Query 004725
Match_columns 733
No_of_seqs 206 out of 1061
Neff 8.6
Searched_HMMs 46136
Date Thu Mar 28 11:51:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004725hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166 Cullins [Cell cycle co 100.0 1E-115 3E-120 985.8 63.9 700 21-731 13-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 2E-113 3E-118 923.7 63.2 714 9-733 6-773 (773)
3 KOG2167 Cullins [Cell cycle co 100.0 1E-111 2E-116 888.8 47.1 650 67-733 1-661 (661)
4 KOG2284 E3 ubiquitin ligase, C 100.0 1E-103 2E-108 791.9 48.8 675 16-733 5-728 (728)
5 PF00888 Cullin: Cullin family 100.0 2E-92 4.4E-97 819.9 62.0 580 29-632 1-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 6.4E-86 1.4E-90 669.5 54.9 704 21-733 9-777 (777)
7 smart00182 CULLIN Cullin. 100.0 2.5E-32 5.4E-37 255.3 17.1 140 412-551 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 8.2E-25 1.8E-29 236.2 51.1 303 405-723 441-758 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 6.4E-20 1.4E-24 147.1 2.5 67 661-727 2-68 (68)
10 PF08539 HbrB: HbrB-like; Int 97.5 0.0032 6.9E-08 59.2 14.4 130 25-156 5-156 (158)
11 KOG2167 Cullins [Cell cycle co 96.3 0.048 1E-06 60.3 12.6 279 25-316 110-418 (661)
12 TIGR01610 phage_O_Nterm phage 94.9 0.089 1.9E-06 45.3 6.8 66 558-632 20-93 (95)
13 PF13412 HTH_24: Winged helix- 94.2 0.12 2.5E-06 38.2 5.1 44 562-605 2-45 (48)
14 PF09339 HTH_IclR: IclR helix- 94.0 0.094 2E-06 39.5 4.3 45 566-613 6-51 (52)
15 PF12802 MarR_2: MarR family; 93.1 0.15 3.2E-06 39.8 4.3 51 561-614 3-55 (62)
16 PF02082 Rrf2: Transcriptional 92.9 0.32 7E-06 40.6 6.4 59 564-630 11-70 (83)
17 PF08220 HTH_DeoR: DeoR-like h 92.1 0.28 6E-06 37.7 4.5 46 565-613 2-47 (57)
18 PF13463 HTH_27: Winged helix 91.5 0.37 8E-06 38.2 4.9 51 561-614 1-52 (68)
19 PF01047 MarR: MarR family; I 91.4 0.19 4E-06 38.8 2.9 50 562-614 2-51 (59)
20 PF12840 HTH_20: Helix-turn-he 90.3 0.49 1.1E-05 36.9 4.4 49 562-613 9-57 (61)
21 TIGR02337 HpaR homoprotocatech 89.4 0.83 1.8E-05 40.9 5.8 52 560-614 25-76 (118)
22 PF01022 HTH_5: Bacterial regu 89.2 0.99 2.2E-05 33.0 5.1 44 564-611 3-46 (47)
23 smart00550 Zalpha Z-DNA-bindin 88.0 1 2.3E-05 35.9 4.8 47 564-613 7-55 (68)
24 smart00346 HTH_ICLR helix_turn 87.6 1.2 2.6E-05 37.6 5.4 56 566-630 8-64 (91)
25 PF04492 Phage_rep_O: Bacterio 87.4 1.7 3.7E-05 37.6 6.1 62 560-632 29-98 (100)
26 PRK11512 DNA-binding transcrip 87.4 1.3 2.8E-05 41.3 5.8 52 560-614 37-88 (144)
27 PF01978 TrmB: Sugar-specific 86.6 0.53 1.1E-05 37.5 2.4 50 562-614 7-56 (68)
28 TIGR01889 Staph_reg_Sar staphy 85.5 2.2 4.9E-05 37.5 6.1 52 560-614 22-77 (109)
29 smart00420 HTH_DEOR helix_turn 84.2 2.4 5.2E-05 31.3 4.9 45 566-613 3-47 (53)
30 TIGR02698 CopY_TcrY copper tra 84.1 1.5 3.2E-05 40.1 4.3 60 669-733 6-65 (130)
31 smart00347 HTH_MARR helix_turn 84.1 2.3 4.9E-05 36.3 5.4 53 558-613 5-57 (101)
32 PF08279 HTH_11: HTH domain; 83.8 3 6.6E-05 31.4 5.4 39 567-605 4-43 (55)
33 COG3355 Predicted transcriptio 83.1 3.1 6.7E-05 37.4 5.8 38 574-614 39-76 (126)
34 PRK15090 DNA-binding transcrip 82.8 2.7 5.9E-05 43.3 6.3 46 566-614 17-62 (257)
35 COG3682 Predicted transcriptio 82.5 1.6 3.5E-05 38.9 3.8 62 667-733 6-67 (123)
36 PRK10857 DNA-binding transcrip 81.7 4.5 9.7E-05 38.6 6.8 45 565-612 12-57 (164)
37 PRK11920 rirA iron-responsive 81.7 4.3 9.4E-05 38.2 6.7 56 566-629 13-68 (153)
38 PF05732 RepL: Firmicute plasm 81.3 2 4.2E-05 41.0 4.2 47 578-634 76-122 (165)
39 smart00419 HTH_CRP helix_turn_ 80.1 4 8.7E-05 29.5 4.7 34 577-613 8-41 (48)
40 PF08784 RPA_C: Replication pr 80.1 3.3 7.2E-05 36.0 4.9 46 560-605 44-93 (102)
41 PF04703 FaeA: FaeA-like prote 80.0 4.5 9.8E-05 31.6 5.1 45 568-615 5-50 (62)
42 PF13601 HTH_34: Winged helix 79.8 1.9 4.2E-05 35.6 3.2 44 566-612 3-46 (80)
43 PRK13777 transcriptional regul 79.5 4.3 9.3E-05 39.5 6.0 53 559-614 41-93 (185)
44 PF05158 RNA_pol_Rpc34: RNA po 79.3 4.3 9.2E-05 43.4 6.4 146 559-725 80-260 (327)
45 TIGR02010 IscR iron-sulfur clu 79.1 5.7 0.00012 36.5 6.4 44 566-612 13-57 (135)
46 PRK03573 transcriptional regul 78.4 4.7 0.0001 37.4 5.7 53 559-614 27-80 (144)
47 cd00090 HTH_ARSR Arsenical Res 78.0 5.4 0.00012 31.6 5.4 48 562-613 6-53 (78)
48 PF03965 Penicillinase_R: Peni 77.6 2.3 5E-05 37.9 3.3 60 669-733 5-64 (115)
49 PF09012 FeoC: FeoC like trans 77.6 0.75 1.6E-05 36.8 0.1 45 672-724 5-49 (69)
50 PHA00738 putative HTH transcri 76.0 6.9 0.00015 34.1 5.5 68 558-632 7-74 (108)
51 COG1414 IclR Transcriptional r 75.9 6.1 0.00013 40.5 6.2 47 566-615 7-54 (246)
52 PRK10870 transcriptional repre 74.9 7.5 0.00016 37.5 6.2 52 560-614 52-105 (176)
53 PRK11569 transcriptional repre 74.7 6.4 0.00014 41.0 6.1 47 565-614 30-77 (274)
54 PRK10163 DNA-binding transcrip 74.5 6.9 0.00015 40.7 6.3 47 565-614 27-74 (271)
55 TIGR00738 rrf2_super rrf2 fami 74.4 8.5 0.00018 35.0 6.2 46 565-613 12-58 (132)
56 smart00344 HTH_ASNC helix_turn 74.0 6.3 0.00014 34.4 5.0 45 564-611 4-48 (108)
57 PF01325 Fe_dep_repress: Iron 73.9 8.2 0.00018 29.9 5.0 44 568-614 13-56 (60)
58 TIGR01884 cas_HTH CRISPR locus 73.9 5.9 0.00013 39.2 5.4 52 560-614 140-191 (203)
59 TIGR03879 near_KaiC_dom probab 73.5 3.9 8.4E-05 33.1 3.1 33 573-605 28-60 (73)
60 smart00345 HTH_GNTR helix_turn 73.4 6.6 0.00014 29.7 4.5 40 572-614 14-54 (60)
61 PF05584 Sulfolobus_pRN: Sulfo 73.1 10 0.00022 30.5 5.3 47 562-613 5-51 (72)
62 COG1959 Predicted transcriptio 72.7 10 0.00022 35.6 6.3 59 564-630 11-70 (150)
63 TIGR02944 suf_reg_Xantho FeS a 72.0 9.6 0.00021 34.6 5.9 44 567-613 13-58 (130)
64 PRK09834 DNA-binding transcrip 71.6 8.1 0.00018 39.9 6.0 47 566-615 14-61 (263)
65 TIGR02431 pcaR_pcaU beta-ketoa 71.6 8.8 0.00019 39.3 6.2 44 566-612 12-56 (248)
66 PF13404 HTH_AsnC-type: AsnC-t 71.6 6.5 0.00014 28.1 3.6 36 566-601 6-41 (42)
67 cd00092 HTH_CRP helix_turn_hel 71.5 9.7 0.00021 29.7 5.2 35 576-613 24-58 (67)
68 PF13730 HTH_36: Helix-turn-he 70.7 10 0.00022 28.5 4.9 27 579-605 27-53 (55)
69 PRK10141 DNA-binding transcrip 70.0 10 0.00023 33.8 5.4 60 564-630 17-76 (117)
70 PF08280 HTH_Mga: M protein tr 69.5 6.9 0.00015 30.2 3.7 39 565-603 7-45 (59)
71 smart00418 HTH_ARSR helix_turn 69.2 10 0.00022 28.9 4.9 36 575-613 8-43 (66)
72 COG2345 Predicted transcriptio 67.7 8.1 0.00018 38.4 4.7 44 566-612 14-57 (218)
73 PRK04172 pheS phenylalanyl-tRN 67.6 33 0.00072 39.0 10.3 50 560-612 3-52 (489)
74 PF01978 TrmB: Sugar-specific 67.3 2.9 6.2E-05 33.2 1.2 54 671-732 12-65 (68)
75 PF09012 FeoC: FeoC like trans 65.8 7.7 0.00017 31.0 3.4 37 569-605 6-42 (69)
76 COG1846 MarR Transcriptional r 65.6 13 0.00029 32.7 5.4 51 561-614 20-70 (126)
77 PF08221 HTH_9: RNA polymerase 65.3 10 0.00022 29.6 3.9 32 574-605 24-55 (62)
78 PF01726 LexA_DNA_bind: LexA D 63.9 18 0.00038 28.6 5.0 51 561-614 4-60 (65)
79 PRK11014 transcriptional repre 63.1 21 0.00045 33.0 6.3 40 572-614 20-59 (141)
80 PF02002 TFIIE_alpha: TFIIE al 62.7 7 0.00015 34.1 2.9 45 564-611 14-58 (105)
81 TIGR02702 SufR_cyano iron-sulf 61.8 19 0.00042 35.5 6.2 44 567-613 5-48 (203)
82 PRK11179 DNA-binding transcrip 61.7 15 0.00032 34.6 5.1 48 561-611 7-54 (153)
83 PRK06266 transcription initiat 59.5 16 0.00034 35.3 4.9 44 565-611 24-67 (178)
84 PF11994 DUF3489: Protein of u 58.5 22 0.00048 28.6 4.7 46 562-607 9-54 (72)
85 PRK11169 leucine-responsive tr 57.5 17 0.00037 34.6 4.8 48 561-611 12-59 (164)
86 cd07377 WHTH_GntR Winged helix 56.7 21 0.00045 27.5 4.4 38 573-613 20-58 (66)
87 COG4189 Predicted transcriptio 56.3 19 0.00041 35.7 4.7 49 562-613 22-70 (308)
