003676 633 ELAVSLFQTVVLMLFN--------DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (804)
Q Consensus 633 ~l~vs~~Qa~ILllFn--------~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (804)
...++.-|+.+|+..- ....+|-.||++.+|++.+.+.+.|..|. +.++|.+.. ....|.+|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~ 91 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTP 91 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCC
Confidence 3567888999888655 45789999999999999999999999999 888987642 2468999988
Q ss_pred CC
Q 003676 705 FT 706 (804)
Q Consensus 705 F~ 706 (804)
.+
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 65
No 13
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=92.70 E-value=0.17 Score=39.44 Aligned_cols=46 Identities=22% Similarity=0.391 Sum_probs=38.8
Q ss_pred HHHHHhHhCCC-CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 641 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 641 a~ILllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+.||-+|.+.+ .+|+.||++.+|++...+.+.|..|. ..+++.+.|
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~--~~g~v~~dp 52 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLV--EEGYVERDP 52 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEECS
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCcCeecCc
Confidence 35788888775 58999999999999999999999999 788887753
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=91.94 E-value=0.44 Score=41.15 Aligned_cols=59 Identities=17% Similarity=0.289 Sum_probs=43.2
Q ss_pred HHHHHHHhHhCCC-CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003676 639 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (804)
Q Consensus 639 ~Qa~ILllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (804)
+++.+.+..+..+ .+|.++|++.+++++..+.+.|+.|. +.+++...+ ..+.-|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-----G~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-----GRGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-----STTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-----CCCCceeecCC
Confidence 4455555545444 49999999999999999999999999 888887543 14567888775
No 15
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=91.39 E-value=0.41 Score=36.55 Aligned_cols=46 Identities=15% Similarity=0.333 Sum_probs=37.3
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCccee
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (804)
+..+.-||....+++.+|..||++.+|++...+.+.|+.|. +.+++
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~--~~g~I 47 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE--EKGLI 47 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH--HTTSE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCcCc
Confidence 44577788888888899999999999999999999999998 55554
No 16
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=91.11 E-value=0.29 Score=39.37 Aligned_cols=51 Identities=20% Similarity=0.292 Sum_probs=43.9
Q ss_pred EcHHHHHHHHhHhCCCC--CCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 636 VSLFQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 636 vs~~Qa~ILllFn~~~~--lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+|+-|+.||..+...+. +|..||++.++++...+.+.+..|. +.+++.+.+
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 46789999988877766 9999999999999999999999999 888887754
No 17
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=89.47 E-value=0.6 Score=37.26 Aligned_cols=47 Identities=23% Similarity=0.483 Sum_probs=40.9
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
|..|+-..++.+.+|++||++.+|+++..+++-|..|. +.+++.+.-
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~~ 48 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 45677788889999999999999999999999999999 777777653
No 18
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=88.99 E-value=0.6 Score=38.23 Aligned_cols=51 Identities=18% Similarity=0.252 Sum_probs=40.1
Q ss_pred EcHHHHHHHHhHh-CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 636 VSLFQTVVLMLFN-DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 636 vs~~Qa~ILllFn-~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+|..|..||.... ....++..+|++.++++...+.+.|+.|. ..+++.+.+
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~--~~glv~~~~ 52 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLE--EKGLVEKER 52 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEecC
Confidence 3667899998888 77899999999999999999999999999 778887643
No 19
>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=88.09 E-value=0.4 Score=38.18 Aligned_cols=50 Identities=14% Similarity=0.282 Sum_probs=43.9
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
|..|+.||....+.+.++..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 2 t~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~~ 51 (59)
T PF01047_consen 2 TPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERER 51 (59)
T ss_dssp THHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEecc
Confidence 67899999888888889999999999999999999999999 788887653
No 20
>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=87.63 E-value=0.79 Score=36.97 Aligned_cols=50 Identities=12% Similarity=0.248 Sum_probs=41.3
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
++.-.-||.++...+++|+.||++.+|++...+.++|.-|. +.+++....
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~--~aGli~~~~ 58 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLE--EAGLIEVER 58 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEec
Confidence 34556788777777899999999999999999999999999 788887643
No 21
>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=87.46 E-value=1.2 Score=41.16 Aligned_cols=52 Identities=15% Similarity=0.257 Sum_probs=46.9
Q ss_pred EEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 635 ~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
.++..|..||......+.+|..+|++.+|++...+.+.+..|. +.+++.+.+
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 4578899999988888899999999999999999999999999 888888754
No 22
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=87.33 E-value=0.64 Score=38.62 Aligned_cols=46 Identities=24% Similarity=0.400 Sum_probs=37.3
Q ss_pred HHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCC
Q 003676 744 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 795 (804)
Q Consensus 744 aIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~ 795 (804)
.|-.+|+.++.++.++|-. .|..+++.+...|+.|+.+|||++.+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAR------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHH------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHH------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 3567899999999999876 589999999999999999999999653
No 23
>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=86.27 E-value=1.7 Score=33.01 Aligned_cols=43 Identities=14% Similarity=0.398 Sum_probs=35.2
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (804)
..-||.+.-+ ++.++.||++.+|++...+.++|..|. +.+++.
T Consensus 4 R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLVE 46 (47)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCee
Confidence 4556766666 789999999999999999999999998 677764
No 24
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=84.81 E-value=2 Score=41.19 Aligned_cols=53 Identities=23% Similarity=0.253 Sum_probs=46.8
Q ss_pred EEEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 634 l~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+.++..|+.||......+.+|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 35678899999877667789999999999999999999999999 889998865
No 25
>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=84.63 E-value=2.9 Score=37.50 Aligned_cols=62 Identities=19% Similarity=0.317 Sum_probs=47.7
Q ss_pred EEcHHHHHHHHh-------HhCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCC
Q 003676 635 AVSLFQTVVLML-------FNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 706 (804)
Q Consensus 635 ~vs~~Qa~ILll-------Fn~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~ 706 (804)
.++.-|.-|++. ||.. +.+|..++++.||++...+.+++..|+ +.+||... +..+.+|.+.+
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 445556666654 4443 589999999999999999999999999 99999763 45677776653
No 26
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=84.33 E-value=2 Score=35.67 Aligned_cols=47 Identities=21% Similarity=0.311 Sum_probs=39.7
Q ss_pred HHHHHHHhHhCCCC--CCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 639 FQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 639 ~Qa~ILllFn~~~~--lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
..-.||.++.+.+. +|..||++.+|++...+.++|..|. +.+++.+.
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 34467777777765 9999999999999999999999999 77777764
No 27
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=82.55 E-value=2.5 Score=37.01 Aligned_cols=53 Identities=23% Similarity=0.397 Sum_probs=46.9
Q ss_pred EEEEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 633 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 633 ~l~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
+..++..+..||.+....+.++..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEec
Confidence 456788899999888887889999999999999999999999999 78888764
No 28
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=82.55 E-value=3.3 Score=37.65 Aligned_cols=53 Identities=23% Similarity=0.339 Sum_probs=45.4
Q ss_pred EEEcHHHHHHHHhHh----CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 634 LAVSLFQTVVLMLFN----DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 634 l~vs~~Qa~ILllFn----~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+.+|..|..||.... ..+.++..+|++.++++...+.+.+..|. +.+.+.+.+
T Consensus 21 ~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~ 77 (109)
T TIGR01889 21 FNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKER 77 (109)
T ss_pred cCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccC
Confidence 346788888886655 55789999999999999999999999999 889998865
No 29
>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=81.81 E-value=4.5 Score=38.17 Aligned_cols=60 Identities=20% Similarity=0.257 Sum_probs=46.4
Q ss_pred HHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 742 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 742 ~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
+..|++++-..+.++..+++..+-+ +..+...-|...|..|.++|||+|..+.+ .|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~--~~~~~~tTv~T~L~rL~~KG~v~~~k~gr-~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAE--KKDWSDSTIKTLLGRLVDKGCLTTEKEGR-KFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhh--ccCCcHHHHHHHHHHHHHCCceeeecCCC-cEEEEe
Confidence 5568888877888888777765433 25678889999999999999999986544 688854
No 30
>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=81.29 E-value=6.2 Score=32.43 Aligned_cols=59 Identities=17% Similarity=0.329 Sum_probs=43.0
Q ss_pred HhhHHHHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCC
Q 003676 735 QDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNP 797 (804)
Q Consensus 735 ~dR~~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~ 797 (804)
-+|+..|=.+|...++.++--.- +.|+.+.+.+. ++.-+...++.|.++|||+|+++-+
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~Pt---~rEIa~~~g~~-S~~tv~~~L~~Le~kG~I~r~~~~~ 63 (65)
T PF01726_consen 5 TERQKEVLEFIREYIEENGYPPT---VREIAEALGLK-STSTVQRHLKALERKGYIRRDPGKA 63 (65)
T ss_dssp -HHHHHHHHHHHHHHHHHSS------HHHHHHHHTSS-SHHHHHHHHHHHHHTTSEEEGCCSC
T ss_pred CHHHHHHHHHHHHHHHHcCCCCC---HHHHHHHhCCC-ChHHHHHHHHHHHHCcCccCCCCCC
Confidence 35677777888888877653322 44555666675 7899999999999999999998643
No 31
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=80.99 E-value=3.7 Score=35.63 Aligned_cols=45 Identities=16% Similarity=0.322 Sum_probs=38.7
Q ss_pred HHHHhHhCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 642 VVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 642 ~ILllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
.||-.+... +.+|..||++.+|++...+.+.|..|. ..++|.+.+
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~~ 54 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQDG 54 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 466667665 689999999999999999999999999 788888753
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=80.87 E-value=3.5 Score=31.38 Aligned_cols=45 Identities=22% Similarity=0.478 Sum_probs=36.9
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
-.|+..+.+...++..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~--~~g~i~~~ 47 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLE--EQGLLTRV 47 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 3456566666789999999999999999999999998 66777654
No 33
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=79.33 E-value=5.8 Score=39.07 Aligned_cols=58 Identities=16% Similarity=0.324 Sum_probs=43.6
Q ss_pred HHHHHHhHhCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003676 640 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (804)
Q Consensus 640 Qa~ILllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (804)
.+++.+.|+.. ..+|.++|++.+|+|...+.+.|+.|. +.+++.... | .++-|.+..+
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s~r-G----~~GGy~Lar~ 70 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSSVR-G----PGGGYLLGKD 70 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeCC-C----CCCCeeccCC
Confidence 44455667654 589999999999999999999999999 889887532 1 2334666554
No 34
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=78.84 E-value=6.1 Score=38.40 Aligned_cols=57 Identities=18% Similarity=0.279 Sum_probs=42.7
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (804)
+++.|..+..+.++..+|++..|+|...|.+.|+.|. +.+++.... | .+.-|.++..
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-G----~~GGy~La~~ 69 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-G----RNGGVRLGRP 69 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-C----CCCCeeecCC
Confidence 3444555666678999999999999999999999999 889887543 2 2344665553
No 35
>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=77.96 E-value=63 Score=35.65 Aligned_cols=160 Identities=13% Similarity=0.235 Sum_probs=93.6
Q ss_pred HHHHHHHHHHHHhhccCCHHHHHHHHHHhccc----ccHHHHHHHHHHHHHHHhhhhhcCc-------hhhHHHHHHHHH
Q 003676 343 HISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMDE-------EKDKDMVSSLLE 411 (804)
Q Consensus 343 ~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~----~~l~~l~~~~~~yi~~~g~~iv~~~-------~~~~~~V~~Ll~ 411 (804)
++..++.+.|..-...+|.+.+.++++||-.+ .|++....-+.+.|.....+.+... ..+.-++..|..
T Consensus 7 ~L~~~f~~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~ 86 (331)
T PF08318_consen 7 SLCEIFLKKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTK 86 (331)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHH
Confidence 34455567788889999999999999999776 5777777777777766666655432 223356666666
Q ss_pred HHHHHHH-------HHHHhcCCcHHh--HHHHHH--------HHHHHhhcCC-CcchHHHHHHHHHHHhc----------
Q 003676 412 FKASLDT-------IWEQSFSKNEAF--CNTIKD--------AFEYLINLRQ-NRPAELIAKFLDEKLRA---------- 463 (804)
Q Consensus 412 l~~~~~~-------li~~~F~~~~~f--~~~l~~--------af~~~lN~~~-~~~~e~La~y~D~~lr~---------- 463 (804)
+++.+-. +|..+||..... ...+.. -+..|...+. .+...-+-.|-...+.+
T Consensus 87 LFe~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~ 166 (331)
T PF08318_consen 87 LFEHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSS 166 (331)
T ss_pred HHHHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhcccccccccccc
Confidence 6666544 456788754321 111111 2233333322 01112233333333322
Q ss_pred --------CCCCCCHHHHHhcccccceeeeeccChhHHHHHHHHHHHHHhcCCC
Q 003676 464 --------GNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGK 509 (804)
Q Consensus 464 --------~~k~~~~~e~e~~l~~i~~lf~~i~~KD~F~~~Y~~~LakRLL~~~ 509 (804)
+....+--+++..|+++..++.... .|.++++.|+....
T Consensus 167 ~~~~~~~~~~~~~d~reld~lL~Eis~i~~~w~-------lY~rFi~~k~~~~~ 213 (331)
T PF08318_consen 167 RAASSSQSEDEGIDPRELDALLNEISLILQRWS-------LYCRFISRKWNEFS 213 (331)
T ss_pred ccccccccccCCCCHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHhccc
Confidence 0011233578888888888775443 79999999987743
No 36
>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=77.86 E-value=5.8 Score=32.28 Aligned_cols=54 Identities=13% Similarity=0.277 Sum_probs=37.2
Q ss_pred HHHHHHHHhh-cCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceee--cCCCCCce
Q 003676 741 VDAAIVRIMK-TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER--DKNNPQIY 800 (804)
Q Consensus 741 i~AaIVRIMK-~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~R--d~~d~~~y 800 (804)
-+..|.+.+. ....++..+|.. .+..+...+-+.|+.|+++|||++ ++.|....