88 PRK10434 srlR DNA-bindng trans 56.0 16 0.00035 37.6 4.6 47 564-613 6-52 (256)
89 TIGR00373 conserved hypothetic 55.7 21 0.00045 33.8 5.0 43 566-611 17-59 (158)
90 PF14394 DUF4423: Domain of un 55.1 32 0.00069 33.1 6.2 55 557-614 18-75 (171)
91 cd07153 Fur_like Ferric uptake 54.9 17 0.00038 32.0 4.2 57 672-731 6-63 (116)
92 COG1349 GlpR Transcriptional r 54.3 19 0.00041 37.0 4.8 47 565-614 7-53 (253)
93 PF00325 Crp: Bacterial regula 54.3 21 0.00045 23.9 3.3 28 578-605 3-30 (32)
94 smart00550 Zalpha Z-DNA-bindin 53.5 21 0.00045 28.4 3.9 54 668-729 7-62 (68)
95 PF04545 Sigma70_r4: Sigma-70, 53.4 31 0.00067 25.3 4.6 33 566-600 11-43 (50)
96 PF06784 UPF0240: Uncharacteri 52.6 25 0.00055 34.0 5.0 64 534-603 97-162 (179)
97 PF08220 HTH_DeoR: DeoR-like h 52.4 8.8 0.00019 29.4 1.5 47 670-724 3-49 (57)
98 PRK00215 LexA repressor; Valid 52.0 33 0.00072 33.8 6.1 52 561-615 2-59 (205)
99 PF09763 Sec3_C: Exocyst compl 52.0 4.9E+02 0.011 31.1 21.1 23 331-353 679-701 (701)
100 PF04967 HTH_10: HTH DNA bindi 51.3 36 0.00079 25.7 4.6 29 572-600 18-46 (53)
101 PRK13509 transcriptional repre 51.1 26 0.00057 35.9 5.3 48 564-614 6-53 (251)
102 PF01726 LexA_DNA_bind: LexA D 50.5 26 0.00057 27.6 4.0 56 663-725 6-62 (65)
103 PF02796 HTH_7: Helix-turn-hel 50.2 20 0.00044 25.8 3.1 31 567-599 13-43 (45)
104 PF14947 HTH_45: Winged helix- 48.8 38 0.00082 27.7 4.9 43 566-612 9-51 (77)
105 PRK04424 fatty acid biosynthes 48.3 18 0.0004 35.2 3.4 46 564-612 8-53 (185)
106 PF04182 B-block_TFIIIC: B-blo 47.5 34 0.00073 27.8 4.4 49 563-614 2-52 (75)
107 PF08281 Sigma70_r4_2: Sigma-7 46.9 37 0.0008 25.2 4.2 24 576-599 25-48 (54)
108 COG1522 Lrp Transcriptional re 46.2 39 0.00085 31.4 5.3 49 561-612 6-54 (154)
109 PF01638 HxlR: HxlR-like helix 46.1 38 0.00083 28.5 4.7 45 565-613 7-52 (90)
110 PRK09802 DNA-binding transcrip 45.9 30 0.00065 35.9 4.8 50 562-614 16-65 (269)
111 PRK10906 DNA-binding transcrip 45.4 33 0.00071 35.3 4.9 48 564-614 6-53 (252)
112 COG4190 Predicted transcriptio 45.2 75 0.0016 28.8 6.3 68 562-632 63-133 (144)
113 smart00421 HTH_LUXR helix_turn 44.2 47 0.001 24.4 4.6 39 562-602 5-43 (58)
114 TIGR00498 lexA SOS regulatory 43.6 28 0.00061 34.2 4.0 51 561-614 4-60 (199)
115 cd06170 LuxR_C_like C-terminal 43.0 51 0.0011 24.3 4.6 39 562-602 2-40 (57)
116 PRK10411 DNA-binding transcrip 42.8 41 0.00089 34.2 5.2 47 564-613 5-51 (240)
117 PF09756 DDRGK: DDRGK domain; 42.7 14 0.0003 36.0 1.6 58 667-733 100-157 (188)
118 PF10771 DUF2582: Protein of u 42.2 39 0.00084 26.7 3.7 37 567-603 12-48 (65)
119 TIGR02844 spore_III_D sporulat 42.1 42 0.00092 27.7 4.1 35 564-599 7-41 (80)
120 PF00392 GntR: Bacterial regul 42.0 35 0.00076 26.6 3.6 38 574-614 20-58 (64)
121 PF08318 COG4: COG4 transport 41.6 4.7E+02 0.01 28.0 17.0 154 274-434 15-212 (331)
122 PF01853 MOZ_SAS: MOZ/SAS fami 41.6 24 0.00051 34.2 2.9 26 577-602 150-175 (188)
123 smart00418 HTH_ARSR helix_turn 41.5 34 0.00074 25.8 3.5 45 673-726 3-47 (66)
124 PRK06474 hypothetical protein; 39.6 82 0.0018 30.4 6.4 53 559-614 7-61 (178)
125 PF13463 HTH_27: Winged helix 39.6 31 0.00066 26.9 2.9 46 669-722 5-51 (68)
126 COG1654 BirA Biotin operon rep 39.5 90 0.002 25.8 5.6 41 570-611 12-52 (79)
127 PF12324 HTH_15: Helix-turn-he 39.3 71 0.0015 26.1 4.8 40 564-603 25-64 (77)
128 PF06163 DUF977: Bacterial pro 38.5 74 0.0016 28.6 5.3 43 563-605 12-54 (127)
129 PF13545 HTH_Crp_2: Crp-like h 38.4 65 0.0014 25.7 4.8 34 577-613 28-61 (76)
130 PF01399 PCI: PCI domain; Int 38.2 56 0.0012 27.8 4.6 42 564-605 47-88 (105)
131 PF10007 DUF2250: Uncharacteri 38.1 68 0.0015 27.3 4.8 53 559-614 3-55 (92)
132 PRK11050 manganese transport r 37.2 74 0.0016 29.8 5.5 44 567-613 41-84 (152)
133 PF03444 HrcA_DNA-bdg: Winged 36.8 1.1E+02 0.0024 25.1 5.6 48 564-614 10-57 (78)
134 PHA02943 hypothetical protein; 36.0 72 0.0016 29.7 4.9 42 568-613 16-57 (165)
135 smart00088 PINT motif in prote 36.0 72 0.0016 26.4 4.8 32 574-605 21-52 (88)
136 smart00753 PAM PCI/PINT associ 36.0 72 0.0016 26.4 4.8 32 574-605 21-52 (88)
137 PF13384 HTH_23: Homeodomain-l 35.9 41 0.0009 24.5 2.9 35 568-604 10-44 (50)
138 PRK03902 manganese transport t 35.4 69 0.0015 29.5 5.0 42 568-612 13-54 (142)
139 PRK10681 DNA-binding transcrip 35.2 53 0.0012 33.7 4.6 40 564-603 8-47 (252)
140 PF13412 HTH_24: Winged helix- 35.1 19 0.00041 26.2 1.0 44 669-720 5-48 (48)
141 COG1318 Predicted transcriptio 35.1 53 0.0011 31.2 4.0 53 530-604 36-88 (182)
142 PRK00135 scpB segregation and 34.8 1.5E+02 0.0034 28.8 7.4 112 513-632 34-153 (188)
143 PF05261 Tra_M: TraM protein, 34.6 3.5E+02 0.0075 24.4 9.5 56 151-206 8-76 (127)
144 KOG4552 Vitamin-D-receptor int 34.6 4.5E+02 0.0098 25.7 12.7 54 331-390 88-142 (272)
145 smart00420 HTH_DEOR helix_turn 34.6 45 0.00097 24.2 3.0 45 672-724 5-49 (53)
146 PRK10430 DNA-binding transcrip 34.4 94 0.002 31.2 6.3 49 561-612 159-210 (239)
147 PF12395 DUF3658: Protein of u 34.3 62 0.0014 28.5 4.3 63 666-731 47-109 (111)
148 smart00344 HTH_ASNC helix_turn 34.1 42 0.0009 29.1 3.2 46 668-721 4-49 (108)
149 COG4742 Predicted transcriptio 33.1 72 0.0016 32.7 5.0 42 568-613 18-59 (260)
150 KOG2747 Histone acetyltransfer 32.9 51 0.0011 35.7 4.1 66 536-602 282-354 (396)
151 TIGR02698 CopY_TcrY copper tra 32.8 1.2E+02 0.0025 27.7 5.9 50 561-613 2-55 (130)
152 KOG2905 Transcription initiati 32.6 63 0.0014 32.4 4.3 58 564-632 187-244 (254)
153 PF12802 MarR_2: MarR family; 32.5 24 0.00053 26.9 1.3 47 670-724 8-56 (62)
154 COG1321 TroR Mn-dependent tran 32.2 91 0.002 29.3 5.2 45 567-614 14-58 (154)
155 TIGR02404 trehalos_R_Bsub treh 32.1 30 0.00065 34.9 2.2 35 695-730 30-64 (233)
156 PF01047 MarR: MarR family; I 32.1 20 0.00044 27.2 0.7 45 671-723 7-51 (59)
157 PF00196 GerE: Bacterial regul 32.0 86 0.0019 23.7 4.2 40 562-603 5-44 (58)
158 PRK10046 dpiA two-component re 31.8 83 0.0018 31.3 5.4 44 567-613 166-210 (225)
159 PF13542 HTH_Tnp_ISL3: Helix-t 31.8 1.1E+02 0.0023 22.4 4.6 34 565-600 17-50 (52)
160 PF02186 TFIIE_beta: TFIIE bet 31.5 35 0.00076 27.0 1.9 54 669-733 7-61 (65)
161 smart00345 HTH_GNTR helix_turn 31.0 36 0.00077 25.5 2.0 28 697-724 28-55 (60)
162 cd06171 Sigma70_r4 Sigma70, re 30.5 1E+02 0.0022 21.9 4.5 39 562-601 12-50 (55)
163 PRK11402 DNA-binding transcrip 30.0 34 0.00073 34.7 2.1 34 696-730 40-73 (241)
164 TIGR00122 birA_repr_reg BirA b 29.6 1.3E+02 0.0028 23.7 5.1 37 569-606 6-42 (69)
165 PF09681 Phage_rep_org_N: N-te 29.5 74 0.0016 28.6 3.9 50 561-613 27-86 (121)
166 PLN03238 probable histone acet 29.5 82 0.0018 32.7 4.7 39 564-602 209-248 (290)
167 PF07106 TBPIP: Tat binding pr 29.4 5E+02 0.011 24.6 10.3 59 565-630 3-64 (169)
168 cd07153 Fur_like Ferric uptake 29.2 1.2E+02 0.0027 26.5 5.4 57 567-629 5-67 (116)
169 PRK14165 winged helix-turn-hel 29.0 1E+02 0.0022 30.8 5.2 45 566-613 10-54 (217)
170 cd07977 TFIIE_beta_winged_heli 28.4 50 0.0011 26.9 2.4 27 666-692 8-36 (75)
171 PRK10079 phosphonate metabolis 28.4 39 0.00084 34.3 2.3 55 668-730 21-75 (241)
172 PF09107 SelB-wing_3: Elongati 28.3 1.5E+02 0.0032 22.1 4.7 41 570-613 3-43 (50)
173 smart00531 TFIIE Transcription 27.7 75 0.0016 29.6 3.9 32 574-605 12-43 (147)
174 TIGR02325 C_P_lyase_phnF phosp 27.6 39 0.00086 34.0 2.2 33 697-730 40-72 (238)
175 PLN02999 photosystem II oxygen 27.1 3E+02 0.0064 26.5 7.5 23 98-120 167-189 (190)
176 PF00165 HTH_AraC: Bacterial r 26.7 83 0.0018 22.0 3.1 28 575-602 6-33 (42)
177 PF02270 TFIIF_beta: Transcrip 26.6 93 0.002 32.4 4.7 59 562-631 215-273 (275)
178 TIGR03433 padR_acidobact trans 26.5 1.2E+02 0.0026 26.0 4.7 53 668-721 5-57 (100)
179 COG5090 TFG2 Transcription ini 26.1 93 0.002 30.9 4.1 55 567-632 199-253 (297)
180 PRK09334 30S ribosomal protein 26.0 39 0.00085 28.3 1.4 39 695-733 47-85 (86)
181 PRK13239 alkylmercury lyase; P 25.7 1.2E+02 0.0026 30.0 4.9 39 564-602 23-61 (206)
182 PF13730 HTH_36: Helix-turn-he 25.6 47 0.001 24.7 1.7 21 699-719 35-55 (55)
183 COG1777 Predicted transcriptio 25.3 5.9E+02 0.013 25.2 9.4 41 568-612 20-60 (217)
184 COG1510 Predicted transcriptio 25.2 76 0.0016 30.2 3.3 41 564-605 29-69 (177)
185 PRK04214 rbn ribonuclease BN/u 25.0 1.8E+02 0.0039 32.3 6.9 39 572-613 305-343 (412)
186 PF09904 HTH_43: Winged helix- 25.0 1.7E+02 0.0036 24.7 4.9 35 570-605 15-49 (90)
187 COG4565 CitB Response regulato 24.8 1.6E+02 0.0035 29.2 5.6 65 559-627 155-221 (224)
188 COG0735 Fur Fe2+/Zn2+ uptake r 24.6 1.2E+02 0.0027 28.1 4.7 52 559-613 17-74 (145)
189 COG1378 Predicted transcriptio 24.5 1.1E+02 0.0025 31.2 4.8 47 559-605 12-58 (247)
190 TIGR01889 Staph_reg_Sar staphy 24.3 60 0.0013 28.4 2.4 38 678-723 40-77 (109)
191 PRK14999 histidine utilization 24.0 48 0.001 33.6 2.0 47 675-730 29-76 (241)
192 PRK09462 fur ferric uptake reg 23.9 1.1E+02 0.0025 28.3 4.3 50 671-723 21-72 (148)
193 PF09114 MotA_activ: Transcrip 23.8 1.5E+02 0.0033 24.9 4.4 46 566-614 19-66 (96)
194 TIGR00721 tfx DNA-binding prot 23.4 1.4E+02 0.0031 27.5 4.7 39 561-601 7-45 (137)
195 COG1522 Lrp Transcriptional re 23.3 65 0.0014 29.9 2.6 51 665-723 6-56 (154)
196 TIGR01714 phage_rep_org_N phag 23.2 1.1E+02 0.0024 27.4 3.8 49 562-613 28-84 (119)
197 PLN03239 histone acetyltransfe 23.0 1.2E+02 0.0025 32.5 4.6 38 564-601 267-308 (351)
198 TIGR02716 C20_methyl_CrtF C-20 22.7 1.1E+02 0.0024 32.1 4.6 35 576-613 22-56 (306)
199 PF14493 HTH_40: Helix-turn-he 22.7 1.8E+02 0.0038 24.5 4.9 36 568-605 6-41 (91)
200 TIGR02147 Fsuc_second hypothet 22.6 2E+02 0.0043 29.9 6.2 34 578-614 138-173 (271)
201 PF00392 GntR: Bacterial regul 22.6 49 0.0011 25.7 1.4 29 696-724 31-59 (64)
202 PRK09333 30S ribosomal protein 22.6 1.2E+02 0.0027 28.2 4.1 50 564-616 54-117 (150)
203 PHA03103 double-strand RNA-bin 22.3 1.9E+02 0.004 28.1 5.4 43 568-613 18-60 (183)
204 COG2188 PhnF Transcriptional r 22.3 55 0.0012 33.2 2.0 36 694-730 36-71 (236)
205 PHA02591 hypothetical protein; 22.2 1E+02 0.0022 25.2 2.9 25 576-600 58-82 (83)
206 TIGR02787 codY_Gpos GTP-sensin 22.1 1.6E+02 0.0035 29.8 5.1 44 568-614 188-232 (251)
207 PF04760 IF2_N: Translation in 22.1 53 0.0011 24.6 1.4 22 577-598 3-24 (54)
208 cd07377 WHTH_GntR Winged helix 21.8 69 0.0015 24.4 2.1 28 696-723 32-59 (66)
209 TIGR02989 Sig-70_gvs1 RNA poly 21.5 1.4E+02 0.0031 27.5 4.6 37 561-599 112-149 (159)
210 COG2771 CsgD DNA-binding HTH d 21.1 2.3E+02 0.005 21.4 5.0 42 560-603 4-45 (65)
211 PLN00104 MYST -like histone ac 20.9 1.4E+02 0.003 33.3 4.7 37 565-601 361-398 (450)
212 KOG4481 Uncharacterized conser 20.8 1.3E+02 0.0028 28.5 3.8 64 533-602 95-160 (194)
213 PF01475 FUR: Ferric uptake re 20.8 95 0.0021 27.5 3.0 58 671-731 12-70 (120)
214 TIGR02018 his_ut_repres histid 20.7 63 0.0014 32.4 2.1 33 697-730 33-65 (230)
215 PF13551 HTH_29: Winged helix- 20.5 1.8E+02 0.004 24.9 4.8 38 567-605 3-40 (112)
216 PF10668 Phage_terminase: Phag 20.3 1.4E+02 0.003 23.3 3.3 22 574-595 19-40 (60)
217 PRK09764 DNA-binding transcrip 20.3 68 0.0015 32.5 2.2 33 697-730 37-69 (240)
218 PF13936 HTH_38: Helix-turn-he 20.3 1.8E+02 0.0038 20.8 3.7 31 568-599 12-42 (44)
219 PRK15431 ferrous iron transpor 20.1 1.3E+02 0.0028 24.7 3.3 32 574-605 13-44 (78)
220 PF03965 Penicillinase_R: Peni 20.1 1.3E+02 0.0028 26.6 3.7 49 562-613 2-54 (115)
221 smart00346 HTH_ICLR helix_turn 20.0 1.3E+02 0.0028 24.9 3.5 44 673-724 11-55 (91)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.3e-115 Score=985.79 Aligned_cols=700 Identities=42% Similarity=0.715 Sum_probs=646.1
Q ss_pred ChhhHHHHHHHHHHHHHHHHhhCCCCCcHHHHHHHHhhhccCCch----HHHHHHHHHHHHHHHHHHH-HHHHhhhhHHH
Q 004725 21 DPKYAEKTWKILEHAIHEIYNHNASGLSFEELYRNAYNMVLHKFG----EKLYSGLVTTMTFHLTEIC-KSIEAAQGGLF 95 (733)
Q Consensus 21 ~~~~~~~~W~~l~~~i~~I~~~~~~~~s~~~lY~~vy~lc~~~~~----~~LY~~l~~~i~~~~~~i~-~~l~~~~~~~~ 95 (733)
+..+++++|..|..+++.+-+......+|+.+|+++|++|.++++ +.||.++++.+.+|+.+++ +.+....++.+
T Consensus 13 ~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~~~~~~~~~ 92 (725)
T KOG2166|consen 13 GWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPALREKHDEYM 92 (725)
T ss_pred cHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHH
Confidence 346667777777777663332223567899999999999999988 9999999999999999955 55556667889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhccccCC-CCCcHHHHH-HHHHHHHHhcchhhHHHHHHHHHHHHHHHhcCCCCC
Q 004725 96 LEELNRKWADHNKALQMIRDILMYMDRTFIPST-HKTPVHELG-LNLWRDVVIHSSKIQTRLQDTLLELVQRERSGEVIN 173 (733)
Q Consensus 96 L~~~~~~W~~~~~~~~~l~~if~YLDr~yv~~~-~~~~i~~~~-l~~f~~~v~~~~~l~~~l~~~il~~I~~~R~g~~i~ 173 (733)
|..+...|.+|+.++.+++++|+||||+|+.++ +..++.+++ +.+|+..++.. ++.++++++++.+|..+|.|+.+|
T Consensus 93 l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~-~~~~~~~~all~lI~~eR~ge~in 171 (725)
T KOG2166|consen 93 LRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKF-EMQSEAIDALLALIHKEREGEQID 171 (725)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHH-HHHHHHHHHHHHHHHhhccccccc
Confidence 999999999999999999999999999999975 666666666 99999999874 599999999999999999999999
Q ss_pred hHHHHHHHHHHHHhC---cccchhhhhHhHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHhhccChhhHHH
Q 004725 174 RGLMRNITKMLMDLG---SFVYQDDFEKHFLEVSADFYRLESQEFIESCDCGDYLKKAERRLNEEMERVSHYLDARSEAK 250 (733)
Q Consensus 174 ~~~lk~ii~~l~~lg---~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~ 250 (733)
+..|+++++++..+| .++|..+||++|++.|..||..++..|+...++++|+.+++.++.+|..|+..|++..+-++
T Consensus 172 ~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~ 251 (725)
T KOG2166|consen 172 RELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEPK 251 (725)
T ss_pred HHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccch
Confidence 999999999999998 67999999999999999999999999999889999999999999999999999999888888
Q ss_pred HHHHHHHHHHHHHHHHHHhcchhhhHHhHccCcHhHHHHHHHhhccCCCChHHHHHHHHHHHHHHHhHhhcCcccC--CC
Q 004725 251 ITNVVEKEMIESHMNRLVHMENSGLVNMLVDDKYEDLGRMYCLFRRVPSGLILIRDVMTSYIRDTGKQLVSDPERL--KD 328 (733)
Q Consensus 251 l~~~~~~~Li~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~--~~ 328 (733)
+...++..++..+.+.+++..++|+..|+++++.++|.+||+++++++.|++.+++.+..|++.+|..++.....+ .+
T Consensus 252 ~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~~~~ 331 (725)
T KOG2166|consen 252 LVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETAATN 331 (725)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhcccc
Confidence 8999999999999999988889999999999999999999999999999999999999999999998888766544 68
Q ss_pred chHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhhcCCCCch-HHHHHHHHHHhhcCCCCCChHHHHHHHHhHh
Q 004725 329 PVDFVQRLLDLKDKYDKVINSAFNNDKTFQNALNSSFEYFINLNSRSP-EFISLFVDDKLRKGLRGVSEEDVENVLDKVM 407 (733)
Q Consensus 329 ~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~ln~~~~~~-e~La~y~D~~l~~~~~~~~~~~~e~~l~~i~ 407 (733)
|..+++.++++++++..++..||+++..|.++++.||..|+|.+..++ |+||.|||.++|+|.++.++++++..+++++
T Consensus 332 ~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~ 411 (725)