T Consensus 4 ~q~~vL~~l~~~~~~~t~~~l~~------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~ 60 (68)
T PF13463_consen 4 PQWQVLRALAHSDGPMTQSDLAE------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSK 60 (68)
T ss_dssp HHHHHHHHHT--TS-BEHHHHHH------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSE
T ss_pred HHHHHHHHHHccCCCcCHHHHHH------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCee
Confidence 3567777888 777888777665 255678889999999999999977 45455433
No 37
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=77.64 E-value=5.2 Score=42.36 Aligned_cols=143 Identities=11% Similarity=0.180 Sum_probs=85.9
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCc----ceEeecc
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPL----YRIKVNA 716 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~----~~iki~~ 716 (804)
..||-+|.....+|+.||++.+|++...+.+.|..|. ..+.|.+.+. +..|.+-..+-.-- ....+..
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~--~~G~l~~~~~------~~~Y~lG~~~~~lg~~~~~~~~l~~ 88 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMK--TLGYVAQEGE------SEKYSLTLKLFELGAKALQNVDLIR 88 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcCC------CCcEEecHHHHHHHHHHHhhCcHHH
Confidence 3478889887789999999999999999999999999 8889987642 34566544331100 0000000
Q ss_pred ---cccc-------cc----------------chhhhhh-hHhHHHhhHHHHHHHHHHHhhcCCCCChHHHHHHHHHhc-
Q 003676 717 ---IQMK-------ET----------------VEENTST-TERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL- 768 (804)
Q Consensus 717 ---i~~k-------~t----------------~~e~~~~-~~~v~~dR~~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l- 768 (804)
..+. +| .+..... ...-...|.+..-++.=|+|=+.-. .+-+..++...
T Consensus 89 ~a~p~l~~La~~~~etv~L~v~~g~~~v~l~~~~~~~~~~~~~~~G~~~Pl~~tA~GkalLA~~~---~~~~~~~l~~~~ 165 (257)
T PRK15090 89 SADIQMREISRLTKETIHLGALDEDSIVYIHKIDSMYNLRMYSRIGRRNPLYSTAIGKVLLAWRD---RDEVREILSGVE 165 (257)
T ss_pred HHHHHHHHHHHHhCCeEEEEEEECCEEEEEEEecCCCceEEEccCCCccchhhhhHHHHHHhCCC---HHHHHHHHccCC
Confidence 0000 00 0000000 0011244566777788888877643 23333444433
Q ss_pred --CCC----CChHHHHHHHHHHhhcCceeecC
Q 003676 769 --KFP----IKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 769 --~F~----~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
+++ .+++.+.+.|+.--++||-.-++
T Consensus 166 ~~~~t~~t~~~~~~l~~~l~~iR~~Gya~~~~ 197 (257)
T PRK15090 166 FKRSTEKTITSTEALLPVLDQVREQGYGEDNE 197 (257)
T ss_pred CCcCCCCCCCCHHHHHHHHHHHHHhCCCcccc
Confidence 232 46788999999999999976543
No 38
>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=77.58 E-value=2.3 Score=35.02 Aligned_cols=49 Identities=18% Similarity=0.261 Sum_probs=40.5
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
|-.++-|+...-..+..|..||++.+|++...+.+.|..|. +.+++.+.
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~--~~GlV~~~ 55 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLE--EKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHH--HTTSEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 44566666555566789999999999999999999999999 77787764
No 39
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=77.34 E-value=5.8 Score=36.83 Aligned_cols=61 Identities=18% Similarity=0.288 Sum_probs=52.9
Q ss_pred HHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeC
Q 003676 740 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYL 803 (804)
Q Consensus 740 ~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yl 803 (804)
..++.|++||=.++..+.++++.++.+. +.++...|+--|..|..||.|.+..++ ..|.|=
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~--~ews~sTV~TLl~RL~KKg~l~~~kdg-r~~~y~ 66 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD--REWSYSTVKTLLNRLVKKGLLTRKKDG-RAFRYS 66 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc--ccccHHHHHHHHHHHHhccchhhhhcC-Ceeeee
Confidence 3678899999999999999999888775 788999999999999999999998754 467774
No 40
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=77.26 E-value=6.6 Score=37.21 Aligned_cols=45 Identities=18% Similarity=0.321 Sum_probs=36.9
Q ss_pred HHHHHHhHhCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 640 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 640 Qa~ILllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
.+++.|.++.. ..+|.++|++.+++|...+.+.|+.|. +.+++..
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 34445565544 479999999999999999999999999 8888864
No 41
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=76.76 E-value=8.7 Score=31.79 Aligned_cols=54 Identities=9% Similarity=0.244 Sum_probs=43.0
Q ss_pred HHHHHHHHhhcCCC--CChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCce
Q 003676 741 VDAAIVRIMKTRKV--LSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIY 800 (804)
Q Consensus 741 i~AaIVRIMK~~K~--l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y 800 (804)
.+..|...|+.+.. ++-.+|-. + .-.+...+.+.+..|.++|||++++..|..|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~----~--lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAK----N--LGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHH----H--HCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 55678899999877 88877765 3 3456778999999999999999988765554
No 42
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=76.68 E-value=2.4 Score=39.03 Aligned_cols=61 Identities=15% Similarity=0.262 Sum_probs=46.8
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 741 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 741 i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
.+..|++++=..+.++..+++..+-+. ..+....|...+..|.+||||.|.... ..|.|-|
T Consensus 4 ~E~~IM~~lW~~~~~t~~eI~~~l~~~--~~~~~sTv~t~L~rL~~Kg~l~~~~~g-r~~~Y~p 64 (115)
T PF03965_consen 4 LELEIMEILWESGEATVREIHEALPEE--RSWAYSTVQTLLNRLVEKGFLTREKIG-RAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHHSSEEHHHHHHHHCTT--SS--HHHHHHHHHHHHHTTSEEEEEET-TCEEEEE
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhc--cccchhHHHHHHHHHHhCCceeEeecC-CceEEEe
Confidence 466788888888888888877655443 567899999999999999999998654 4688854
No 43
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=76.20 E-value=5.5 Score=32.42 Aligned_cols=47 Identities=26% Similarity=0.360 Sum_probs=36.4
Q ss_pred HHHhHhC-CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCC
Q 003676 643 VLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGR 691 (804)
Q Consensus 643 ILllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~ 691 (804)
||-.++. +.+++..||++.+|++....++.|..|. +.+.+.+.|.++
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~r 52 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRR 52 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SS
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCC
Confidence 4555566 6789999999999999999999999999 777777766543
No 44
>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=75.47 E-value=2.2 Score=35.12 Aligned_cols=57 Identities=16% Similarity=0.323 Sum_probs=42.9
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeC
Q 003676 741 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYL 803 (804)
Q Consensus 741 i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yl 803 (804)
.++.|-..|-.++.++..+|... ...+...+-+.++.|.++|+++|.+.++..|..+
T Consensus 9 ~E~~vy~~Ll~~~~~t~~eIa~~------l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 9 NEAKVYLALLKNGPATAEEIAEE------LGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHHCHEEHHHHHHH------HTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 45555556557777888776653 2457889999999999999999998776666554
No 45
>PHA00738 putative HTH transcription regulator
Probab=75.09 E-value=7.2 Score=35.28 Aligned_cols=68 Identities=18% Similarity=0.199 Sum_probs=52.8
Q ss_pred EEEEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCC
Q 003676 633 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 706 (804)
Q Consensus 633 ~l~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~ 706 (804)
++...+.=-.||.+..+++.+++.+|++.++|+...+-++|.-|- ..+|+.....|+.+ .|++|.+-.
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr~v----yY~Ln~~~~ 74 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGRTL----YAKIRENSK 74 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECCEE----EEEECCCcc
Confidence 344555555677666677789999999999999999999999998 88999877665433 577887643
No 46
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=75.09 E-value=6.6 Score=39.48 Aligned_cols=53 Identities=9% Similarity=0.008 Sum_probs=47.2
Q ss_pred EEEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 634 l~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+.++..|..||......+.+|..+|++.++++...+.+.|..|. +.+++.+.+
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 45678899999999888899999999999999999999999999 888888754
No 47
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=74.12 E-value=6.1 Score=37.69 Aligned_cols=53 Identities=25% Similarity=0.293 Sum_probs=45.7
Q ss_pred EEEcHHHHHHHHhHhCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 634 LAVSLFQTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 634 l~vs~~Qa~ILllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+.++..|..||...... +.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 45778898998877654 568999999999999999999999999 889998765
No 48
>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=74.06 E-value=7.5 Score=31.64 Aligned_cols=48 Identities=15% Similarity=0.327 Sum_probs=40.0
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
+..+..|+..+.+.. ++..||++.+|++...+.+.|..|. ..+++...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~--~~g~i~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLE--EAGLVESR 53 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHH--HCCCeEEE
Confidence 456777887777766 9999999999999999999999998 66777653
No 49
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=73.03 E-value=8.4 Score=28.74 Aligned_cols=34 Identities=26% Similarity=0.433 Sum_probs=30.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 652 ~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
.++..+|++.+|++...+.+.|..|. +.+++.+.
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 57899999999999999999999999 88888763
No 50
>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=72.59 E-value=7.8 Score=30.23 Aligned_cols=36 Identities=17% Similarity=0.492 Sum_probs=29.1
Q ss_pred HHH-hHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhc
Q 003676 643 VLM-LFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 678 (804)
Q Consensus 643 ILl-lFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 678 (804)
||. +.+..+.+|.++|++.+|++...+.+.|..|..
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 443 446666799999999999999999999999973
No 51
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=72.33 E-value=9.5 Score=35.64 Aligned_cols=37 Identities=14% Similarity=0.299 Sum_probs=34.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 649 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
.++.+|+++|++.++.+...+.++|+.|. ..+++.++
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~--~~GlV~Re 75 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLL--EAGLVERE 75 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHH--HcCCeeee
Confidence 67899999999999999999999999999 88898875
No 52
>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=71.95 E-value=6.7 Score=31.20 Aligned_cols=47 Identities=15% Similarity=0.351 Sum_probs=41.6
Q ss_pred HHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCC
Q 003676 743 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 795 (804)
Q Consensus 743 AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~ 795 (804)
..|+..++.++.++..+|.. .|.++...|.+-+..|-++|+|.|.-+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~------~~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAE------EFGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHH------HHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 46888899999999999886 488999999999999999999999643
No 53
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=71.89 E-value=3.2 Score=35.58 Aligned_cols=44 Identities=20% Similarity=0.458 Sum_probs=34.1
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
..||...+..+.+++.+|.+.+|+++..|.++|..|. +.+.+..
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le--~~GyV~~ 46 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLE--EAGYVEV 46 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEE
Confidence 3456555667789999999999999999999999999 6666543
No 54
>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=71.50 E-value=5.4 Score=39.31 Aligned_cols=49 Identities=16% Similarity=0.378 Sum_probs=42.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCc
Q 003676 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPL 709 (804)
Q Consensus 652 ~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~ 709 (804)
-+|..+|++.+|++...+.+++..|. +.+||.+.. ...|.+|++|--+-
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~~-------~G~Y~iNP~~~~kG 123 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKIR-------NGAYMINPNFFFKG 123 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEcc-------CCeEEECcHHheeC
Confidence 47899999999999999999999999 888998753 45899999986543
No 55
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=71.10 E-value=8 Score=30.24 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=33.8
Q ss_pred HhCCCCC-CHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 647 FNDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 647 Fn~~~~l-t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+...+.+ |..+|++.+|++...+.++|..|. +.+++...+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEec
Confidence 4445567 899999999999999999999999 778887654
No 56
>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=71.03 E-value=4.7 Score=33.91 Aligned_cols=42 Identities=19% Similarity=0.238 Sum_probs=32.0
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
+..++...+.+|+.||++.+|++...++..+..+. +.++|.+
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~~ 64 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLVK 64 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHHH
Confidence 33333444679999999999999999999988776 6666643
No 57
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=71.03 E-value=6.6 Score=36.36 Aligned_cols=57 Identities=16% Similarity=0.247 Sum_probs=43.8
Q ss_pred HHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003676 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (804)
Q Consensus 642 ~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (804)
.||.+.-+.++.++.||++.+|++...+-++|.-|. ..+++.....|+. -.|.+|.+
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr~----~~Y~l~~~ 76 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGKW----VHYRLSPH 76 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcCE----EEEEECch
Confidence 455444445679999999999999999999999999 8999987665532 24667653
No 58
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=70.96 E-value=6.7 Score=39.94 Aligned_cols=52 Identities=19% Similarity=0.222 Sum_probs=46.7
Q ss_pred EEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 635 ~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
.++.-|..||..+.+++.++..+|++.+|++...+.+.|..|. +.+++.+.+
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 5678899999999887889999999999999999999999999 888888754
No 59
>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=70.88 E-value=10 Score=35.50 Aligned_cols=47 Identities=17% Similarity=0.400 Sum_probs=37.0
Q ss_pred HHHHHHHhHhCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 639 FQTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 639 ~Qa~ILllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
+++++.+.-++. ..+|.++|++.+|++...+.+.|..|. +.+++...
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~~ 58 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVESV 58 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 344445544433 389999999999999999999999999 78888653
No 60
>PRK10870 transcriptional repressor MprA; Provisional
Probab=69.90 E-value=11 Score=37.48 Aligned_cols=52 Identities=12% Similarity=0.158 Sum_probs=44.3
Q ss_pred EEcHHHHHHHHhHhC--CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 635 AVSLFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 635 ~vs~~Qa~ILllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
.++..|..||..... ..++|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~ 105 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRE 105 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 456778888877754 4579999999999999999999999999 889998865
No 61
>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=69.40 E-value=13 Score=31.23 Aligned_cols=41 Identities=22% Similarity=0.476 Sum_probs=34.5
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
||+..... ..|+++|.+.||++.+.|...|.-|. +.+++.+
T Consensus 10 IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 10 ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 44444444 89999999999999999999999999 8888865
No 62
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=68.05 E-value=13 Score=35.97 Aligned_cols=59 Identities=14% Similarity=0.282 Sum_probs=44.4
Q ss_pred HHHHHHHhHhCCC-CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003676 639 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (804)
Q Consensus 639 ~Qa~ILllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (804)
+.+.+.|.-+..+ ..|.++|++..|+++..|.+.|..|. |.+++...+. .+.-|.++.+
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~rG-----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVRG-----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeecC-----CCCCccCCCC
Confidence 3445555555554 68899999999999999999999999 8999876432 3455666664
No 63
>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=67.22 E-value=5.6 Score=31.47 Aligned_cols=46 Identities=22% Similarity=0.356 Sum_probs=35.3
Q ss_pred HHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeec
Q 003676 742 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 793 (804)
Q Consensus 742 ~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd 793 (804)
+..|..++-....++..+|-. .+..+...+-+.|..|+++|||+|.