T KOG2166|consen 332 PVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKVV 411 (725)
T ss_pred hHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhcce
Confidence 999999999999999999999999999999999999999999877666 9999999999999888899999999999999
Q ss_pred hhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhhCchhhhhHHHHHhhHHHHHHHHHHHHhhhhcCCC
Q 004725 408 MLFRFLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMQGFYASLGAESG 487 (733)
Q Consensus 408 ~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~ 487 (733)
.+|+|+.+||+|+.+|++.||+|||+++|.|+++|+.||.+|++.||.+||.+|++|++|+..|++++..|.++...+..
T Consensus 412 ~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~~~~~~~ 491 (725)
T KOG2166|consen 412 KLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADYANYSAN 491 (725)
T ss_pred eeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhhhchhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999975201112
Q ss_pred CCCceEEEEecCCCCCCCCCCCCCCcHHHHHHHHHHHHHHhccCCCceeEeecCcceEEEEEeeCCCceEEEEeeHHHHH
Q 004725 488 DSPTLTVQVLTTGSWPTQPSATCNLPAEIMGICEKFRSYYLGTHTGRRLTWQTNMGTADLKGTFGKGQKHELNVSTYQMC 567 (733)
Q Consensus 488 ~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~~l~~s~~Qa~ 567 (733)
.+++|.|.|||+|+||.+++.++.||++|.++++.|+.||..+|+||+|+|+|++|+++|.++|.+ ++++++||++||+
T Consensus 492 ~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~-~~~~l~vst~Qm~ 570 (725)
T KOG2166|consen 492 LGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDK-KTVELQVSTYQMA 570 (725)
T ss_pred CCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecC-ceEEEEEEhHHHH
Confidence 369999999999999998888899999999999999999999999999999999999999999997 7999999999999
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCcCCcceEEeccccccC
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFTSKFVKVKIGTVVAQR 647 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~~~~~ki~i~~~~~~~ 647 (733)
||++||+.+.+|+++|.+.|+++.+++.++|+||++.|.. ++.. |.++. ++++.|.+|.+|+++..|++++.++.+
T Consensus 571 VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~-v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~- 646 (725)
T KOG2166|consen 571 VLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYK-ILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMD- 646 (725)
T ss_pred HHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHh-hccC-ccccC-CCCcEEEeeccccCcceeeccCCCCch-
Confidence 9999999999999999999999999999999999887744 6666 66666 899999999999999999999863332
Q ss_pred CCchhhHHHHHHHHhhhhhhhhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCc
Q 004725 648 ESEPENQETRQRVEEDRKPQIEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRK 727 (733)
Q Consensus 648 ~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~ 727 (733)
+.+.+.+.+++||+..|+||||||||+||.+.|++|+.+|.+|+++||.|++.+||+|||.|||||||+|| +|++
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 77788999999999999999999999999999999999999999999999999999999999999999999 8999
Q ss_pred ceee
Q 004725 728 LYRY 731 (733)
Q Consensus 728 ~y~Y 731 (733)
+|+|
T Consensus 722 ~Y~Y 725 (725)
T KOG2166|consen 722 IYRY 725 (725)
T ss_pred cccC
Confidence 9998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.5e-113 Score=923.68 Aligned_cols=714 Identities=34% Similarity=0.568 Sum_probs=639.0
Q ss_pred cceecCCCCCCCChhhHHHHHHHHHHHHHHHHhhC---CCCCcHHHHHHHHhhhccCC----------------chHHHH
Q 004725 9 FQIEAFKHRVVVDPKYAEKTWKILEHAIHEIYNHN---ASGLSFEELYRNAYNMVLHK----------------FGEKLY 69 (733)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~W~~l~~~i~~I~~~~---~~~~s~~~lY~~vy~lc~~~----------------~~~~LY 69 (733)
++|.-++. +.+++.|+..|+.+++||..|+... ...++|+++|+.+|+.|.++ .++.||
T Consensus 6 ~ki~vp~~--~~~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li 83 (773)
T COG5647 6 IKIDVPRK--TLSEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLI 83 (773)
T ss_pred cccccCcc--CCchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHH
Confidence 44444443 5667779999999999999999544 35688999999999999986 467788
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccc-----CCCCCcHHHHHHHHHHHH
Q 004725 70 SGLVTTMTFHLTEICKSIEAAQGGLFLEELNRKWADHNKALQMIRDILMYMDRTFIP-----STHKTPVHELGLNLWRDV 144 (733)
Q Consensus 70 ~~l~~~i~~~~~~i~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLDr~yv~-----~~~~~~i~~~~l~~f~~~ 144 (733)
+++.....+++.....+......+.+|..++..|.+|+.++.++..+|.||||+|++ ......+.++++..|+-.
T Consensus 84 ~~L~~~~k~~i~~~~~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~ 163 (773)
T COG5647 84 QKLVDYAKNYIEEYNRGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIE 163 (773)
T ss_pred HHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHH
Confidence 888888888887644332223447999999999999999999999999999999999 234557778999999999
Q ss_pred HhcchhhHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHhC---------cccchhhhhHhHHHHHHHHHHHHHHHH
Q 004725 145 VIHSSKIQTRLQDTLLELVQRERSGEVINRGLMRNITKMLMDLG---------SFVYQDDFEKHFLEVSADFYRLESQEF 215 (733)
Q Consensus 145 v~~~~~l~~~l~~~il~~I~~~R~g~~i~~~~lk~ii~~l~~lg---------~~~Y~~~FE~~~L~~t~~yY~~~s~~~ 215 (733)
+|. .+.+.+++.++..+.+.|.|+.+|+..+..++.|+..++ .++|.+.||+.||+.|..||..++++.
T Consensus 164 ~f~--~i~~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~ 241 (773)
T COG5647 164 SFR--LIVDSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEV 241 (773)
T ss_pred HHH--hhhHHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHH
Confidence 999 999999999999999999999999999999999999994 368999999999999999999999999
Q ss_pred HhhCCHHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHHHHHHHhcchhhhHHhHccCcHhHHHHHHHhhc
Q 004725 216 IESCDCGDYLKKAERRLNEEMERVSHYLDARSEAKITNVVEKEMIESHMNRLVHMENSGLVNMLVDDKYEDLGRMYCLFR 295 (733)
Q Consensus 216 l~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~l~~ 295 (733)
+..+++.+||.+|+.++++|.+++..|++.++..++..+++++||..|.+.+.+. .+|+..+++..+.+.|..+|++++
T Consensus 242 i~~~~~~eyL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~-~s~f~~~~d~~~~e~l~~lY~l~s 320 (773)
T COG5647 242 IELLSVTEYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQ-GSGFREALDASNLEKLQVLYRLLS 320 (773)
T ss_pred HHHcCHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhc-hHHHHHHHHhhhHHHHHHHHHHhh
Confidence 9999999999999999999999999999999999999999999999999999876 379999999999999999999999
Q ss_pred cCCCChHHHHHHHHHHHHHHH---hH----hhcCcc-------cCCCchHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHH
Q 004725 296 RVPSGLILIRDVMTSYIRDTG---KQ----LVSDPE-------RLKDPVDFVQRLLDLKDKYDKVINSAFNNDKTFQNAL 361 (733)
Q Consensus 296 ~~~~~l~~l~~~~~~~i~~~g---~~----~~~~~~-------~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l 361 (733)
+.+.++.+|++.|.+||+..| .. ++.... ....|..+++.++++++.+..++.+.|.+|..+.+++
T Consensus 321 e~~~~v~pl~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l 400 (773)
T COG5647 321 ETKYGVQPLQEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKAL 400 (773)
T ss_pred hhhhhhhhHHHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHH
Confidence 999999999999999999999 11 111111 1126789999999999999999999999999999999
Q ss_pred HHHHHHhhcC----CCCchHHHHHHHHHHhhcCCCCCChHHHHHHHHhHhhhhccccchHHHHHHHHHHHHhHhcCCCCC
Q 004725 362 NSSFEYFINL----NSRSPEFISLFVDDKLRKGLRGVSEEDVENVLDKVMMLFRFLQEKDVFEKYYKQHLAKRLLSGKTV 437 (733)
Q Consensus 362 ~~af~~~ln~----~~~~~e~La~y~D~~l~~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~ 437 (733)
++||+.|+|+ +..++|+||+|+|.+++++.+..-...++..+.+++.||+|+.+||+|+.+|+++||||||+++|.