T Consensus 5 q~~iL~~l~~~~~~~~~~la~------~~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAE------KLGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHH------HHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHH------HHCCChhHHHHHHHHHHHCCCEEec
Confidence 456666677777788877664 2456899999999999999999994
No 64
>PRK11569 transcriptional repressor IclR; Provisional
Probab=66.59 E-value=12 Score=40.00 Aligned_cols=45 Identities=9% Similarity=0.315 Sum_probs=39.8
Q ss_pred HHHHhHhCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 642 VVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 642 ~ILllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
.||-+|.+. ..+++.||++.+|++...+.+.|.+|. ..+.|.+.+
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~ 77 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVG 77 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 478889875 579999999999999999999999999 888998754
No 65
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=66.09 E-value=14 Score=39.55 Aligned_cols=56 Identities=14% Similarity=0.100 Sum_probs=45.1
Q ss_pred HHHHHhHhCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003676 641 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (804)
Q Consensus 641 a~ILllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (804)
..||-+|... ..+|+.||++.+|++...+.+.|.+|. ..+.|.+.+ .+..|.+...
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~--~~G~l~~~~------~~~~Y~lG~~ 84 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQ--AADFVYQDS------QLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC------CCCeEEecHH
Confidence 3488899865 479999999999999999999999999 888898754 2445665443
No 66
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=65.53 E-value=14 Score=38.85 Aligned_cols=46 Identities=22% Similarity=0.446 Sum_probs=40.3
Q ss_pred HHHHHhHhCCCC-CCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 641 TVVLMLFNDAQK-LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 641 a~ILllFn~~~~-lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
..||-+|..... +++.||++.+|+|...+.+.|..|. ..+.+.+.+
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 357888887554 7899999999999999999999999 899999875
No 67
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=65.25 E-value=13 Score=39.47 Aligned_cols=45 Identities=20% Similarity=0.326 Sum_probs=39.7
Q ss_pred HHHHhHhCCC-CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 642 VVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 642 ~ILllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
.||.+|.+.+ .+|..||++.+|++...+.+.|..|. ..++|.+.+
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~ 60 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSA 60 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 4778887655 59999999999999999999999999 889998865
No 68
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=65.17 E-value=12 Score=33.71 Aligned_cols=46 Identities=11% Similarity=0.314 Sum_probs=39.4
Q ss_pred HHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
..-.||..+.....+|+.+|++.+|++...+.+.++.|. +.+++.+
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~--~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLE--EEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeec
Confidence 345677788777889999999999999999999999999 7777763
No 69
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=64.78 E-value=66 Score=37.57 Aligned_cols=50 Identities=10% Similarity=0.242 Sum_probs=44.6
Q ss_pred EEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 635 ~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
.++..|..||......+.++..+|++.+|++...+.+.+.+|. +.+++..
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le--~kGlV~~ 52 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLE--EKGLVKV 52 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHH--hCCCEEE
Confidence 4678999999999888899999999999999999999999998 6667664
No 70
>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=64.66 E-value=16 Score=34.22 Aligned_cols=43 Identities=21% Similarity=0.358 Sum_probs=35.5
Q ss_pred HHHhHhC--CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 643 VLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 643 ILllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
+|+.+.. .+.+|..||++.+|++...+.+.|..|. +.+++...
T Consensus 14 ~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~ 58 (130)
T TIGR02944 14 VLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSK 58 (130)
T ss_pred HHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 4444443 3579999999999999999999999999 88888653
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=64.31 E-value=15 Score=38.55 Aligned_cols=43 Identities=26% Similarity=0.466 Sum_probs=38.3
Q ss_pred HHHHhHhC-CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 642 VVLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 642 ~ILllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
.||-+|.. ...+++.||++.+|++...+.+.|..|. ..+.|.+
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~--~~G~l~~ 56 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLV--ELGYVTS 56 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 47888986 4579999999999999999999999999 7888876
No 72
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=64.17 E-value=1.7e+02 Score=29.61 Aligned_cols=85 Identities=18% Similarity=0.311 Sum_probs=48.9
Q ss_pred HHHHHHHHHhcccccHHHHHHHHHHHHHHHhhhhhcCchhhHHHHHHHHHHHHHHHHHHH-HhcCCcHHhHHHHHHHHHH
Q 003676 362 EDLQRMYSLFSRVNALESLRQALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWE-QSFSKNEAFCNTIKDAFEY 440 (804)
Q Consensus 362 ~~L~~ly~Ll~~~~~l~~l~~~~~~yi~~~g~~iv~~~~~~~~~V~~Ll~l~~~~~~li~-~~F~~~~~f~~~l~~af~~ 440 (804)
++++.|..|--.-...+.+...+..+|.++- ..|+.|-.-....+.++. -||..+..+ +.|++|
T Consensus 57 ~ef~~llkla~eq~k~e~~m~~Lea~VEkrD-----------~~IQqLqk~LK~aE~iLtta~fqA~qKL-ksi~~A--- 121 (272)
T KOG4552|consen 57 DEFKTLLKLAPEQQKREQLMRTLEAHVEKRD-----------EVIQQLQKNLKSAEVILTTACFQANQKL-KSIKEA--- 121 (272)
T ss_pred HHHHHHHHHhHhHHHHHHHHHHHHHHHHHhH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH---
Confidence 4555555444333445566666666665543 345555444444454443 467655554 345554
Q ss_pred HhhcCCCcchHHHHHHHHHHHhcC
Q 003676 441 LINLRQNRPAELIAKFLDEKLRAG 464 (804)
Q Consensus 441 ~lN~~~~~~~e~La~y~D~~lr~~ 464 (804)
++++ -.+|.|-||.|.+-+.+
T Consensus 122 --~krp-vsSEelIKyAHrIS~~N 142 (272)
T KOG4552|consen 122 --EKRP-VSSEELIKYAHRISKHN 142 (272)
T ss_pred --hcCC-CCHHHHHHHHHHhhhcc
Confidence 4555 36799999999987654
No 73
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=64.03 E-value=15 Score=28.83 Aligned_cols=49 Identities=12% Similarity=0.310 Sum_probs=35.0
Q ss_pred HHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCce
Q 003676 745 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIY 800 (804)
Q Consensus 745 IVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y 800 (804)
|++.+. .+.++..++... +..+...+.+.|+.|.++|++.+..+.+..|
T Consensus 2 il~~l~-~~~~~~~~i~~~------l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~ 50 (66)
T smart00418 2 ILKLLA-EGELCVCELAEI------LGLSQSTVSHHLKKLREAGLVESRREGKRVY 50 (66)
T ss_pred HHHHhh-cCCccHHHHHHH------HCCCHHHHHHHHHHHHHCCCeeeeecCCEEE
Confidence 445555 667777765542 3457888999999999999999876544333
No 74
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=63.05 E-value=15 Score=28.78 Aligned_cols=36 Identities=11% Similarity=0.303 Sum_probs=31.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 650 AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 650 ~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
.+..|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~--~~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR--EAGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 5678999999999999999999999999 77777654
No 75
>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=62.45 E-value=13 Score=30.61 Aligned_cols=43 Identities=33% Similarity=0.427 Sum_probs=34.7
Q ss_pred HHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhc-CCccee
Q 003676 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC-GKVRVL 684 (804)
Q Consensus 642 ~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~-~k~~iL 684 (804)
.|--+.++...+|+.+|+..||++++++..+|--|+. +|..+-
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~ 55 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFE 55 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEE
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEE
Confidence 4556778888999999999999999999999999995 344443
No 76
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=61.46 E-value=17 Score=27.44 Aligned_cols=45 Identities=11% Similarity=0.299 Sum_probs=36.3
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCcee
Q 003676 741 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLE 791 (804)
Q Consensus 741 i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~ 791 (804)
.+-.|+..+.....++..+|-.. +..+.+.+.+.|..|.+.|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEK------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHH------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHH------hCCCHHHHHHHHHHHHHCcCcC
Confidence 56678888999999999888763 3468999999999999999986
No 77
>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=59.80 E-value=15 Score=32.82 Aligned_cols=44 Identities=23% Similarity=0.422 Sum_probs=37.3
Q ss_pred EEcHHHHHHHHhHhC----CCCCCHHHHHHHhCCCHHHHHHHHhHhhc
Q 003676 635 AVSLFQTVVLMLFND----AQKLSFQDIKDATGIEDKELRRTLQSLAC 678 (804)
Q Consensus 635 ~vs~~Qa~ILllFn~----~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 678 (804)
.++..|-.||-.+.. .+.+++++|++.++++.++++.+|..|+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSN 91 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 578899999988887 35799999999999999999999999984
No 78
>PF13730 HTH_36: Helix-turn-helix domain
Probab=59.29 E-value=20 Score=27.83 Aligned_cols=28 Identities=14% Similarity=0.385 Sum_probs=25.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHhHhhcCCcce
Q 003676 654 SFQDIKDATGIEDKELRRTLQSLACGKVRV 683 (804)
Q Consensus 654 t~~ei~~~t~i~~~~l~~~L~sL~~~k~~i 683 (804)
|.+.|++.+|++...+.+++..|. +.++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~--~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE--EKGL 54 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH--HCcC
Confidence 899999999999999999999998 5544
No 79
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=58.88 E-value=20 Score=32.31 Aligned_cols=51 Identities=18% Similarity=0.373 Sum_probs=44.6
Q ss_pred EcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 636 vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
++..|..||......+..+..+|++.++++...+.+.+..|. +.+++.+.+
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 788899999888877766668999999999999999999999 888888754
No 80
>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=58.87 E-value=17 Score=27.08 Aligned_cols=35 Identities=20% Similarity=0.546 Sum_probs=26.4
Q ss_pred HHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHh
Q 003676 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (804)
Q Consensus 642 ~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL 676 (804)
.||-.+......++.+|++.+|++...+.+-++-|
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 46666666688999999999999999998877654
No 81
>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=58.66 E-value=8.4 Score=38.69 Aligned_cols=58 Identities=19% Similarity=0.309 Sum_probs=41.0
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 741 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 741 i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
+=...|...|.+|.+..++|-. .|...++++-.+|..|...|-|.---+|++.|+||.
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 4444568889999999998875 488899999999999999999988778899999984
No 82
>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=57.94 E-value=14 Score=30.05 Aligned_cols=35 Identities=23% Similarity=0.473 Sum_probs=28.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003676 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (804)
Q Consensus 649 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (804)
..+.+|+.+|.+.|+++.+.++.+|-.|+ +.+++.
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~Li--Qh~~v~ 58 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLI--QHNLVQ 58 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHH--HTTSEE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHH--HcCCee
Confidence 34689999999999999999999999999 777664
No 83
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=57.19 E-value=31 Score=32.86 Aligned_cols=40 Identities=8% Similarity=0.325 Sum_probs=34.5
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 647 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 647 Fn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+..+..++..+|++..|++...+++.|+.|. +.+++...+
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 3344578999999999999999999999999 888887654
No 84
>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=55.81 E-value=27 Score=28.16 Aligned_cols=44 Identities=18% Similarity=0.326 Sum_probs=36.0
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
|..+-.+...++..+|++.+|+++..+...|..|. +.+++...|
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 44444577899999999999999999999999999 778887754
No 85
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=55.49 E-value=21 Score=28.63 Aligned_cols=36 Identities=25% Similarity=0.380 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 651 QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 651 ~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
..+|..+|++.+|++...+.+.|..|. +.+++...+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE--EEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 479999999999999999999999999 788888753
No 86
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=54.75 E-value=27 Score=26.31 Aligned_cols=46 Identities=13% Similarity=0.254 Sum_probs=36.1
Q ss_pred HHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCC
Q 003676 744 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 795 (804)
Q Consensus 744 aIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~ 795 (804)
.|.+.+..+..++..+|... |..++..+.+.|..|.++|+|.+..+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQGKVSVEELAEL------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 35566666777888777753 46689999999999999999998653
No 87
>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=54.48 E-value=40 Score=30.83 Aligned_cols=62 Identities=21% Similarity=0.201 Sum_probs=46.8
Q ss_pred HHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceee
Q 003676 740 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 802 (804)
Q Consensus 740 ~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Y 802 (804)
.+|+.|++-- ...=.....++.+|+.+....++..-+--||+.||+.|.|+-.++-..+.+|
T Consensus 48 ~yD~~Il~~~-~~~~~~~arvIg~vl~~~~~~i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQA-PDEFQKAARVIGEVLGHSDQGIGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhcC-CccccHHHHHHHHHHHhcCcCCChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 5778887722 2233456788999999886557889999999999999999998765555544
No 88
>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=54.17 E-value=4.9e+02 Score=31.86 Aligned_cols=65 Identities=14% Similarity=0.335 Sum_probs=36.6
Q ss_pred HHHHHHHHHhc--cc-ccHHHHHHHHHHHHHHHhhhhhcCch-hh---HHHHHHHHHHHHHHHHHHHHhcCC
Q 003676 362 EDLQRMYSLFS--RV-NALESLRQALAMYIRRTGHGIVMDEE-KD---KDMVSSLLEFKASLDTIWEQSFSK 426 (804)
Q Consensus 362 ~~L~~ly~Ll~--~~-~~l~~l~~~~~~yi~~~g~~iv~~~~-~~---~~~V~~Ll~l~~~~~~li~~~F~~ 426 (804)
..|+.+-.-+. .+ .+++.|.+.+.+|+...+..-..+.. -+ ..+-..++..|.++..++..|+.|
T Consensus 630 ~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~vW~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 630 QELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQVVWSAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 44555544432 12 56777777777776221110000000 00 256777889999999999999864
No 89
>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=53.87 E-value=22 Score=29.22 Aligned_cols=55 Identities=24% Similarity=0.273 Sum_probs=33.6
Q ss_pred HHHHHHHHhhcC-CCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 741 VDAAIVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 741 i~AaIVRIMK~~-K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
.=|.||..||++ +.++.++|..++ .+..+ ++.++.|-+.+-|+-|+++ +.|.|.|
T Consensus 6 ql~~~VeymK~r~~Plt~~eI~d~l----~~d~~----~~~~~~Lk~npKI~~d~~~-~~f~fkp 61 (65)
T PF02186_consen 6 QLAKAVEYMKKRDHPLTLEEILDYL----SLDIG----KKLKQWLKNNPKIEYDPDG-NTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHHH----TSSS-----HHHHHHHHH-TTEEEE-TT--CEEE--
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHH----cCCCC----HHHHHHHHcCCCEEEecCC-CEEEecc
Confidence 447899999997 566766666544 44443 2455677799999999853 6899975
No 90
>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=53.44 E-value=42 Score=30.44 Aligned_cols=58 Identities=16% Similarity=0.128 Sum_probs=43.7
Q ss_pred HHHHHhhc-CCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceee
Q 003676 744 AIVRIMKT-RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 802 (804)
Q Consensus 744 aIVRIMK~-~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Y 802 (804)
+|..+|.. .+-++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.+.+.|
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~-~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKG-PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcC-CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 46666665 56799999998887653 467899999999999999999996433333444
No 91
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=53.37 E-value=20 Score=36.83 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=37.5
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
..||.+.+..+++|.+||++.+||+..-++++|+.|. .-+++..