T Consensus 401 ~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~ 480 (773)
T COG5647 401 GNAFKTFINGNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSA 480 (773)
T ss_pred HHHHHHHhccccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCc
Confidence 9999999997 247899999999999999876554556788889999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHhhCchhhhhHHHHHhhHHHHHHHHHHHHhhhhcCCCCCCceEEEEecCCCCCCC-CCCCCCCcHHH
Q 004725 438 SDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMQGFYASLGAESGDSPTLTVQVLTTGSWPTQ-PSATCNLPAEI 516 (733)
Q Consensus 438 ~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~VLt~~~WP~~-~~~~~~lP~~l 516 (733)
+.++|..||++||+.||.+||+|+++||+||..|.++...|++...+.+ ..+++.|.||+..+||.. +...+.||++|
T Consensus 481 s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s~~-~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l 559 (773)
T COG5647 481 SAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQSYN-KYLDLFVWVLTQAYWPLSPEEVSIRLPKEL 559 (773)
T ss_pred chHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchhhc-cccchhHHHHHHhcCCCCccccccCCChHH
Confidence 9999999999999999999999999999999999999999987541222 258999999999999954 56899999999
Q ss_pred HHHHHHHHHHHhccCCCceeEeecCcceEEEEEeeCCCc-eEEEE-eeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHH
Q 004725 517 MGICEKFRSYYLGTHTGRRLTWQTNMGTADLKGTFGKGQ-KHELN-VSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPEL 594 (733)
Q Consensus 517 ~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~-~~~l~-~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l 594 (733)
.+.++.|++||.+||+||+|+|.|+||+|+|+++|+.|+ .+.+. ++++|+.|+++||+++++|+++|.+.|+++.+++
T Consensus 560 ~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl 639 (773)
T COG5647 560 VPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDL 639 (773)
T ss_pred HHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhH
Confidence 999999999999999999999999999999999999852 23333 6788999999999999999999999999999999
Q ss_pred HHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCcCCcceEEeccccccCCCchhhHHHHHHHHhhhhhhhhhheeh
Q 004725 595 KRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFTSKFVKVKIGTVVAQRESEPENQETRQRVEEDRKPQIEAAIVR 674 (733)
Q Consensus 595 ~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~~~~~ki~i~~~~~~~~~~~e~~~~~~~~~~~r~~~i~A~IVR 674 (733)
+++|+||++++ ++...++++.++|++.|.+|.+|+++..+|+++.+..+ +..+++..+++.+++||+..+||+|||
T Consensus 640 ~~~L~sl~~ak---~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~-~~~q~~~~~h~~v~edR~~~lqA~IVR 715 (773)
T COG5647 640 KRVLQSLSCAK---LVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAES-ECMQDNLDTHETVEEDRQAELQACIVR 715 (773)
T ss_pred HHHHHHHHhhh---eeeeccccccCCCCceEEEccccccccceeeecccccc-hhhccchhhHHHHHHHHHHHHHHHHHH
Confidence 99999999998 55445557889999999999999999999999986544 333466677899999999999999999
Q ss_pred hcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 675 IMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 675 imK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
|||+||+|+|++|+++|+.+.++||.|++.+||++|+.|||||||+|.++| .+|+|+|
T Consensus 716 IMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 716 IMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred HHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999999999999999999999999999999999999999999888 7999997
No 3
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.1e-111 Score=888.76 Aligned_cols=650 Identities=42% Similarity=0.703 Sum_probs=612.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh--hhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccC-CC-CCcHHHHHHHHHH
Q 004725 67 KLYSGLVTTMTFHLTEICKSIEA--AQGGLFLEELNRKWADHNKALQMIRDILMYMDRTFIPS-TH-KTPVHELGLNLWR 142 (733)
Q Consensus 67 ~LY~~l~~~i~~~~~~i~~~l~~--~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLDr~yv~~-~~-~~~i~~~~l~~f~ 142 (733)
.||..|+..++.|+.+-+.++.. .+...+|..+.++|..|+..+..++++|.||||.|+.. ++ .+|+|++|+.+|+
T Consensus 1 ~ly~~l~~~~~~~~~~~~~q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp~v~siWem~l~LFR 80 (661)
T KOG2167|consen 1 VLYKQLRQICEQHIKAQIEQLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNPYVLSIWEMGLQLFR 80 (661)
T ss_pred ChHHHHHHHHHHHHHHHHhhCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCCCcCCHHHhhHHHHH
Confidence 38999999999999974444432 22367999999999999999999999999999999998 43 7899999999999
Q ss_pred HHHhc--chhhHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHhCcccchhhhhHhHHHHHHHHHHHHHHHHHhhCC
Q 004725 143 DVVIH--SSKIQTRLQDTLLELVQRERSGEVINRGLMRNITKMLMDLGSFVYQDDFEKHFLEVSADFYRLESQEFIESCD 220 (733)
Q Consensus 143 ~~v~~--~~~l~~~l~~~il~~I~~~R~g~~i~~~~lk~ii~~l~~lg~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~ 220 (733)
.+++. .|.+..+..++++..++++|.|+++|+.+++.++.|+.+++ .|.+.|++.|++.+..+|.++.....++..
T Consensus 81 ~~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~~--iY~esF~~~fls~f~~lY~aE~~d~~Qel~ 158 (661)
T KOG2167|consen 81 AHFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDLQ--IYKESFELTFLSLFRELYAAEGQDKRQELE 158 (661)
T ss_pred HHhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHH--hhhhhhHHHHHHHHHHHHHHHhcchhhhcc
Confidence 99999 77888999999999999999999999999999999999986 899999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHHHHHHHhcchhhhHHhHccCcHhHHHHHHHhhccCCCC
Q 004725 221 CGDYLKKAERRLNEEMERVSHYLDARSEAKITNVVEKEMIESHMNRLVHMENSGLVNMLVDDKYEDLGRMYCLFRRVPSG 300 (733)
Q Consensus 221 ~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~l~~~~~~~ 300 (733)
+++||++++..+.+|..++..+++.+|...+..+++..|+..|++.++.+ |+..+++.++..++.++|.|++++..+
T Consensus 159 v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~k---gl~~lvDm~q~~d~~rly~L~~r~~~g 235 (661)
T KOG2167|consen 159 VPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTK---GLDSLVDMRQTSDLTRLYMLFSRVQGG 235 (661)
T ss_pred cHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhc---chHHhhhhhhccchHhHHHHHHHHhcc
Confidence 99999999999999999999999988877799999999999999999976 899999999999999999999999888
Q ss_pred hHHHHHHHHHHHHHHHhHhhcCcccCCCchHHHHHHHHHHHHHHHHHHHhcCCc--HHHHHHHHHHHHHhhcC-CCCchH
Q 004725 301 LILIRDVMTSYIRDTGKQLVSDPERLKDPVDFVQRLLDLKDKYDKVINSAFNND--KTFQNALNSSFEYFINL-NSRSPE 377 (733)
Q Consensus 301 l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~--~~f~~~l~~af~~~ln~-~~~~~e 377 (733)
...++..|++|+++.|.+++.+... ...++..++.|+++.+-++..||-.+ ..|..++++||+.|+|. .+++||
T Consensus 236 ~l~l~qq~sdylk~~G~KlV~de~k---Dk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fink~~~rpAe 312 (661)
T KOG2167|consen 236 QLSLLQQWSDYLKKPGFKLVIDEEK---DKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFINKRRNRPAE 312 (661)
T ss_pred hHHHHHHHHHHHhcccceeccCchh---hHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHhcccCCHHH
Confidence 8899999999999999999987654 48999999999999999999999888 99999999999999996 568999
Q ss_pred HHHHHHHHHhhcCCCCCChHHHHHHHHhHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhhCchh
Q 004725 378 FISLFVDDKLRKGLRGVSEEDVENVLDKVMMLFRFLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQF 457 (733)
Q Consensus 378 ~La~y~D~~l~~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~ 457 (733)
+||+|.|..|+.|+++.++++++..++.++.||+|+..||+|+.+|++.||+|||.++|++.|+|..|+.+|+.+||..|
T Consensus 313 lIak~~dt~Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~f 392 (661)
T KOG2167|consen 313 LIAKYVDTKLRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAF 392 (661)
T ss_pred HHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHhhHHHHHHHHHHHHhhhhcCCC--CCCceEEEEecCCCCCCCCCCCCCCcHHHHHHHHHHHHHHhccCCCce
Q 004725 458 TSKLEGMFTDMKTSQDTMQGFYASLGAESG--DSPTLTVQVLTTGSWPTQPSATCNLPAEIMGICEKFRSYYLGTHTGRR 535 (733)
Q Consensus 458 ~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~--~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~ 535 (733)
|++|++|++|+..|++++..|+++.+.++. .++ +.+.|+|.++||++++.++.||++|..+++.|..||-.+|.||+
T Consensus 393 t~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrk 471 (661)
T KOG2167|consen 393 TYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRK 471 (661)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHHHHHHHhccccccCcc
Confidence 999999999999999999999998543332 234 99999999999999999999999999999999999999999999
Q ss_pred eEeecCcceEEEEEeeCCCceEEEEeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCC
Q 004725 536 LTWQTNMGTADLKGTFGKGQKHELNVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPM 615 (733)
Q Consensus 536 L~w~~~l~~~~i~~~~~~~~~~~l~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~ 615 (733)
|.|++++|+|.+++.|+. |++++.+|++|++||++||+++++|++||.+.|||.+.+|.++|+||.+++.+ +|.+.|.
T Consensus 472 lqW~~~lg~~v~ka~f~~-gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~r-vl~~~pk 549 (661)
T KOG2167|consen 472 LQWQDSLGHCVLKAEFKE-GKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRAR-VLQKVPK 549 (661)
T ss_pred eeeecCCcchhhhhhccC-CchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccce-eeeeCCC
Confidence 999999999999999998 68999999999999999999999999999999999999999999999999888 9999999
Q ss_pred CCCCCCCCeEeecccCcCCcceEEeccccccCCCchhhHHHHHHHHhhhhhhhhhheehhcccCCCCChHHHHHHHHHHh
Q 004725 616 SKDIAEDDAFFFNDKFTSKFVKVKIGTVVAQRESEPENQETRQRVEEDRKPQIEAAIVRIMKARRVLDHNNIVTEVTKQL 695 (733)
Q Consensus 616 ~~~~~~~~~f~~N~~f~~~~~ki~i~~~~~~~~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l 695 (733)
|+.+.+++.|.+|..|+.+..||+|+++ +.+++.+|+.+|.++|.+||++.||||||||||+||+|+|+.|++++.+++
T Consensus 550 g~~~~~~~~f~~n~~f~~kl~rikinqi-~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~ql 628 (661)
T KOG2167|consen 550 GKEVEDGDKFIVNDKFTHKLYRIKINQI-QMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQL 628 (661)
T ss_pred CCCCCCCCEEEechhhcchhheehHhhh-hHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhc
Confidence 9999999999999999999999999985 445777888899999999999999999999999999999999999999999
Q ss_pred ccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 696 QSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 696 ~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
+ ||..+ ++|+|||+||+|||++|| +| +.|.|||
T Consensus 629 k--fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 629 K--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred C--CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 7 99998 999999999999999999 45 8999998
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-103 Score=791.88 Aligned_cols=675 Identities=27% Similarity=0.527 Sum_probs=625.0
Q ss_pred CCCCCChhhHHHHHHHHHHHHHHHHhhCC-CCCcHHHHHHHHhhhccC---CchHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 004725 16 HRVVVDPKYAEKTWKILEHAIHEIYNHNA-SGLSFEELYRNAYNMVLH---KFGEKLYSGLVTTMTFHLTEICKSIEAAQ 91 (733)
Q Consensus 16 ~~~~~~~~~~~~~W~~l~~~i~~I~~~~~-~~~s~~~lY~~vy~lc~~---~~~~~LY~~l~~~i~~~~~~i~~~l~~~~ 91 (733)
.|+.++ |+..|..|-+.|..|..-.+ .+..|..-|+.||.+|.. +-|+.||...+.+|++|++.-+...-..+
T Consensus 5 kp~vv~---fd~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v~~~ 81 (728)
T KOG2284|consen 5 KPKVVE---FDKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIVDVD 81 (728)
T ss_pred Cceeee---HHHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhhcCC
Confidence 357789 99999999999999998776 567899999999999986 47999999999999999997454443445
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCCC---------------CC---cHHHHHHHHHHHHHhcchhhHH
Q 004725 92 GGLFLEELNRKWADHNKALQMIRDILMYMDRTFIPSTH---------------KT---PVHELGLNLWRDVVIHSSKIQT 153 (733)
Q Consensus 92 ~~~~L~~~~~~W~~~~~~~~~l~~if~YLDr~yv~~~~---------------~~---~i~~~~l~~f~~~v~~~~~l~~ 153 (733)
.+.+|..|++-|+.|..+..++..+|.||+..|++.+. .+ .|..+|+.+|++.+.. ++..
T Consensus 82 p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~--~i~~ 159 (728)
T KOG2284|consen 82 PDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVK--TILP 159 (728)
T ss_pred HHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHH--HHHH
Confidence 46799999999999999999999999999999998742 22 4567889999999999 9999
Q ss_pred HHHHHHHHHHHHHhcCCCCC-hHHHHHHHHHHHHhC--------------------cccchhhhhHhHHHHHHHHHHHHH
Q 004725 154 RLQDTLLELVQRERSGEVIN-RGLMRNITKMLMDLG--------------------SFVYQDDFEKHFLEVSADFYRLES 212 (733)
Q Consensus 154 ~l~~~il~~I~~~R~g~~i~-~~~lk~ii~~l~~lg--------------------~~~Y~~~FE~~~L~~t~~yY~~~s 212 (733)
.|+.-++..|.++|.|+..+ ...+.+++..|+.+. ..+|++.||+|||.+|..||++++
T Consensus 160 ~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a 239 (728)
T KOG2284|consen 160 QLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALA 239 (728)
T ss_pred HHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHH
Confidence 99999999999999999888 678889999888652 257999999999999999999999
Q ss_pred HHHHhhCCHHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHHHHHHHhcchhhhHHhHccCcHhHHHHHHH
Q 004725 213 QEFIESCDCGDYLKKAERRLNEEMERVSHYLDARSEAKITNVVEKEMIESHMNRLVHMENSGLVNMLVDDKYEDLGRMYC 292 (733)
Q Consensus 213 ~~~l~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~ 292 (733)
+..+++.++++|+.+|..++++|+-||..||++++..+++..|++.+|.+|.+.+ +..|..++.+.+..|++.||.
T Consensus 240 ~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~~d~~nmy~ 315 (728)
T KOG2284|consen 240 QKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEENKDLRNMYR 315 (728)
T ss_pred HHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhhhHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999 668999999999999999999
Q ss_pred hhccCCCChHHHHHHHHHHHHHHHhHhhcCcccCCCchHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhhcC-
Q 004725 293 LFRRVPSGLILIRDVMTSYIRDTGKQLVSDPERLKDPVDFVQRLLDLKDKYDKVINSAFNNDKTFQNALNSSFEYFINL- 371 (733)
Q Consensus 293 l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~ln~- 371 (733)
|+..+..|++.+...|++||...|.+.++.......|..||+.++.+|.+|..++...|.+|..|..+++.|+..++|.
T Consensus 316 ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~ 395 (728)
T KOG2284|consen 316 LLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSK 395 (728)
T ss_pred HHHHHhcCchHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccC
Confidence 9999999999999999999999999999877766789999999999999999999999999999999999999999995
Q ss_pred -----CCCchHHHHHHHHHHhhcCCCCCChHHHHHHHHhHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHH
Q 004725 372 -----NSRSPEFISLFVDDKLRKGLRGVSEEDVENVLDKVMMLFRFLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLI 446 (733)
Q Consensus 372 -----~~~~~e~La~y~D~~l~~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i 446 (733)
-.+.+|.||+|||.+++++.+++++.++|.+|+..+.+|+|++|||+|.++|.+.||+||+.+.|.|.|.|..||
T Consensus 396 epg~sv~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~mi 475 (728)
T KOG2284|consen 396 EPGQSVPKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMI 475 (728)
T ss_pred CCCccccchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHH
Confidence 258899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCchhhhhHHHHHhhHHHHHHHHHHHHhhhhcCCCCCCceEEEEecCCCCCCCCCCCCCCcHHHHHHHHHHHHH
Q 004725 447 VKLKTECGYQFTSKLEGMFTDMKTSQDTMQGFYASLGAESGDSPTLTVQVLTTGSWPTQPSATCNLPAEIMGICEKFRSY 526 (733)
Q Consensus 447 ~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~ 526 (733)
++|++.||.+||+++- +.|+..|.+++++|.+.+ . ++.+|.+|+...+.|+.|
T Consensus 476 nklkqacgyefts~~~--~td~~~s~~lnn~f~~~i-~------------------------nf~~pq~l~~~iq~fe~f 528 (728)
T KOG2284|consen 476 NKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDI-A------------------------NFHLPQILQPVIQEFEKF 528 (728)
T ss_pred HHHHHHhCceecccCC--CCChhhccccchhHHHHH-H------------------------hccchHHHHHHHHHHHHH
Confidence 9999999999999988 999999999999998876 1 178999999999999999
Q ss_pred HhccCCCceeEeecCcceEEEEEeeCCCceEEEEeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccC
Q 004725 527 YLGTHTGRRLTWQTNMGTADLKGTFGKGQKHELNVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKG 606 (733)
Q Consensus 527 Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~~l~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~ 606 (733)
|..+|+||+|+|++.+++++++++|-+ +.|.-.++++||++||+||..+.+++.+|.+.+|++.+++.+.+.++.+.+
T Consensus 529 yt~~~~grkltwl~~~~~g~v~~~yl~-k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~tildv~- 606 (728)
T KOG2284|consen 529 YTGKHNGRKLTWLFNMSQGDVRLTYLD-KQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTILDVT- 606 (728)
T ss_pred hccccCCceehhhhhhcccceeeeecC-chHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHHhce-
Confidence 999999999999999999999999996 899999999999999999999999999999999999999999999999988
Q ss_pred cceeeccCCCCCCCCCCeEeecccCcCCcceEEeccccccCCCchhhHHHHHHHHhhhhhhhhhheehhcccCCCCChHH
Q 004725 607 KHVLRKEPMSKDIAEDDAFFFNDKFTSKFVKVKIGTVVAQRESEPENQETRQRVEEDRKPQIEAAIVRIMKARRVLDHNN 686 (733)
Q Consensus 607 ~~iL~~~~~~~~~~~~~~f~~N~~f~~~~~ki~i~~~~~~~~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~ 686 (733)
+|+.... .+..+..|++|.+|++++.|.++.+....+.+.+|.+.+...|.+||++.++||||||||+||.+.|+.
T Consensus 607 --~~~~d~~--~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hna 682 (728)
T KOG2284|consen 607 --LLTCDDQ--NLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNA 682 (728)
T ss_pred --eeccccc--ccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 8876543 567788999999999999999997644455666777788889999999999999999999999999999
Q ss_pred HHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 687 IVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 687 L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
|+++|+.|.+.||.|++++||++||.||++.||+|...+ +.|.|+|
T Consensus 683 lv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 683 LVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 999999999999999999999999999999999998765 8899997
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=2e-92 Score=819.85 Aligned_cols=580 Identities=41% Similarity=0.731 Sum_probs=530.2
Q ss_pred HHHHHHHHHHHHhhCCCCCcHHHHHHHHhhhccCCchHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 004725 29 WKILEHAIHEIYNHNASGLSFEELYRNAYNMVLHKFGEKLYSGLVTTMTFHLTEICKSIEAAQGGLFLEELNRKWADHNK 108 (733)
Q Consensus 29 W~~l~~~i~~I~~~~~~~~s~~~lY~~vy~lc~~~~~~~LY~~l~~~i~~~~~~i~~~l~~~~~~~~L~~~~~~W~~~~~ 108 (733)
|+.|++||+.|+.+..++.+|+.+|++||++|.+++|+.||+++++.+.+++..+++++....++++|..|...|.+|+.