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le--~~Glv~~ 57 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLE--AEGLVEV 57 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHH--hCcceee
Confidence 3567777888899999999999999999999999999 6565543
No 92
>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=52.95 E-value=20 Score=28.72 Aligned_cols=38 Identities=13% Similarity=0.348 Sum_probs=29.2
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
|.-+|-++-+.+.+++++|++.+|++...++.-+.-|-
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 44555444447889999999999999999998887775
No 93
>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=52.13 E-value=18 Score=28.71 Aligned_cols=49 Identities=12% Similarity=0.273 Sum_probs=36.0
Q ss_pred HHHHHHHHhhcCCC--CChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCC
Q 003676 741 VDAAIVRIMKTRKV--LSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 795 (804)
Q Consensus 741 i~AaIVRIMK~~K~--l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~ 795 (804)
.+..|...+..+.. ++..+|... +..+.+-+.+.|..|+++|||+|..+
T Consensus 6 ~q~~vL~~l~~~~~~~~t~~~la~~------l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 6 SQFRVLMALARHPGEELTQSELAER------LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHHSTTSGEEHHHHHHH------HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 35566677777766 777776652 34578999999999999999999653
No 94
>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=52.12 E-value=11 Score=34.04 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=31.0
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (804)
.+.|+..+..++.++-++|++.+|++..++++.|..|. ..+++.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~--~~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLY--EDGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHH--HHSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeE
Confidence 34566666666789999999999999999999999998 666653
No 95
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=52.10 E-value=37 Score=33.66 Aligned_cols=54 Identities=20% Similarity=0.170 Sum_probs=41.7
Q ss_pred EEEEcHHHHHHHHhHhCCCC-CCHHHHHHHh--CCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 633 ELAVSLFQTVVLMLFNDAQK-LSFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 633 ~l~vs~~Qa~ILllFn~~~~-lt~~ei~~~t--~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
++.-+.+..+|+-+..-.+. -+..+|++.+ +++.++++.+|..|. +.++|.+..
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 33344555566655554443 3899999999 999999999999999 999999853
No 96
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=51.37 E-value=27 Score=31.28 Aligned_cols=46 Identities=15% Similarity=0.328 Sum_probs=40.2
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceee
Q 003676 741 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 792 (804)
Q Consensus 741 i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~R 792 (804)
+|-.|++.+.....++..+|-.. +..++..+.++|..|.++|+|+|
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 67789999999999999888763 46789999999999999999995
No 97
>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=51.18 E-value=31 Score=27.39 Aligned_cols=38 Identities=16% Similarity=0.386 Sum_probs=31.2
Q ss_pred hCCCCC-CHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 648 NDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 648 n~~~~l-t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
.....+ |..+|++.+|++...+.++|..|. +.++|...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~--~~G~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELE--AEGLVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 333444 499999999999999999999999 77788654
No 98
>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=50.35 E-value=23 Score=29.25 Aligned_cols=40 Identities=15% Similarity=0.329 Sum_probs=29.9
Q ss_pred HhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 645 MLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 645 llFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
-...+.+.+|+.||+..++++.+.+...|.-|. +.+-+.+
T Consensus 7 ~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~--~kG~I~~ 46 (69)
T PF09012_consen 7 DYLRERGRVSLAELAREFGISPEAVEAMLEQLI--RKGYIRK 46 (69)
T ss_dssp HHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHH--CCTSCEE
T ss_pred HHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEE
Confidence 334566789999999999999999999999999 5444444
No 99
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=50.14 E-value=22 Score=37.66 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=42.2
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
|..|+-+.++.+.+++.||++.+|++...++|-|..|. +.++|.+.-
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~~ 53 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEEE
Confidence 66788889999999999999999999999999999999 778787753
No 100
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=46.68 E-value=47 Score=25.26 Aligned_cols=33 Identities=24% Similarity=0.532 Sum_probs=24.3
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHh
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~ 674 (804)
+.+|-+.| ...+|+.||++.+|++...+.+.+.
T Consensus 10 r~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 10 REVIRLRY--FEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 34445666 4568999999999999988876654
No 101
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=46.56 E-value=2.3e+02 Score=28.58 Aligned_cols=34 Identities=24% Similarity=0.490 Sum_probs=30.1
Q ss_pred HHhHhCCCC-CCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 644 LMLFNDAQK-LSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 644 LllFn~~~~-lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
-++|-..++ +|+++|++.++++..++...|..|.
T Consensus 11 A~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~ 45 (188)
T PRK00135 11 ALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQ 45 (188)
T ss_pred HHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 367878886 9999999999999999999999986
No 102
>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=46.29 E-value=33 Score=33.49 Aligned_cols=43 Identities=21% Similarity=0.285 Sum_probs=35.4
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (804)
..|+...=.++.+|-+||++.+||+..++++.|..|. ..+++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~--e~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALY--DAGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCce
Confidence 3455544455689999999999999999999999999 777774
No 103
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=45.67 E-value=31 Score=34.45 Aligned_cols=44 Identities=23% Similarity=0.298 Sum_probs=36.9
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (804)
...||.+.-.++.+|-++|++.+||+...++++|..|. ..+++.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~--e~gLv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLY--DARLAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeE
Confidence 34566656676789999999999999999999999999 667765
No 104
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=45.40 E-value=39 Score=26.05 Aligned_cols=24 Identities=29% Similarity=0.645 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 003676 651 QKLSFQDIKDATGIEDKELRRTLQ 674 (804)
Q Consensus 651 ~~lt~~ei~~~t~i~~~~l~~~L~ 674 (804)
+.+|+.||++.+|++...++..|.
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 358999999999999998887664
No 105
>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=44.74 E-value=52 Score=33.39 Aligned_cols=44 Identities=16% Similarity=0.239 Sum_probs=36.6
Q ss_pred HHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 642 ~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
.||......+.+|..+|++.+|++...+.++|..|. +.+++.+.
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 455444455679999999999999999999999999 77888765
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=44.33 E-value=30 Score=28.44 Aligned_cols=51 Identities=20% Similarity=0.374 Sum_probs=36.3
Q ss_pred EcHHHHHHHHhHhC-----CCCCCHHHHHHHhCCC-HHHHHHHHhHhhcCCcceeeeCC
Q 003676 636 VSLFQTVVLMLFND-----AQKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 636 vs~~Qa~ILllFn~-----~~~lt~~ei~~~t~i~-~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
++.-|.-||...-+ +-.-|+.||++.+|+. ...+..+|..|. +.+.|.+.|
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 34556666654432 2367999999999996 999999999999 788888765
No 107
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=44.06 E-value=37 Score=34.96 Aligned_cols=49 Identities=18% Similarity=0.368 Sum_probs=42.7
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
|..-..||-+...+..+.+.||++.+|+|...+..+++.|. +.+++..+
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 44455688888888999999999999999999999999999 99998754
No 108
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=44.06 E-value=38 Score=35.78 Aligned_cols=50 Identities=20% Similarity=0.355 Sum_probs=43.1
Q ss_pred HHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003676 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (804)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (804)
-|..|+-.+++++.++..||++.+|++...++|-|..|. +.+++.+...|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~gg 55 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVRNG 55 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecCC
Confidence 356788889999999999999999999999999999998 77788775444
No 109
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=43.86 E-value=64 Score=30.31 Aligned_cols=65 Identities=22% Similarity=0.333 Sum_probs=49.7
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCC---CCeEEEecCCC
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVED---DDSFVFNEGFT 706 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~---~d~f~~N~~F~ 706 (804)
-...|-+..+.+..|+.|+++.+|=+.+.+.+.|..|. ..+|+..+..|+...+ -+.|.++-.|.
T Consensus 66 nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 66 NLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 33456677788999999999999999999999999999 8999987665554333 24455555554
No 110
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=43.41 E-value=33 Score=36.28 Aligned_cols=49 Identities=22% Similarity=0.478 Sum_probs=43.2
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (804)
|-.||-+.++.+.++++||++.+|+++..++|=|..|. +.++|.+...|
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~hGG 55 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRVHGG 55 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEEeCC
Confidence 55688888999999999999999999999999999999 88888875443
No 111
>PRK00215 LexA repressor; Validated
Probab=43.10 E-value=52 Score=33.36 Aligned_cols=52 Identities=21% Similarity=0.329 Sum_probs=42.2
Q ss_pred EcHHHHHHHHhHhC-----CCCCCHHHHHHHhCC-CHHHHHHHHhHhhcCCcceeeeCCC
Q 003676 636 VSLFQTVVLMLFND-----AQKLSFQDIKDATGI-EDKELRRTLQSLACGKVRVLQKLPK 689 (804)
Q Consensus 636 vs~~Qa~ILllFn~-----~~~lt~~ei~~~t~i-~~~~l~~~L~sL~~~k~~iL~k~~~ 689 (804)
++.-|..||....+ ....|+.||++.+|+ +...+.+.|+.|. +.+++.+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~~ 59 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDPG 59 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCCC
Confidence 35668888865542 347899999999999 9999999999999 8888887654
No 112
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=41.96 E-value=25 Score=35.26 Aligned_cols=26 Identities=38% Similarity=0.617 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 652 KLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 652 ~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
.+|+++|++.|||..+++..+|+.|-
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 79999999999999999999999885
No 113
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=41.39 E-value=47 Score=32.06 Aligned_cols=49 Identities=4% Similarity=0.249 Sum_probs=42.1
Q ss_pred EcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 636 vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
+...--.||-.+..+...|+.+|++.+|+++..+.+-++.|. ..+++..
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~--~~GvI~~ 55 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMK--QAGIITG 55 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeee
Confidence 455666788888888899999999999999999999999999 6777753
No 114
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=40.41 E-value=44 Score=32.73 Aligned_cols=49 Identities=10% Similarity=0.199 Sum_probs=42.3
Q ss_pred EcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 636 vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
+.-.-.-||-...++..+|+.+|++.+|++...+.+-++.|. +.+++..
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~--~~GvI~~ 60 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLE--RQGFIQG 60 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEE
Confidence 344566788888888999999999999999999999999999 7777763
No 115
>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=39.44 E-value=47 Score=28.94 Aligned_cols=45 Identities=18% Similarity=0.370 Sum_probs=37.3
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHh-CCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t-~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
-+.||..... +...|.||.+.+ |+++..|.+.|..|. ..+++.+.
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 3567766666 789999999999 999999999999999 88888763
No 116
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=38.99 E-value=44 Score=35.28 Aligned_cols=49 Identities=16% Similarity=0.325 Sum_probs=42.1
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (804)
|..|+-+.++.+.+++.||++.++++...++|-|..|. +.++|.+.-.|
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le--~~g~l~r~~GG 55 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLA--EQNKILRHHGG 55 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCC
Confidence 55677778888999999999999999999999999999 77788775433
No 117
>PF07516 SecA_SW: SecA Wing and Scaffold domain; InterPro: IPR011116 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner. This domain is composed of two C-terminal alpha helical subdomains: the wing and scaffold subdomains.; GO: 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 2IPC_D 3JUX_A 3DIN_B ....
Probab=38.52 E-value=4.5e+02 Score=26.83 Aligned_cols=131 Identities=19% Similarity=0.266 Sum_probs=73.9
Q ss_pred hHHHHHHHHHHHHHHHHhcC------CCCccHHHHHHHHHhhhccC------------chhHHHHHHHHHHHHHHHHHHH
Q 003676 103 FEEDTWAKLKLAIKAIFLKQ------PTSCDLEKLYQAVNDLCLHK------------MGGNLYQRIEKECEEHISAAIR 164 (804)
Q Consensus 103 ~~e~~W~~L~~aI~~I~~~~------~~~~s~e~LY~~Vy~lC~~k------------~~e~LY~~L~~~~~~~l~~~~~ 164 (804)
..+..-..++++|+.+.... +..-.++.+...+....... ..+.+-+.|.+.+.........