T Consensus 1 W~~l~~~i~~i~~~~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~~~~l~~~~~~w~~~~~ 80 (588)
T PF00888_consen 1 WEILEEAIDQIFKKSISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNIIESLLSSSDEDLLEEYVQEWEKYKK 80 (588)
T ss_dssp HHHHHHHHHHHHTT-GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTCHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHcCCCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHH
Confidence 99999999999988888999999999999999999999999999999999999999998776778999999999999999
Q ss_pred HHHHHHHHhhhhhhccccCCCCCcHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHhC
Q 004725 109 ALQMIRDILMYMDRTFIPSTHKTPVHELGLNLWRDVVIHSSKIQTRLQDTLLELVQRERSGEVINRGLMRNITKMLMDLG 188 (733)
Q Consensus 109 ~~~~l~~if~YLDr~yv~~~~~~~i~~~~l~~f~~~v~~~~~l~~~l~~~il~~I~~~R~g~~i~~~~lk~ii~~l~~lg 188 (733)
++.+++++|+||||+|+.++ +|++.++. ++.+.++++++.+|.++|.|+.+|+.+++++++++.++|
T Consensus 81 ~~~~i~~if~yLdr~yv~~~-----------~f~~~v~~--~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~ 147 (588)
T PF00888_consen 81 AIKYISDIFSYLDRNYVKRN-----------LFREQVFK--PLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELG 147 (588)
T ss_dssp HHHHHHHHTHHHHHTSTTTT-----------HHHHHTTT--SHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhHhhhhhh-----------hHHHHHHH--HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccc
Confidence 99999999999999999876 99999999 799999999999999999999999999999999999997
Q ss_pred -cccchhhhhHhHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHHHHHH
Q 004725 189 -SFVYQDDFEKHFLEVSADFYRLESQEFIESCDCGDYLKKAERRLNEEMERVSHYLDARSEAKITNVVEKEMIESHMNRL 267 (733)
Q Consensus 189 -~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~l 267 (733)
..+|.+.||++|+++|.+||++++ +++.++.+|+++|+.++++|.+|+..|++++|.+++.+++.++||.+|.+.+
T Consensus 148 ~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l 224 (588)
T PF00888_consen 148 SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDEL 224 (588)
T ss_dssp HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHH
T ss_pred hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999999 6778999999999999999999999999999999999999999999999999
Q ss_pred HhcchhhhHHhHccCcHhHHHHHHHhhccCCCChHHHHHHHHHHHHHHHhHhhcCcccCCCchHHHHHHHHHHHHHHHHH
Q 004725 268 VHMENSGLVNMLVDDKYEDLGRMYCLFRRVPSGLILIRDVMTSYIRDTGKQLVSDPERLKDPVDFVQRLLDLKDKYDKVI 347 (733)
Q Consensus 268 l~~~~~~~~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~ 347 (733)
.+|+..|+++++.++|+++|+++++++++++.+++.|++||...|.++++.......+..+|+.+++++++++.++
T Consensus 225 ----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~ 300 (588)
T PF00888_consen 225 ----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLI 300 (588)
T ss_dssp ----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHH
T ss_pred ----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999999999999999999999999876544568899999999999999999
Q ss_pred HHhcCCcHHHHHHHHHHHHHhhcCC-CCchHHHHHHHHHHhhcCCCCCChHHHHHHHHhHhhhhccccchHHHHHHHHHH
Q 004725 348 NSAFNNDKTFQNALNSSFEYFINLN-SRSPEFISLFVDDKLRKGLRGVSEEDVENVLDKVMMLFRFLQEKDVFEKYYKQH 426 (733)
Q Consensus 348 ~~~F~~~~~f~~~l~~af~~~ln~~-~~~~e~La~y~D~~l~~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~ 426 (733)
.+||++++.|..++++||+.++|.. ..++++||+|||.+++++.++.++++.+..++.++.+|+|+++||+|+.+|+++
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 9999999999999999999999987 899999999999999998877888899999999999999999999999999999
Q ss_pred HHhHhcCCCCCChHHHHHHHHHHHHhhCchhhhhHHHHHhhHHHHHHHHHHHHhhhhcCCC-C--CCceEEEEecCCCCC
Q 004725 427 LAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMQGFYASLGAESG-D--SPTLTVQVLTTGSWP 503 (733)
Q Consensus 427 L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~-~--~~~~~~~VLt~~~WP 503 (733)
||+|||.+++.+.+.|..+|++|+.+||.+++++|++|++|+..|++++++|++.....+. . +++|+|.||++++||
T Consensus 381 L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp 460 (588)
T PF00888_consen 381 LAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWP 460 (588)
T ss_dssp HHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-
T ss_pred HHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCC
Confidence 9999999999999999999999999999999999999999999999999999988732211 1 789999999999999
Q ss_pred CCCCCC-CCCcHHHHHHHHHHHHHHhccCCCceeEeecCcceEEEEEeeCCCceEEEEeeHHHHHHHHHHhCCCCcCHHH
Q 004725 504 TQPSAT-CNLPAEIMGICEKFRSYYLGTHTGRRLTWQTNMGTADLKGTFGKGQKHELNVSTYQMCVLMLFNSIDRLSYKE 582 (733)
Q Consensus 504 ~~~~~~-~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~~l~~s~~Qa~iLl~Fn~~~~~t~~e 582 (733)
..+..+ +.+|++|+.+++.|++||+.+|+||+|+|++++|+|+|++++++ ++++++||++||+||++||+++++|+++
T Consensus 461 ~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~-~~~~l~~s~~q~~iLl~Fn~~~~~t~~e 539 (588)
T PF00888_consen 461 KYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNN-GKYELTVSTLQAAILLLFNDNDSLTVEE 539 (588)
T ss_dssp S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSS-SEEEEEEEHHHHHHHHGGGSSSEEEHHH
T ss_pred CCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecC-CceeEEeeHHHHHHHHHHccCCCccHHH
Confidence 887665 99999999999999999999999999999999999999999997 7899999999999999999999999999
Q ss_pred HHHHcCCChHHHHHHHHHhhhccCcceee--ccCCCCCCCCCCeEeecccCc
Q 004725 583 IEQATEIPAPELKRCLQSLACVKGKHVLR--KEPMSKDIAEDDAFFFNDKFT 632 (733)
Q Consensus 583 i~~~t~i~~~~l~~~L~~L~~~k~~~iL~--~~~~~~~~~~~~~f~~N~~f~ 632 (733)
|++.||+++++++++|.+|+..| +|. +.+++.++++++.|.+|.+|+
T Consensus 540 i~~~~~~~~~~l~~~L~~l~~~~---~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 540 ISEKTGISEEELKRALKSLVKSK---ILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp HHHHC---HHHHHHHHHCCCTTT---TCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHHHHCcCHHHHHHHHHHHHhCC---cceeecCCccCCCCCCCEEEeCCCCC
Confidence 99999999999999999999988 555 678889999999999999996
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.4e-86 Score=669.47 Aligned_cols=704 Identities=26% Similarity=0.474 Sum_probs=619.3
Q ss_pred ChhhHHHHHHHHHHHHHHHHhhCC-CCCcHHHHHHHHhhhccCC--chHHHHHHHHHHHHHHHHHHHHHHHhhh-hHHHH
Q 004725 21 DPKYAEKTWKILEHAIHEIYNHNA-SGLSFEELYRNAYNMVLHK--FGEKLYSGLVTTMTFHLTEICKSIEAAQ-GGLFL 96 (733)
Q Consensus 21 ~~~~~~~~W~~l~~~i~~I~~~~~-~~~s~~~lY~~vy~lc~~~--~~~~LY~~l~~~i~~~~~~i~~~l~~~~-~~~~L 96 (733)
|.+-|++.|+...+.+-+++...+ ++..|++||..||..|... .....|+.++..|.+++.....++...+ +..+|
T Consensus 9 ~r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d~aLL 88 (777)
T KOG2285|consen 9 DRDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTDGALL 88 (777)
T ss_pred chhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccccHHH
Confidence 345699999999999999999886 5677999999999999974 5678999999999999988666655444 46899
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhccccCC--------CCCcHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHhc
Q 004725 97 EELNRKWADHNKALQMIRDILMYMDRTFIPST--------HKTPVHELGLNLWRDVVIHSSKIQTRLQDTLLELVQRERS 168 (733)
Q Consensus 97 ~~~~~~W~~~~~~~~~l~~if~YLDr~yv~~~--------~~~~i~~~~l~~f~~~v~~~~~l~~~l~~~il~~I~~~R~ 168 (733)
..|...|.+|....+++.--|.-||.+-.... .-.+++.+.+..|.+++|. .++.++..+.+.++..+|.