T Consensus 56 ~~~~i~~~~~~~i~~~v~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~k~~ 135 (214)
T PF07516_consen 56 LEEIILEMIEDVIDDIVDEYIPEKDSPEEWDIEGLKDFLNQNFNLDFDISPEDLINNKDKEELKKYLFEQVEESYERKEE 135 (214)
T ss_dssp CHHHHHHHHHHHHHHHHHHHSSSSSSSTSSCHHHHHHHHHHCSSSSSCHCSCHHSSSSTCHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHcccccCcccccHHHHHHHHHHHcCCCcchhHHHHhccCCHHHHHHHHHHHHHHHHHHHHh
Confidence 33455567777887777532 22346777777776665432 1233444444444444433222
Q ss_pred hhhcCC---CcHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccceeccccccccHHH---HHHHHHHHHhccccchHHHHH
Q 003676 165 SLVGQS---PDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWD---MGLQLFRKYLSSYSEVEHKTV 238 (804)
Q Consensus 165 ~l~~~~---~d~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDr~yv~~~~~~~sI~~---lgl~lFr~~v~~~~~i~~~l~ 238 (804)
.+.... -....+|..+..+|.+|-..|..|+..-.. |.|-.. .|+.+ -|..+|.... ..+...++
T Consensus 136 ~~~~~~~~~~eR~ilL~~ID~~W~~HL~~m~~Lr~~I~l--R~y~Qk----dPl~EYk~Ea~~lF~~m~---~~i~~~i~ 206 (214)
T PF07516_consen 136 EIGEEQFNEFERYILLKAIDQNWKDHLDNMDQLREGIGL--RSYGQK----DPLVEYKREAFELFEEML---ENIREDII 206 (214)
T ss_dssp HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTC--TTSSSS----SHHHHHHHHHHHHHHHHH---HHHHHHHH
T ss_pred hccHHHHHHHHHHhHHHHHhHHHHHHHHHHHHHHHHHHH--HhHccC----CHHHHHHHHHHHHHHHHH---HHHHHHHH
Confidence 221100 012568999999999999999999987522 555444 44554 4666666544 24555555
Q ss_pred HHHH
Q 003676 239 TGLL 242 (804)
Q Consensus 239 ~~ll 242 (804)
..++
T Consensus 207 ~~l~ 210 (214)
T PF07516_consen 207 RNLF 210 (214)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 5544
No 118
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=38.21 E-value=45 Score=35.61 Aligned_cols=49 Identities=12% Similarity=0.179 Sum_probs=42.7
Q ss_pred HHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 638 ~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
--|..|+-+.+..+.+++.||++.+|++...++|-|..|. ..+++.+..
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le--~~G~l~r~~ 65 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLE--KQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHH--hCCCeEEEe
Confidence 3577888889998899999999999999999999999998 667777654
No 119
>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=37.44 E-value=38 Score=23.73 Aligned_cols=25 Identities=32% Similarity=0.517 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 653 LSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 653 lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
+|-+||++.+|+..+.+-|.|..|.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 6789999999999999999999887
No 120
>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=36.50 E-value=78 Score=27.74 Aligned_cols=40 Identities=15% Similarity=0.414 Sum_probs=26.8
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (804)
+..+..+... ++..|.+.||||.-.++.+|.+|. ..+|-+
T Consensus 13 la~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~--~~~I~~ 52 (90)
T PF09904_consen 13 LAYLIDSGER-NVPALMEATGMPRRTIQDTIKALP--ELGIEC 52 (90)
T ss_dssp HHHHHHHS-B--HHHHHHHH---HHHHHHHHHGGG--GGT-EE
T ss_pred HHHHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhh--cCCeEE
Confidence 4445555556 999999999999999999999998 655543
No 121
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=36.03 E-value=51 Score=31.51 Aligned_cols=48 Identities=15% Similarity=0.335 Sum_probs=41.7
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
.-.-.-||-.+.+....++.+|++.+|++...+.+-+.-|. +.+|+..
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~--~~GiI~~ 54 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLE--EEGVIKG 54 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCceee
Confidence 44556788888888889999999999999999999999999 8888875
No 122
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.94 E-value=82 Score=27.13 Aligned_cols=49 Identities=16% Similarity=0.299 Sum_probs=38.3
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCC
Q 003676 741 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 795 (804)
Q Consensus 741 i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~ 795 (804)
.+..|...+.....++..+|... +.++...|.+.|..|.++|+|++..+
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~------~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKR------LGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHH------HCCCchhHHHHHHHHHHCCCeEecCC
Confidence 45677778877788888877653 34577889999999999999997643
No 123
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=35.92 E-value=35 Score=34.21 Aligned_cols=46 Identities=11% Similarity=0.177 Sum_probs=40.0
Q ss_pred HHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
-+..|+...+.++.+++.+|++.+|++...++|=|..|. ..+++.+
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~--~~g~~~r 53 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELG--IPELRER 53 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHh--cchHHHH
Confidence 466788889999999999999999999999999999998 5555544
No 124
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=35.47 E-value=61 Score=33.95 Aligned_cols=46 Identities=15% Similarity=0.295 Sum_probs=38.8
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
|..|+..+++++.++.+||++.+|+++..++|-|.-|. ..+.|.+.
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~--~~~~l~r~ 51 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQ--TQGKILRN 51 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEe
Confidence 55688888888899999999999999999999999997 44555553
No 125
>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=35.38 E-value=41 Score=25.93 Aligned_cols=44 Identities=18% Similarity=0.413 Sum_probs=31.0
Q ss_pred HHHHhhcCC-CCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 745 IVRIMKTRK-VLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 745 IVRIMK~~K-~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
|.+.+...+ .++..+|.. .+. .+..-+-+.+..|.+.||++||+
T Consensus 8 iL~~l~~~~~~~t~~eia~----~~g--l~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIAR----ALG--LPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHH----HHT--S-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHcCCCCCCHHHHHH----HHC--cCHHHHHHHHHHHHHCcCeecCc
Confidence 445555544 367766664 333 45778999999999999999986
No 126
>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=35.31 E-value=44 Score=33.73 Aligned_cols=51 Identities=22% Similarity=0.308 Sum_probs=42.1
Q ss_pred EcHHHHHHHHhHhC-----CCCCCHHHHHHHhCCC-HHHHHHHHhHhhcCCcceeeeCC
Q 003676 636 VSLFQTVVLMLFND-----AQKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 636 vs~~Qa~ILllFn~-----~~~lt~~ei~~~t~i~-~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
++..|..||....+ .-..|..||++.+|++ ...+.++|..|. +.++|.+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecCC
Confidence 46778888866653 2358999999999998 999999999999 888998754
No 127
>PHA02943 hypothetical protein; Provisional
Probab=35.23 E-value=70 Score=30.88 Aligned_cols=54 Identities=22% Similarity=0.289 Sum_probs=39.4
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEec
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 703 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~ 703 (804)
||-.+ ..+..|..||++.+|++-.+++-+|.-|. +-+.+.+..-| ....+.+|+
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLE--rEG~VkrV~~G----~~tyw~l~~ 69 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLA--KEGMVLKVEIG----RAAIWCLDE 69 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCceEEEeec----ceEEEEECh
Confidence 44444 66678999999999999999999999998 77777664432 234455555
No 128
>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=34.94 E-value=53 Score=29.27 Aligned_cols=46 Identities=11% Similarity=0.234 Sum_probs=33.4
Q ss_pred HHHHHHHHHhhc----CCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCcee
Q 003676 740 QVDAAIVRIMKT----RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLE 791 (804)
Q Consensus 740 ~i~AaIVRIMK~----~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~ 791 (804)
.++..|..++|. .-.++.++|.. +| ..+..+|+++|+.|++.|+|=
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~----~l--~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQ----QL--GMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHH----HS--TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHH----Hh--CcCHHHHHHHHHHHHhCCeEe
Confidence 456667777777 45577766664 44 457999999999999999873
No 129
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=34.75 E-value=87 Score=29.85 Aligned_cols=50 Identities=18% Similarity=0.359 Sum_probs=43.0
Q ss_pred HHHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 739 YQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 739 ~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
..+|..|.+++.....++..+|-.++ ..++..+..||+.|.++|.|++-.
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 45889999999999999998887644 368899999999999999999853
No 130
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=34.63 E-value=79 Score=27.98 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=44.7
Q ss_pred EEEcHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 634 l~vs~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
+..+....-||..+...+.=...-|+..|+++.+++...|..|. ..++|.+..
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 44566777899888887776777899999999999999999999 899998753
No 131
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=34.21 E-value=75 Score=27.71 Aligned_cols=57 Identities=25% Similarity=0.278 Sum_probs=42.3
Q ss_pred HHHHHHHhhcC---CCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 742 DAAIVRIMKTR---KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 742 ~AaIVRIMK~~---K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
++..=|++|.= |-++...|.+ ++.+..+.-++.|..|.++|.|..-..+...-.|.|
T Consensus 26 k~t~dkl~kEV~~~K~ITps~lse------rlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 26 EELLKRVAKEVKKEKIVTPYTLAS------KYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHHHHHHHHHhccCcEEcHHHHHH------HhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 34444666653 4445544443 678889999999999999999998877888888875
No 132
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=33.96 E-value=49 Score=36.98 Aligned_cols=64 Identities=30% Similarity=0.404 Sum_probs=40.6
Q ss_pred eEeecCCceEEEEEEecCceEEEEE-------cHHHHHHHHhHhC-CC-CCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 612 LMWQNSLGHCVLKAEFPKGKKELAV-------SLFQTVVLMLFND-AQ-KLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 612 L~W~~~lg~~~l~~~f~~~~~~l~v-------s~~Qa~ILllFn~-~~-~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
+.+.+.||..+=++--|. +=|.= +-+-..||-++-+ .+ .+|+++|++.|||..+++..+|++|-
T Consensus 282 IdFSYeLSr~E~~~GsPE--KPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 282 IDFSYELSRREGKIGSPE--KPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhcccCcCCCCC--CCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 467777777665432222 21211 2233344433333 22 39999999999999999999999985
No 133
>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=33.79 E-value=1.1e+02 Score=27.94 Aligned_cols=47 Identities=23% Similarity=0.202 Sum_probs=33.8
Q ss_pred HHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 742 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 742 ~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
+..|...+.....++..+|-. . ...+.+.+-+.|..|.++|||+|..
T Consensus 30 q~~iL~~l~~~~~~t~~ela~----~--~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 30 QWRILRILAEQGSMEFTQLAN----Q--ACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHHHHcCCcCHHHHHH----H--hCCCchhHHHHHHHHHHCCCEEecc
Confidence 344556666677787766654 2 3345667899999999999999954
No 134
>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=33.19 E-value=91 Score=23.63 Aligned_cols=38 Identities=24% Similarity=0.369 Sum_probs=27.5
Q ss_pred HHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 638 ~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
..|.-|+.++- +.+|..+|++.+|++...+...+..+.
T Consensus 3 ~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 3 PREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34444554442 458999999999999998888776553
No 135
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.79 E-value=93 Score=23.47 Aligned_cols=39 Identities=23% Similarity=0.398 Sum_probs=29.0
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
+.-|.-|+.++. ..++..+|++.+|++...+.+.+..+.
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 444555555553 347999999999999999988877654
No 136
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=32.66 E-value=5.3e+02 Score=25.95 Aligned_cols=33 Identities=18% Similarity=0.404 Sum_probs=25.7
Q ss_pred HhHhCCCC-CCHHHHHHHhCCC-HHHHHHHHhHhh
Q 003676 645 MLFNDAQK-LSFQDIKDATGIE-DKELRRTLQSLA 677 (804)
Q Consensus 645 llFn~~~~-lt~~ei~~~t~i~-~~~l~~~L~sL~ 677 (804)
++|-..++ +|.++|++.++++ .+.+...+.-|.
T Consensus 9 lLF~sg~pgls~~~La~il~~~~~~~~~~~l~~l~ 43 (186)
T TIGR00281 9 LLFVSGEPGVTLAELVRILGKEKAEKLNAIMELLE 43 (186)
T ss_pred HHHHcCCCCCCHHHHHHHhCCCchHHHHHHHHHHH
Confidence 67777887 9999999999998 456666666554
No 137
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=32.36 E-value=1.7e+02 Score=25.41 Aligned_cols=56 Identities=9% Similarity=0.180 Sum_probs=40.8
Q ss_pred HHHHH-HHHHHHHHHHHhc-CCCCccHHHHHHHHHhhhccCchhHHHHHHHHHHHHHH
Q 003676 104 EEDTW-AKLKLAIKAIFLK-QPTSCDLEKLYQAVNDLCLHKMGGNLYQRIEKECEEHI 159 (804)
Q Consensus 104 ~e~~W-~~L~~aI~~I~~~-~~~~~s~e~LY~~Vy~lC~~k~~e~LY~~L~~~~~~~l 159 (804)
.+.+| ..++..+..+... ....++|++|+..|.-.++....+.+...+-..+..++
T Consensus 28 ~e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L 85 (86)
T PF10163_consen 28 IECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFL 85 (86)
T ss_dssp HHTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH
T ss_pred HHCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHh
Confidence 36688 4788877777765 55678999999999999988877776666666666554
No 138
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=32.20 E-value=1.1e+02 Score=25.15 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=41.4
Q ss_pred HHHHHhhcC-CCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 744 AIVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 744 aIVRIMK~~-K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
.|.++++.. +.++...|...+... .+..+.+.|..++..|-++||+++..
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~-g~~~se~avRrrLr~me~~Glt~~~g 52 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLR-GEELSEEAVRRRLRAMERDGLTRKVG 52 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhc-ChhhhHHHHHHHHHHHHHCCCccccC
Confidence 477888876 569999988766554 78899999999999999999998764
No 139
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=32.11 E-value=91 Score=29.59 Aligned_cols=45 Identities=11% Similarity=0.258 Sum_probs=32.2
Q ss_pred HHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 744 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 744 aIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
.|...+-....++..+|-. .+..+.+.+-+.|+.|.++|||+|.+
T Consensus 44 ~vL~~l~~~~~~t~~eLa~------~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 44 KVLCSIRCAACITPVELKK------VLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HHHHHHHHcCCCCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 3333333455666666654 25568899999999999999999953
No 140
>PF10408 Ufd2P_core: Ubiquitin elongating factor core; InterPro: IPR019474 This entry represents the most conserved part of the core region of ubiquitin conjugation factor E4 (or Ub elongating factor, or Ufd2P), running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C terminus, (IPR003613 from INTERPRO), which has ligase activity. Ubiquitin conjugation factor E4 is involved in N-terminal ubiquitin fusion degradation proteolytic pathway (UFD pathway). E4 binds to the ubiquitin moieties of preformed conjugates and catalyses ubiquitin chain assembly in conjunction with E1, E2, and E3. E4 appears to influence the formation and topology of the multi-Ub chain as it enhances ubiquitination at 'Lys-48' but not at 'Lys-29' of the N-terminal Ub moiety.; GO: 0034450 ubiquitin-ubiquitin ligase activity, 0006511 ubiquitin-dependent protein catabolic process, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 2KRE_A 3M63_A 2QIZ_A 2QJ0_A 3M62_A.
Probab=31.92 E-value=3.4e+02 Score=32.74 Aligned_cols=59 Identities=17% Similarity=0.294 Sum_probs=32.4
Q ss_pred cccHHHHHHHHHHHH-hccccchHHHHHHHHHHHHHHHhcCCc-C-----------ChHHHHHHHHHHhhhh
Q 003676 212 VRSLWDMGLQLFRKY-LSSYSEVEHKTVTGLLRMIERERLGEA-V-----------DRTLLNHLLKMFTALG 270 (804)
Q Consensus 212 ~~sI~~lgl~lFr~~-v~~~~~i~~~l~~~ll~lI~~eR~g~~-i-----------d~~llk~ii~ml~~L~ 270 (804)
..++-.+.+...... .+.||.++.+++..+.-.+...+.+.. + -..++.++++.+++.+
T Consensus 321 ~~~l~~f~i~fm~s~~~ikNP~LraklvevL~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~sLm~~yidvE 392 (629)
T PF10408_consen 321 LDELVTFCITFMGSPEYIKNPHLRAKLVEVLFSLLPPDRDGRRGVLGSLFESHPLAQEHLVPSLMKFYIDVE 392 (629)
T ss_dssp HHHHHHHHHHHHH-TTS---HHHHHHHHHHHHHCCS--TTS---TTHHHHHH-HHHHCCHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHhCChhhcCCHHHHHHHHHHHHHhcCcccccccccHHHHHHcCHHHHHHHHHHHHHHHHHHH
Confidence 345666666666555 677888999998888877766662211 1 1124556666666653
No 141
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.88 E-value=1.3e+02 Score=28.07 Aligned_cols=52 Identities=17% Similarity=0.280 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCC
Q 003676 738 QYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 795 (804)
Q Consensus 738 ~~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~ 795 (804)
...|.+-||-..+.++.++..+|+.+ +-.+...+++.+..|+++|.|-+.+.
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 34699999999999999999999863 45678889999999999999988653
No 142
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=31.70 E-value=78 Score=33.55 Aligned_cols=42 Identities=12% Similarity=0.319 Sum_probs=35.4
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
||++.-+ ++.|++||.+.++++...+..+|.-|. +.+++.+.
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 4444444 789999999999999999999999998 78888774
No 143
>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=31.39 E-value=1.1e+02 Score=27.71 Aligned_cols=41 Identities=24% Similarity=0.383 Sum_probs=31.0
Q ss_pred cCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceee--cCCCC
Q 003676 751 TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER--DKNNP 797 (804)
Q Consensus 751 ~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~R--d~~d~ 797 (804)
....++..+|.. ....+..-+-+.|..|.++|||.| ++.|+
T Consensus 40 ~~~~~t~~eL~~------~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 40 NEGKLTLKEIIK------EILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred cCCcCcHHHHHH------HHCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 446677777665 245578889999999999999997 45554
No 144
>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=31.36 E-value=36 Score=37.47 Aligned_cols=50 Identities=22% Similarity=0.357 Sum_probs=37.1
Q ss_pred EEEcHHHHHHHHhHhC--CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003676 634 LAVSLFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (804)
Q Consensus 634 l~vs~~Qa~ILllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (804)
-.++..+..|.-+..+ ...+-..+|...|||+...|.++|.+|.. -+++.
T Consensus 80 ~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~--k~lIK 131 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLES--KKLIK 131 (327)
T ss_dssp -SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHH--TTSEE
T ss_pred cCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHh--CCCEE
Confidence 3567778888877765 35788999999999999999999999983 34544
No 145
>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=31.35 E-value=1.3e+02 Score=25.82 Aligned_cols=48 Identities=13% Similarity=0.349 Sum_probs=39.8
Q ss_pred HHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
++++|=+.-..+..+.-.+|++.++.+...++..+..|- ..++|.+.|
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 455555556667899999999999999999999999998 888987544
No 146
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=31.24 E-value=77 Score=31.70 Aligned_cols=64 Identities=19% Similarity=0.307 Sum_probs=49.2
Q ss_pred CceeEeecCCceEEEEEEecCceEEEEEcHHHHHHHHhHhCC--CCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 609 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 609 ~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~--~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
.|.-.|.+.+|.++++- .+.|. ||+.||.-||.-... ..||.+.|++..+|+.+++...|..+.
T Consensus 96 ~r~~~~~~~fg~~ep~~-vPkGk----ltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEK-VPKGK----LTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCCcccccccccCccc-CCCCc----eeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 34455888899888763 45554 577899887764433 489999999999999999999888876
No 147
>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=31.16 E-value=63 Score=24.17 Aligned_cols=30 Identities=20% Similarity=0.427 Sum_probs=21.5
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHh
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~ 674 (804)
|+-++.++ +|+.+|++.+|++...+.+.|.
T Consensus 14 i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 44455554 8999999999999999988774
No 148
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.97 E-value=76 Score=33.99 Aligned_cols=39 Identities=33% Similarity=0.472 Sum_probs=30.8
Q ss_pred HHHHHHHhH-hCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 639 FQTVVLMLF-NDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 639 ~Qa~ILllF-n~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
+...|+-.+ +....+|+++|++.|||..+++..+|++|-
T Consensus 209 W~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~ 248 (290)
T PLN03238 209 WTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLN 248 (290)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 444555443 335689999999999999999999999874
No 149
>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=30.85 E-value=73 Score=34.18 Aligned_cols=58 Identities=21% Similarity=0.362 Sum_probs=32.8
Q ss_pred HHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCC
Q 003676 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 705 (804)
Q Consensus 638 ~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F 705 (804)
-+--.|.-+|.++..|++.+|.+.|+-|+..|+.+|..++ ++.+.+. ....|.+=..|
T Consensus 216 eL~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 216 ELLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 3445677899999999999999999999999999999987 5665421 23456655544
No 150
>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=30.77 E-value=98 Score=26.03 Aligned_cols=47 Identities=19% Similarity=0.296 Sum_probs=39.0
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcce
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRV 683 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~i 683 (804)
.+=|+.|+-++...+.-|+++|++.||-..-.++-+|..+.-.|.++
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 44589999888888899999999999999999999998886334444
No 151
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=30.61 E-value=64 Score=34.13 Aligned_cols=45 Identities=20% Similarity=0.187 Sum_probs=40.3
Q ss_pred HHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeec
Q 003676 743 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 793 (804)
Q Consensus 743 AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd 793 (804)
..|+..++.++.++.++|.. .|.++...|.+-|+.|-++|.|.|.
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~------~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQ------YFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 46788899999999999886 5889999999999999999999984
No 152
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=30.35 E-value=1.4e+02 Score=25.41 Aligned_cols=45 Identities=18% Similarity=0.325 Sum_probs=35.2
Q ss_pred HHHHhhcC-CCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCC
Q 003676 745 IVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 795 (804)
Q Consensus 745 IVRIMK~~-K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~ 795 (804)
|...+... ..++..+|..++ ..+...+.+.+..|.+.|||++++.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 44555555 678888887644 4578899999999999999999854
No 153
>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=30.03 E-value=96 Score=27.36 Aligned_cols=38 Identities=16% Similarity=0.222 Sum_probs=30.8
Q ss_pred cCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 751 TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 751 ~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
....+++.+|... .-.+.+.+.+.|..|.++|+|+|..
T Consensus 44 ~~~~is~~eLa~~------~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAEL------TGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHH------HCcCHHHHHHHHHHHHHCCCeeeec
Confidence 5677888877752 3457889999999999999999876
No 154
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=29.84 E-value=2e+02 Score=24.21 Aligned_cols=54 Identities=20% Similarity=0.233 Sum_probs=42.7
Q ss_pred HHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCC----hHHHHHHHHHHhhcCceeecC
Q 003676 740 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIK----PADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 740 ~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~----~~~iK~~Ie~LIereyi~Rd~ 794 (804)
.|..|| .-|+.++..+...+...+...-+...+ ...+++.|..++++|-|++..
T Consensus 8 mI~eAI-~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 8 MILEAI-KALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHH-HHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHH-HHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 355555 688999999999999988886543333 367999999999999999865
No 155
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.81 E-value=86 Score=32.47 Aligned_cols=58 Identities=21% Similarity=0.344 Sum_probs=48.4
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeCC
Q 003676 741 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 804 (804)
Q Consensus 741 i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yla 804 (804)
+=+--|-..|+.|.+...||-. .|....++.-.+|..|+..|.|.-.-+|++.|+||.
T Consensus 201 ll~eFv~YIk~nKvV~ledLas------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 201 LLSEFVEYIKKNKVVPLEDLAS------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHHHHHhcCeeeHHHHHH------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 4455677888899988888875 377778888889999999999999889999999984
No 156
>PRK11050 manganese transport regulator MntR; Provisional
Probab=29.25 E-value=1.1e+02 Score=29.52 Aligned_cols=44 Identities=16% Similarity=0.264 Sum_probs=36.6
Q ss_pred HHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 642 ~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
.|+.++...+.++..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le--~~GlI~r~ 84 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLA--RDGLVEMR 84 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 355566677889999999999999999999999999 66777653
No 157
>PF07393 Sec10: Exocyst complex component Sec10; InterPro: IPR009976 This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which specifically affects the synthesis and delivery of secretory and basolateral plasma membrane proteins [].; GO: 0006887 exocytosis, 0048278 vesicle docking, 0005737 cytoplasm
Probab=29.11 E-value=1.1e+03 Score=28.74 Aligned_cols=98 Identities=15% Similarity=0.248 Sum_probs=55.0
Q ss_pred cHHHHHHHHHhhhccCc----------hhHHHHHHHHHHHHHHHHHHHhhhcCCC--cHHHHHHHHHHHHHHHHHHHHHH
Q 003676 127 DLEKLYQAVNDLCLHKM----------GGNLYQRIEKECEEHISAAIRSLVGQSP--DLVVFLSLVERCWQDLCDQMLMI 194 (804)
Q Consensus 127 s~e~LY~~Vy~lC~~k~----------~e~LY~~L~~~~~~~l~~~~~~l~~~~~--d~~~~L~~~~~~W~~~~~~~~~i 194 (804)
++..+|..+-..|.... ..-+..-+...+.+.|...+..++.... +...||+.+...+..-..-+.-|
T Consensus 192 ~l~~~~~~i~~~i~~e~~iI~~VFp~~~~Vm~~fiervf~~~I~~~i~~lL~~a~~~s~~~YLr~l~~~y~~t~~lv~~L 271 (710)
T PF07393_consen 192 SLDAFFEDIRDVINEESKIIDRVFPNPEPVMQKFIERVFEQVIQEYIESLLEEASSISTLAYLRTLHGLYSQTKKLVDDL 271 (710)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778888888777651 2335555566666666666666665433 45678888877665433333333
Q ss_pred HHhhhhcccceeccc-cccccHHHHHHHHHHHHh
Q 003676 195 RGIALYLDRTYVKQT-PNVRSLWDMGLQLFRKYL 227 (804)
Q Consensus 195 ~~iF~YLDr~yv~~~-~~~~sI~~lgl~lFr~~v 227 (804)
.. ++....+... .....+..+.-.+|..++
T Consensus 272 ~~---~~~~~~~~~~~~~~~~l~~~~~~lF~~~l 302 (710)
T PF07393_consen 272 KE---FFSGENPDPDSSDSAFLDQLVESLFEPYL 302 (710)
T ss_pred HH---hhcccCCCccchHHHHHHHHHHHHHHHHc
Confidence 33 3222111110 112446666777777777
No 158
>PF03037 KMP11: Kinetoplastid membrane protein 11; InterPro: IPR004132 Kinetoplastid membrane protein 11 is a major cell surface glycoprotein of the parasite Leishmania donovani. It stimulates T-cell proliferation and may play a role in the immunlogy of the dieases Leishmaniasis.; GO: 0006952 defense response, 0008284 positive regulation of cell proliferation
Probab=29.10 E-value=2.8e+02 Score=23.08 Aligned_cols=64 Identities=9% Similarity=0.244 Sum_probs=46.3
Q ss_pred cHHHHHHHHHHHHHHHhhhhhcCchhhHHHHHHHHHHHHHHHHHHHHhcCCcHHhHHHHHHHHHHHh
Q 003676 376 ALESLRQALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLI 442 (804)
Q Consensus 376 ~l~~l~~~~~~yi~~~g~~iv~~~~~~~~~V~~Ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~l 442 (804)
.++.|-..|..-..........|.-.+..+-..+-+-|++++.+|++- ...|.+.+++--+.|-
T Consensus 11 kldrld~ef~kkm~eqn~kffadkpdestlspemkehyekfe~miqeh---tdkfnkkm~ehsehfk 74 (90)
T PF03037_consen 11 KLDRLDAEFNKKMQEQNKKFFADKPDESTLSPEMKEHYEKFERMIQEH---TDKFNKKMHEHSEHFK 74 (90)
T ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCcccccCHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Confidence 456666777777777777777776666677788888899999999873 5577777776655553
No 159
>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=28.66 E-value=89 Score=26.26 Aligned_cols=49 Identities=18% Similarity=0.226 Sum_probs=40.5
Q ss_pred HHHHHHHHhHhC--CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 638 LFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 638 ~~Qa~ILllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
..|.++|...-. ...++-.+|...+|++...+-..++.|. +.+++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEEE
Confidence 457778877764 3578899999999999999999999999 788887753
No 160
>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=28.60 E-value=67 Score=25.84 Aligned_cols=38 Identities=18% Similarity=0.440 Sum_probs=31.4
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 649 DAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 649 ~~~~l-t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
.++.+ |..+|++..|++-..++++|..|. ..+++...|
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~--~~g~i~~~~ 58 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLE--AEGLIERRP 58 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHH--HCCcEEEEC
Confidence 34678 999999999999999999999999 778887755
No 161
>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=28.26 E-value=99 Score=26.59 Aligned_cols=33 Identities=6% Similarity=0.170 Sum_probs=28.8
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHH
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTL 673 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L 673 (804)
|+.|+-...+ +.+|+.+|++.+|++...+.+.|
T Consensus 8 ~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 8 VLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 5677877788 89999999999999999988866
No 162
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=28.26 E-value=78 Score=33.44 Aligned_cols=46 Identities=20% Similarity=0.484 Sum_probs=41.1
Q ss_pred HHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeec
Q 003676 742 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 793 (804)
Q Consensus 742 ~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd 793 (804)
...|+.++++++.++..+|.+ .|.++...|.+-|+.|-++|+|.|-
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVE------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHH------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 456788889999999999887 5789999999999999999999994
No 163
>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=28.18 E-value=3.5e+02 Score=29.71 Aligned_cols=53 Identities=15% Similarity=0.378 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHhhccCCHHHHHHHHHHhccc----ccHHHHHHHHHHHHHHHhhhh
Q 003676 343 HISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGI 395 (804)
Q Consensus 343 ~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~----~~l~~l~~~~~~yi~~~g~~i 395 (804)
.+..++.+.|..-.+++|...+.++++||-.+ .|++....-+.+.|......+
T Consensus 7 ~L~~~~~~~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~ 63 (324)
T smart00762 7 TLTELFKERFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSL 63 (324)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHH
Confidence 34455667788889999999999999999876 466666666665555544443
No 164
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=28.06 E-value=79 Score=33.58 Aligned_cols=50 Identities=18% Similarity=0.370 Sum_probs=42.6
Q ss_pred HHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003676 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (804)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (804)
-|.++-+.-+.++.++-.||.+++|+|...+-|+|+.|. |.+++.+...|
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE--k~GlIe~~K~G 246 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE--KRGLIEKEKKG 246 (258)
T ss_pred HHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH--hCCceEEEEeC
Confidence 456666777777889999999999999999999999999 98998876544
No 165
>PRK06474 hypothetical protein; Provisional
Probab=27.92 E-value=1.6e+02 Score=29.26 Aligned_cols=52 Identities=12% Similarity=0.185 Sum_probs=40.6
Q ss_pred EEcHHHHHHHHhHhCCC-CCCHHHHHHHh-CCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 635 AVSLFQTVVLMLFNDAQ-KLSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 635 ~vs~~Qa~ILllFn~~~-~lt~~ei~~~t-~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
..++.-..||-.+-..+ .+|..+|.+.+ +++...+-++|..|. +.+++...+
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~~ 61 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVVK 61 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEee
Confidence 34555666775554444 49999999999 799999999999999 888887643
No 166
>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=27.67 E-value=1.5e+02 Score=25.34 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=27.5
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
.-.+|-+.-....+|..+|+..+|.+.+++...|..+.
T Consensus 26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 33456666778899999999999999999999998875
No 167
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=26.96 E-value=71 Score=33.78 Aligned_cols=45 Identities=18% Similarity=0.307 Sum_probs=41.0
Q ss_pred HHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeec
Q 003676 743 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 793 (804)
Q Consensus 743 AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd 793 (804)
-.|+..++.++.++.++|.. .|.++...|.+=|..|-++|+|.|.
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~------~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKEKGKVSVEELAE------LFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHH------HhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 35789999999999999986 6999999999999999999999994
No 168
>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=26.51 E-value=1e+02 Score=28.77 Aligned_cols=51 Identities=12% Similarity=0.134 Sum_probs=40.2
Q ss_pred EEcHHHHHHHHh--HhC--------CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 635 AVSLFQTVVLML--FND--------AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 635 ~vs~~Qa~ILll--Fn~--------~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
.+-.+.-..++. .|. .-+.+.++|+..++-+.+.++.+|..|. +.+++...
T Consensus 26 ~~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 26 YTVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred eHHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 334555556666 443 4589999999999999999999999999 88888763
No 169
>smart00526 H15 Domain in histone families 1 and 5.
Probab=26.39 E-value=3e+02 Score=22.25 Aligned_cols=53 Identities=21% Similarity=0.130 Sum_probs=39.1
Q ss_pred HHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCC--hHHHHHHHHHHhhcCceeec
Q 003676 740 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIK--PADLKKRIESLIDREYLERD 793 (804)
Q Consensus 740 ~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~--~~~iK~~Ie~LIereyi~Rd 793 (804)
.|..||+. |+.++..+...+...+...-...+. ...++..|..++++|-|.+-
T Consensus 10 mI~eAI~~-l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 10 MITEAISA-LKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred HHHHHHHH-cCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeec
Confidence 46667766 6999999999988877665322222 25688889999999988764
No 170
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=25.80 E-value=1.2e+02 Score=28.81 Aligned_cols=42 Identities=19% Similarity=0.296 Sum_probs=35.4
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
|..+.+..+..+..+|++.++++...+.+.|..|. +.+++.+
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~--~~Gli~~ 54 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD--KDEYLIY 54 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH--HCCCEEE
Confidence 44455667788999999999999999999999999 7777764
No 171
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=25.76 E-value=1.3e+02 Score=29.06 Aligned_cols=47 Identities=13% Similarity=0.268 Sum_probs=41.2
Q ss_pred HHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceee
Q 003676 740 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 792 (804)
Q Consensus 740 ~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~R 792 (804)
.+|-.|.+.|.....+++.+|-.++ ..+++.+..||+.|.+.|+|++
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l------glS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF------GVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeee
Confidence 4788899999999999999987644 5689999999999999999985
No 172
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=25.53 E-value=1.3e+02 Score=29.44 Aligned_cols=48 Identities=15% Similarity=0.297 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceee
Q 003676 739 YQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 792 (804)
Q Consensus 739 ~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~R 792 (804)
..+|-.|.+++.....++..+|=.+| ..++..+.+||..|.+.|.|++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l------glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV------GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeEE
Confidence 35899999999999999998877644 5688999999999999999986
No 173
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=25.52 E-value=3.1e+02 Score=22.94 Aligned_cols=60 Identities=13% Similarity=0.265 Sum_probs=40.2
Q ss_pred HHHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCceeeC
Q 003676 739 YQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYL 803 (804)
Q Consensus 739 ~~i~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~Yl 803 (804)
..-+++|-.+.+.+..-+..+|+..+.+. .|.++-+.|-+-|..| +-++ .++..+.|.|.
T Consensus 4 ~~R~~~I~~li~~~~i~sQ~eL~~~L~~~-Gi~vTQaTiSRDLkeL---~~vK-v~~~~g~~~Y~ 63 (70)
T PF01316_consen 4 SKRQELIKELISEHEISSQEELVELLEEE-GIEVTQATISRDLKEL---GAVK-VPDGNGKYRYV 63 (70)
T ss_dssp HHHHHHHHHHHHHS---SHHHHHHHHHHT-T-T--HHHHHHHHHHH---T-EE-EECTTSSEEEE
T ss_pred HHHHHHHHHHHHHCCcCCHHHHHHHHHHc-CCCcchhHHHHHHHHc---CcEE-eeCCCCCEEEE
Confidence 34578899999999999999999877665 8999999998888777 3333 33444678874
No 174
>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=25.37 E-value=1.6e+02 Score=23.33 Aligned_cols=46 Identities=13% Similarity=0.317 Sum_probs=32.9
Q ss_pred HHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCC
Q 003676 744 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNN 796 (804)
Q Consensus 744 aIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d 796 (804)
.|...+.... ++..++.. . +..+...+.+.++.|.+.|+|.+..+.
T Consensus 11 ~il~~l~~~~-~~~~ei~~----~--~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 11 RILRLLLEGP-LTVSELAE----R--LGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHHCC-cCHHHHHH----H--HCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 3444444555 77777544 2 356788999999999999999986544
No 175
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=25.09 E-value=1.7e+02 Score=22.45 Aligned_cols=39 Identities=13% Similarity=0.227 Sum_probs=29.3
Q ss_pred cCCCC-ChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCC
Q 003676 751 TRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 795 (804)
Q Consensus 751 ~~K~l-~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~ 795 (804)
....+ +..+|.. .|..+...+.+.+..|.+.|+|.+.++
T Consensus 16 ~~~~l~s~~~la~------~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 16 PGDKLPSERELAA------QLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred CCCcCcCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 33344 4555443 467789999999999999999998764
No 176
>smart00753 PAM PCI/PINT associated module.
Probab=24.80 E-value=1e+02 Score=26.28 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=28.8
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCccee
Q 003676 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (804)
Q Consensus 649 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (804)
....+++++|++.++++.+++...+..++ ..+.|
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i--~~~~l 54 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAI--RDGEI 54 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHH--HCCCe
Confidence 45789999999999999999999999888 44444
No 177
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=24.80 E-value=1e+02 Score=26.28 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=28.8
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCccee
Q 003676 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (804)
Q Consensus 649 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (804)
....+++++|++.++++.+++...+..++ ..+.|
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i--~~~~l 54 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAI--RDGEI 54 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHH--HCCCe
Confidence 45789999999999999999999999888 44444
No 178
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=24.79 E-value=1.8e+02 Score=33.07 Aligned_cols=39 Identities=21% Similarity=0.301 Sum_probs=35.2
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 647 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 647 Fn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
+.....+|.++|++.++++...+.+.|..|. +.+++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~--~agLI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELA--RIGLLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--hCCCeEec
Confidence 5667799999999999999999999999999 88998753
No 179
>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=24.69 E-value=1.3e+02 Score=24.74 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=29.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 652 ~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
.+|-++|++.+|++...+.+.|.-|. +.+++..
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~--~~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLK--DEGIIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHH--HTTSEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 48999999999999999999999999 7778765
No 180
>PRK09462 fur ferric uptake regulator; Provisional
Probab=24.62 E-value=2.3e+02 Score=27.02 Aligned_cols=51 Identities=16% Similarity=0.169 Sum_probs=40.6
Q ss_pred HHHHHHhhc--CCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 743 AAIVRIMKT--RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 743 AaIVRIMK~--~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
-+|.+++.. .+-++.++|...+.+.. ..++.+.|=+.|+.|.+.|.|.+-.
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~-~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMG-EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 355666664 36899999998886653 5678999999999999999998843
No 181
>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=24.50 E-value=1.7e+02 Score=26.42 Aligned_cols=57 Identities=18% Similarity=0.325 Sum_probs=40.7
Q ss_pred HHHHhHhC-CCCCCHHHHHHHh-----CCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEec
Q 003676 642 VVLMLFND-AQKLSFQDIKDAT-----GIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 703 (804)
Q Consensus 642 ~ILllFn~-~~~lt~~ei~~~t-----~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~ 703 (804)
.||-.+.+ ...+|.+||.+.+ +++...+-|+|..|. ..+++.+...+. ....|..+.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~--~~Gli~~~~~~~---~~~~y~~~~ 67 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLE--EAGLVREIELGD---GKARYELNT 67 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHH--hCCCEEEEEeCC---CceEEEeCC
Confidence 35544444 4579999999988 688999999999999 888887743211 124566654
No 182
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=24.39 E-value=1.1e+02 Score=35.07 Aligned_cols=37 Identities=32% Similarity=0.478 Sum_probs=29.4
Q ss_pred HHHHH-hHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 641 TVVLM-LFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 641 a~ILl-lFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
..||- +.+....+|+++|++.|||..+++..+|+.|-
T Consensus 362 ~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l~ 399 (450)
T PLN00104 362 RVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSLN 399 (450)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 34442 33444689999999999999999999999884
No 183
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=24.12 E-value=1.5e+02 Score=27.99 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=21.5
Q ss_pred CCCChHHHHHHHHHHhhcCceeecC
Q 003676 770 FPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 770 F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
+..+.+.+.+.|+.|.++|||+|..
T Consensus 56 l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 56 IGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred hCCChhhHHHHHHHHHHCCCEeeec
Confidence 4557788999999999999999953
No 184
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.07 E-value=1.8e+02 Score=22.00 Aligned_cols=35 Identities=23% Similarity=0.484 Sum_probs=25.6
Q ss_pred HHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhH
Q 003676 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (804)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~s 675 (804)
+...|+.+.-+. .|+.+|+..+|++...+.+.+..
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 344444433332 69999999999999999988764
No 185
>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=24.04 E-value=1.1e+02 Score=26.60 Aligned_cols=39 Identities=18% Similarity=0.241 Sum_probs=31.4
Q ss_pred HHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhc
Q 003676 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 678 (804)
Q Consensus 640 Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 678 (804)
...+.-++....++++++|++.++++.+++...|..++.
T Consensus 48 ~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~ 86 (105)
T PF01399_consen 48 RRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLIS 86 (105)
T ss_dssp HHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHH
Confidence 344445555778999999999999999999999999883
No 186
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=23.96 E-value=1.1e+02 Score=32.23 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=36.2
Q ss_pred HHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
=|..|+-+.+.++.+++.+|++.+|+++..++|=|..|.
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 467899999999999999999999999999999999887
No 187
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.82 E-value=95 Score=29.85 Aligned_cols=30 Identities=27% Similarity=0.348 Sum_probs=27.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhc
Q 003676 649 DAQKLSFQDIKDATGIEDKELRRTLQSLAC 678 (804)
Q Consensus 649 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 678 (804)
.++.+|-++|++.+||+...|++.|..|..
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 345799999999999999999999999983
No 188
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=23.75 E-value=1e+02 Score=24.94 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=26.9
Q ss_pred CCCChHHHHHHHHHhcCCCCCh--HHHHHHHHHHhhcCcee
Q 003676 753 KVLSHTLLITELFQQLKFPIKP--ADLKKRIESLIDREYLE 791 (804)
Q Consensus 753 K~l~~~~Li~ev~~~l~F~~~~--~~iK~~Ie~LIereyi~ 791 (804)
++++++||+. +.|++.. ..|+++=+.|+++||=-
T Consensus 2 ~tv~k~dLi~-----lGf~~~tA~~IIrqAK~~lV~~G~~~ 37 (59)
T PF11372_consen 2 KTVTKKDLIE-----LGFSESTARDIIRQAKALLVQKGFSF 37 (59)
T ss_pred CccCHHHHHH-----cCCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 5788999984 4787644 58999999999999743
No 189
>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=23.13 E-value=1.8e+02 Score=21.27 Aligned_cols=39 Identities=23% Similarity=0.376 Sum_probs=27.6
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHh
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL 676 (804)
+..+..++.++- .+.++..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444445554432 245899999999999999888777653
No 190
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=22.98 E-value=1.5e+02 Score=28.79 Aligned_cols=44 Identities=14% Similarity=0.277 Sum_probs=37.3
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (804)
|..++.+.......+|++.+++++..+...|+-|. +.+++...|
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~~ 58 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYEP 58 (154)
T ss_pred HHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEec
Confidence 44455567789999999999999999999999999 788887754
No 191
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=22.61 E-value=2.2e+02 Score=26.69 Aligned_cols=50 Identities=16% Similarity=0.092 Sum_probs=39.6
Q ss_pred EcHHHHHHHHhHhCCCCCCHHHHHHHh----CCCHHHHHHHHhHhhcCCcceeeeC
Q 003676 636 VSLFQTVVLMLFNDAQKLSFQDIKDAT----GIEDKELRRTLQSLACGKVRVLQKL 687 (804)
Q Consensus 636 vs~~Qa~ILllFn~~~~lt~~ei~~~t----~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (804)
+|..+..|+..+=+.+..|..+|.+.+ ++....+...|.-|. +.+++.+.
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~--~KG~v~~~ 55 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLV--DKGCLTTE 55 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHH--HCCceeee
Confidence 466778888777667789999977765 788899999999999 77777653
No 192
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=22.51 E-value=2.4e+02 Score=28.41 Aligned_cols=111 Identities=16% Similarity=0.161 Sum_probs=61.7
Q ss_pred ChHHHHHHHHHHHHHHhcCCCceeEeecCCceEEEEEE--ec-------CceEEEEEcHHHHHHHHhHhCCCCCCHHHHH
Q 003676 589 PHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAE--FP-------KGKKELAVSLFQTVVLMLFNDAQKLSFQDIK 659 (804)
Q Consensus 589 P~~l~~~~~~F~~~Y~~k~~~RkL~W~~~lg~~~l~~~--f~-------~~~~~l~vs~~Qa~ILllFn~~~~lt~~ei~ 659 (804)
|.++..+++....-|.....| +.-...=|...+..+ +. .....-..|...+-+|-..--+.++|-.||.
T Consensus 34 ~~~v~~~l~~L~~~y~~~~~g--i~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~ 111 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGDDRG--LKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEID 111 (188)
T ss_pred HHHHHHHHHHHHHHHhhCCCC--EEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHH
Confidence 357889999999999865333 333222222222221 00 0111223444444455444445689999999
Q ss_pred HHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCC
Q 003676 660 DATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 706 (804)
Q Consensus 660 ~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~ 706 (804)
+.+|++. ..++..|. ..+++..............|.++..|-
T Consensus 112 ~irGv~~---~~ii~~L~--~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNS---DGALQTLL--AKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCH---HHHHHHHH--HCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999986 44566666 556665432221122345577777764
No 193
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=22.47 E-value=2.6e+02 Score=24.04 Aligned_cols=42 Identities=19% Similarity=0.268 Sum_probs=32.8
Q ss_pred HHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003676 644 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (804)
Q Consensus 644 LllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (804)
++.-++.+.+|=++|++.+|++...+-++++.|-...+.|..
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEe
Confidence 344556678999999999999999999999999733344443
No 194
>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=22.27 E-value=1.2e+02 Score=28.24 Aligned_cols=49 Identities=18% Similarity=0.316 Sum_probs=39.5
Q ss_pred EcHHHHHHHHhHhCC--------CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 636 VSLFQTVVLMLFNDA--------QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 636 vs~~Qa~ILllFn~~--------~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
+..+.-..|+..|.. -+.+.+.|+..++-+.+.++.+|..|. +.+++..
T Consensus 27 ~~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~ 83 (119)
T TIGR01714 27 TIIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEK 83 (119)
T ss_pred HHHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 344555566665554 478999999999999999999999999 8988876
No 195
>PLN03239 histone acetyltransferase; Provisional
Probab=22.15 E-value=1.2e+02 Score=33.33 Aligned_cols=39 Identities=23% Similarity=0.397 Sum_probs=29.7
Q ss_pred HHHHHHHhH-hCC---CCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 639 FQTVVLMLF-NDA---QKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 639 ~Qa~ILllF-n~~---~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
+...|+-.+ +.. ..+|+++|++.|||..+++..+|+.|-
T Consensus 267 W~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l~ 309 (351)
T PLN03239 267 WGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQLG 309 (351)
T ss_pred HHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 444555433 322 469999999999999999999998874
No 196
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=22.12 E-value=1e+02 Score=26.37 Aligned_cols=47 Identities=21% Similarity=0.364 Sum_probs=36.3
Q ss_pred HHHHHHHhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 742 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 742 ~AaIVRIMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
.-+|+-++.....+++.+|... ...+...+-+.+..|.+.|||++..
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~------l~lt~g~Ls~hL~~Le~~GyV~~~k 48 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEE------LGLTDGNLSKHLKKLEEAGYVEVEK 48 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHH------TT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHH------hCcCHHHHHHHHHHHHHCCCEEEEE
Confidence 3467777788888888887752 3458999999999999999999853
No 197
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=22.01 E-value=1.2e+02 Score=22.62 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=22.7
Q ss_pred hHHHHHHHHHHHhhcCCCcchHHHHHHHHH
Q 003676 430 FCNTIKDAFEYLINLRQNRPAELIAKFLDE 459 (804)
Q Consensus 430 f~~~l~~af~~~lN~~~~~~~e~La~y~D~ 459 (804)
+...+.+|+......++..+.++||.|+-.
T Consensus 10 v~p~L~~gL~~l~~~rP~DPi~~La~~Ll~ 39 (42)
T PF05186_consen 10 VGPVLTEGLAELAKERPEDPIEFLAEYLLK 39 (42)
T ss_dssp THHHHHHHHHHHHHH--SSHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHCCCChHHHHHHHHHH
Confidence 456677888888888888899999999753
No 198
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=22.01 E-value=1.5e+02 Score=24.92 Aligned_cols=43 Identities=14% Similarity=0.222 Sum_probs=31.1
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
+-||.... .+..++.+|+..+|++...+.+.|..|. +.+++..
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~--~~gLI~~ 51 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELE--EKGLIKK 51 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHH--HTTSEEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCcCeeC
Confidence 34566665 5678899999999999999999999999 7777743
No 199
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=21.79 E-value=7.6e+02 Score=28.90 Aligned_cols=30 Identities=23% Similarity=0.288 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCcCchHHHHHHHHH
Q 003676 305 LKHVEIRLHEEHERCLLYLDVSTRKPLIATAER 337 (804)
Q Consensus 305 L~~ve~~l~eE~~r~~~yl~~~t~~~l~~~l~~ 337 (804)
++.+..++.....+.++| +..++++..|++
T Consensus 468 ~~~i~~rI~~h~~~Lrk~---syGKhIia~lek 497 (503)
T KOG1488|consen 468 RELIKSRVKPHASRLRKF---SYGKHIIAKLEK 497 (503)
T ss_pred HHHHHHHHHHHHHHHccC---ccHHHHHHHHHH
Confidence 566667777777776665 455666666554
No 200
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=21.74 E-value=1.4e+02 Score=21.70 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 650 AQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 650 ~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
.+.+++++|++..|++..-+.+..+...
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 4579999999999999999988887654
No 201
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=21.71 E-value=1.2e+02 Score=31.54 Aligned_cols=55 Identities=16% Similarity=0.323 Sum_probs=41.3
Q ss_pred HHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCC
Q 003676 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 705 (804)
Q Consensus 641 a~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F 705 (804)
..+.-+|.++..||+.+|.+.|+=|...|+..|..++ |+.+... ...+|.+-..|
T Consensus 189 d~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-----v~NkKg~-----~k~tyeLKPEY 243 (254)
T KOG2905|consen 189 DMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-----VLNKKGP-----YKNTYELKPEY 243 (254)
T ss_pred HHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-----HHhccCc-----ccCceecCHHH
Confidence 3455688899999999999999999999999999987 4544211 23456665555
No 202
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=21.61 E-value=1.7e+02 Score=30.15 Aligned_cols=36 Identities=19% Similarity=0.265 Sum_probs=32.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003676 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (804)
Q Consensus 649 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (804)
....+|.++|++.+++++..++.++..|+ .++++..
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~--~~~~~~~ 210 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLV--NCHILFT 210 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHH--hCCEEEE
Confidence 35689999999999999999999999999 8888844
No 203
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=21.56 E-value=1.9e+02 Score=24.55 Aligned_cols=58 Identities=24% Similarity=0.290 Sum_probs=33.9
Q ss_pred HHHHHHHHHHhhcCC--CCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCce---eecCCCCCceeeCC
Q 003676 739 YQVDAAIVRIMKTRK--VLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYL---ERDKNNPQIYNYLA 804 (804)
Q Consensus 739 ~~i~AaIVRIMK~~K--~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi---~Rd~~d~~~y~Yla 804 (804)
...=|.||-.||++. .++.+|++.++-. +... ..++ +.|-+-+-+ +.++. .+.|.|.|
T Consensus 8 ~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~---~d~~-~~~~---~~L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 8 FTQLAKIVDYMKKRHQHPLTLDEILDYLSL---LDIG-PKLK---EWLKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhhHHHHHHHHHhcCCCCccHHHHHHHHhc---cCcc-HHHH---HHHHhhhhccCceeccC-CCEEEecc
Confidence 345688999999986 6777777766532 3332 1222 333333333 44443 36888865
No 204
>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=21.15 E-value=1.8e+02 Score=22.81 Aligned_cols=39 Identities=21% Similarity=0.341 Sum_probs=30.8
Q ss_pred cHHHHHHHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
|.-+..||.++..+ .+..+|++..|+++..+..++..+.
T Consensus 5 T~~E~~vl~~l~~G--~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 5 TERELEVLRLLAQG--MSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp -HHHHHHHHHHHTT--S-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhc--CCcchhHHhcCcchhhHHHHHHHHH
Confidence 45567777777664 7899999999999999999988876
No 205
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.08 E-value=1.2e+02 Score=22.83 Aligned_cols=33 Identities=15% Similarity=0.358 Sum_probs=21.6
Q ss_pred HHHhHhCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003676 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (804)
Q Consensus 643 ILllFn~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 677 (804)
|+.++.+ .+|..+|++.+|++...+.+-+.-+.
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 4445544 68999999999999999888776654
No 206
>PF07393 Sec10: Exocyst complex component Sec10; InterPro: IPR009976 This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which specifically affects the synthesis and delivery of secretory and basolateral plasma membrane proteins [].; GO: 0006887 exocytosis, 0048278 vesicle docking, 0005737 cytoplasm
Probab=21.03 E-value=1.6e+03 Score=27.53 Aligned_cols=136 Identities=13% Similarity=0.133 Sum_probs=75.2
Q ss_pred chHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHhhhhcchHhhHHhHHHHHHHHHHHHH----------HHh--h---
Q 003676 232 EVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEG----------MKY--M--- 296 (804)
Q Consensus 232 ~i~~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~~L~iY~~~FE~~fL~~t~~yY~~~s----------~~~--i--- 296 (804)
...+.+-..+|+.++..=. .-|...++.+...|..++-+.. .=..|++...-|+.... ..| +
T Consensus 106 ~~~e~fE~~LL~eFe~ay~--~~d~~~M~~~A~vL~~fngg~~-~i~~fi~k~~~f~~~~~~~~~~~~~~~~~~~~l~d~ 182 (710)
T PF07393_consen 106 KYCEIFENALLREFEIAYR--EGDYERMKEFAKVLLEFNGGSS-CIDFFINKHEFFIDEDQLDESNGFEDEEIWEKLSDP 182 (710)
T ss_pred HHHHHHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHcCCCcH-HHHHHHHhChhhhhhhhhccccccchhHHHHhccCc
Confidence 3445666677777653321 2267889999999999875543 22334444433431100 011 0
Q ss_pred ------hcCChhhHHHHHHHHHHHHHHHHhhhcCc--CchHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHH
Q 003676 297 ------QQSDVPDYLKHVEIRLHEEHERCLLYLDV--STRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMY 368 (804)
Q Consensus 297 ------~~~~~~eYL~~ve~~l~eE~~r~~~yl~~--~t~~~l~~~l~~~Li~~~~~~ll~~gl~~ll~~~~~~~L~~ly 368 (804)
....+.+++..+...+++|...+...++. .....+++.+-..-|..++..+|+ .........-|+.++
T Consensus 183 ~~~~~~~~~~l~~~~~~i~~~i~~e~~iI~~VFp~~~~Vm~~fiervf~~~I~~~i~~lL~----~a~~~s~~~YLr~l~ 258 (710)
T PF07393_consen 183 DSHPPINEESLDAFFEDIRDVINEESKIIDRVFPNPEPVMQKFIERVFEQVIQEYIESLLE----EASSISTLAYLRTLH 258 (710)
T ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHH----hhccCCHHHHHHHHH
Confidence 11236688999999999999999887643 233344444444444444444442 222222334466777
Q ss_pred HHhccc
Q 003676 369 SLFSRV 374 (804)
Q Consensus 369 ~Ll~~~ 374 (804)
.++..+
T Consensus 259 ~~y~~t 264 (710)
T PF07393_consen 259 GLYSQT 264 (710)
T ss_pred HHHHHH
Confidence 766654
No 207
>PRK14999 histidine utilization repressor; Provisional
Probab=20.51 E-value=1.7e+02 Score=30.35 Aligned_cols=47 Identities=13% Similarity=0.309 Sum_probs=36.1
Q ss_pred HhhcCCCC-ChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecCCCCCcee
Q 003676 748 IMKTRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 801 (804)
Q Consensus 748 IMK~~K~l-~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~~d~~~y~ 801 (804)
..+....| +-.+|.. .|.++...|+++|+.|.+.|+|.|..+ +++|+
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 44555556 5666665 589999999999999999999999764 45654
No 208
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=20.18 E-value=1.8e+02 Score=27.37 Aligned_cols=41 Identities=17% Similarity=0.310 Sum_probs=32.5
Q ss_pred HhhcCCCCChHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCceeecC
Q 003676 748 IMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 794 (804)
Q Consensus 748 IMK~~K~l~~~~Li~ev~~~l~F~~~~~~iK~~Ie~LIereyi~Rd~ 794 (804)
+|..++.++.++|-+.+ ..+.+.+-+.+.+|++.|.+.|..
T Consensus 36 LL~~~~~~tvdelae~l------nr~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 36 LLEENGPLTVDELAEIL------NRSRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HHhhcCCcCHHHHHHHH------CccHHHHHHHHHHHHHcCCeeeee
Confidence 34478888888876533 457888999999999999999954
Done!