T Consensus 89 ~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~--nIk~rLq~sAmklVhaER~ 166 (777)
T KOG2285|consen 89 IGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFM--NIKERLQVSAMKLVHAERD 166 (777)
T ss_pred HHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999998754432 1348899999999999999 8999999999999999999
Q ss_pred CCCCChHHHHHHHHHHHHhC------cccchhhhhHhHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHhhc
Q 004725 169 GEVINRGLMRNITKMLMDLG------SFVYQDDFEKHFLEVSADFYRLESQEFIESCDCGDYLKKAERRLNEEMERVSHY 242 (733)
Q Consensus 169 g~~i~~~~lk~ii~~l~~lg------~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~~~~~l~~E~~r~~~~ 242 (733)
|+.+|.+++-++-+.|+.|. ..+|++.||..||++|.+||+..+.+++++.++.+|+++|...+++|+.|+.+|
T Consensus 167 G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRY 246 (777)
T KOG2285|consen 167 GNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKRY 246 (777)
T ss_pred cchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHh
Confidence 99999999999999999985 468999999999999999999999999999999999999999999999999999
Q ss_pred cCh--hhHHHHHHHHHHHHHHHHHHHHHhcchhhhHHhHccCcHhHHHHHHHhhccCCCChHHHHHHHHHHHHHHHhHhh
Q 004725 243 LDA--RSEAKITNVVEKEMIESHMNRLVHMENSGLVNMLVDDKYEDLGRMYCLFRRVPSGLILIRDVMTSYIRDTGKQLV 320 (733)
Q Consensus 243 l~~--~t~~~l~~~~~~~Li~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~ 320 (733)
|.. .+..+++..+...||.++.+.|+. .|..|+...+.+.|.+||+|+.+++.|++++...+..||...|..-+
T Consensus 247 LE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM 322 (777)
T KOG2285|consen 247 LEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADM 322 (777)
T ss_pred hccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHH
Confidence 976 588999999999999999999985 68899999999999999999999999999999999999999998655
Q ss_pred cC-ccc-CCCchHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhhcC---------------------CCCchH
Q 004725 321 SD-PER-LKDPVDFVQRLLDLKDKYDKVINSAFNNDKTFQNALNSSFEYFINL---------------------NSRSPE 377 (733)
Q Consensus 321 ~~-~~~-~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~ln~---------------------~~~~~e 377 (733)
-. .+. +.++..||+.|+.++++|..++.+.|.+|+.|..|-+.||+.++|. ..+.||
T Consensus 323 ~~aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpE 402 (777)
T KOG2285|consen 323 RNAAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPE 402 (777)
T ss_pred HhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHH
Confidence 33 222 2378999999999999999999999999999999999999999993 147899
Q ss_pred HHHHHHHHHhhcCC--CCCChHHHHHHHHhHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhhCc
Q 004725 378 FISLFVDDKLRKGL--RGVSEEDVENVLDKVMMLFRFLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGY 455 (733)
Q Consensus 378 ~La~y~D~~l~~~~--~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~ 455 (733)
+||.|||.++|+.. +.++.++++.+|++++-+++|+.+||+|+.+++.+|++||+...|+..+.|..|++.|+ +||.
T Consensus 403 LLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGM 481 (777)
T KOG2285|consen 403 LLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGM 481 (777)
T ss_pred HHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCC
Confidence 99999999999976 67899999999999999999999999999999999999999999999999999999998 5774
Q ss_pred --hhhhhHHHHHhhHHHHHHHHHHHHhhhhcC-CC-CCCceEEEEecCCCCCCC-CCCCCCCcHHHHHHHHHHHHHHhcc
Q 004725 456 --QFTSKLEGMFTDMKTSQDTMQGFYASLGAE-SG-DSPTLTVQVLTTGSWPTQ-PSATCNLPAEIMGICEKFRSYYLGT 530 (733)
Q Consensus 456 --~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~-~~-~~~~~~~~VLt~~~WP~~-~~~~~~lP~~l~~~~~~f~~~Y~~~ 530 (733)
+|.++|..|++|++.|++++..|+...... +. ..-.+++.||+.|.|... ....+.||.+|++.+-..+.||+.+
T Consensus 482 PaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~ 561 (777)
T KOG2285|consen 482 PADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKK 561 (777)
T ss_pred cHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcc
Confidence 799999999999999999999999876321 11 123678999999999964 3467899999999999999999999
Q ss_pred CCCceeEeecCcceEEEEEeeCCCceEEEEeeHHHHHHHHHHhC--CCCcCHHHHHHHcCCChHHHHHHHHHhhhc---c
Q 004725 531 HTGRRLTWQTNMGTADLKGTFGKGQKHELNVSTYQMCVLMLFNS--IDRLSYKEIEQATEIPAPELKRCLQSLACV---K 605 (733)
Q Consensus 531 ~~~R~L~w~~~l~~~~i~~~~~~~~~~~l~~s~~Qa~iLl~Fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~---k 605 (733)
|+||+|+|.|+++.++|++.-.- +.|++.|+++||+||.+||+ ++.+|++.+.-.|.+|+.++.+.|-||+.- |
T Consensus 562 hsgrkl~w~h~msNG~itf~n~~-GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k 640 (777)
T KOG2285|consen 562 HSGRKLQWYHHMSNGTITFVNNF-GRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMK 640 (777)
T ss_pred cCccchhhhhhccCCeeEeeccc-ccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhh
Confidence 99999999999999988543222 68999999999999999997 678999999999999999999999999874 3
Q ss_pred CcceeeccCC----CCCCCCCCeEeecccCcCC-----cceEEecccc-ccCCCchhhHHHHHHHHhhhhhhhhhheehh
Q 004725 606 GKHVLRKEPM----SKDIAEDDAFFFNDKFTSK-----FVKVKIGTVV-AQRESEPENQETRQRVEEDRKPQIEAAIVRI 675 (733)
Q Consensus 606 ~~~iL~~~~~----~~~~~~~~~f~~N~~f~~~-----~~ki~i~~~~-~~~~~~~e~~~~~~~~~~~r~~~i~A~IVRi 675 (733)
.. ||..+|+ .+++.+++.|.+|.+|.-- .++-+++-+. .+..+....++..+.+.+-|....|-+|++|
T Consensus 641 ~Q-iLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikI 719 (777)
T KOG2285|consen 641 YQ-ILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKI 719 (777)
T ss_pred hh-eeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHH
Confidence 34 7777765 3567888999999999631 1233333321 1122223334445677888999999999999
Q ss_pred cccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 676 MKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 676 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
||.||+++..+|..+.++.+++.|-|+..+||+.||.|||..|++||++|-++|.|+|
T Consensus 720 mK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 720 MKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 9999999999999999999999999999999999999999999999999999999997
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=2.5e-32 Score=255.31 Aligned_cols=140 Identities=49% Similarity=0.877 Sum_probs=131.0
Q ss_pred cccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhhCchhhhhHHHHHhhHHHHHHHHHHHHhhhhcC-CCCCC
Q 004725 412 FLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMQGFYASLGAE-SGDSP 490 (733)
Q Consensus 412 ~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~-~~~~~ 490 (733)
|+++||+|+.+|+++||+|||..++++.+.|..+|++|+.+||.+++++|++|++|+..|++++++|++..... ...++
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~~~~~~ 80 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNSNKPII 80 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999876321 23368
Q ss_pred ceEEEEecCCCCCCCCC-CCCCCcHHHHHHHHHHHHHHhccCCCceeEeecCcceEEEEEee
Q 004725 491 TLTVQVLTTGSWPTQPS-ATCNLPAEIMGICEKFRSYYLGTHTGRRLTWQTNMGTADLKGTF 551 (733)
Q Consensus 491 ~~~~~VLt~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~ 551 (733)
+|+|.|||+++||..+. .++.||++|+.+++.|++||..+|+||+|+|++++|+|+|+++|
T Consensus 81 ~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 81 DLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred ceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 99999999999998877 89999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=8.2e-25 Score=236.17 Aligned_cols=303 Identities=23% Similarity=0.296 Sum_probs=241.5
Q ss_pred hHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhhCchhhhhHHHHHhhHHHHHHHHHHHHhhh--
Q 004725 405 KVMMLFRFLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMQGFYASL-- 482 (733)
Q Consensus 405 ~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~-- 482 (733)
-+..+.+.+.+|+.|++.||.+||.||+....++.+.|..-++.||-.+|..-.+.|++|++|+..|+++++.++...
T Consensus 441 i~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~ 520 (765)
T KOG2165|consen 441 IFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESEL 520 (765)
T ss_pred HHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhh
Confidence 455667777899999999999999999999999999999999999999999999999999999999999999998742
Q ss_pred hcC--CCCCCceEEEEecCCCCCCCCCCCCCCcHHHHHHHHHHHHHHhccCCCceeEeecCcceEEEEEeeCCCceEEEE
Q 004725 483 GAE--SGDSPTLTVQVLTTGSWPTQPSATCNLPAEIMGICEKFRSYYLGTHTGRRLTWQTNMGTADLKGTFGKGQKHELN 560 (733)
Q Consensus 483 ~~~--~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~~l~ 560 (733)
..+ +...+.+++.+||+.+||......+.+|.+++..++.|.+-|.+...+|+|.|.+++|.|++++.|.+ ++.+++
T Consensus 521 ~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~D-Rtl~~t 599 (765)
T KOG2165|consen 521 SRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFED-RTLVLT 599 (765)
T ss_pred hcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcC-eEEEEe
Confidence 111 11247889999999999998888999999999999999999999999999999999999999999998 999999
Q ss_pred eeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCcCCcceEEe
Q 004725 561 VSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFTSKFVKVKI 640 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~~~~~ki~i 640 (733)
||+.||+|+.+|.+..+||++++++.+|+|...+.+.|..|++.| +|..+|. +++.+.|++++.=.+..+- -
T Consensus 600 Vsp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~G---vL~e~~~---~s~tgt~T~iEse~d~~q~--~ 671 (765)
T KOG2165|consen 600 VSPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKG---VLREEPI---ISDTGTLTVIESEMDFDQA--E 671 (765)
T ss_pred eCHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcC---eeecCCC---CCCCceeeecccccccccc--C
Confidence 999999999999999999999999999999999999999999988 9998764 3678899999854332110 1
Q ss_pred ccccccCCCchhhHH--HHHHHHhhh--hhhhhhheehhcccCCCCChHHHHHHHHHHhccCCCCCh-------HHHHHH
Q 004725 641 GTVVAQRESEPENQE--TRQRVEEDR--KPQIEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNP-------VVIKKR 709 (733)
Q Consensus 641 ~~~~~~~~~~~e~~~--~~~~~~~~r--~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~-------~~ik~~ 709 (733)
+++ +.+..++..+ ....+.+-+ -..-...||-.+-.-+.|+.+-+.+. -+.|.|.. ++++.-
T Consensus 672 ~~~--~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnm-----LkmF~~~~~~~~~TlqeL~~f 744 (765)
T KOG2165|consen 672 GTV--LLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNM-----LKMFVPPDGSAEITLQELQGF 744 (765)
T ss_pred CCc--ccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHH-----HeeeecCCCCCcccHHHHHHH
Confidence 110 1111112111 111222211 23334588888888899998777642 23566544 567767
Q ss_pred HHHhhhhhcccccC
Q 004725 710 IESLIEREFLERDK 723 (733)
Q Consensus 710 Ie~LIereyi~rd~ 723 (733)
+..++.-|-++-.+
T Consensus 745 Lq~kV~e~kL~f~~ 758 (765)
T KOG2165|consen 745 LQRKVREGKLEFIA 758 (765)
T ss_pred HHHHhhccceEEec
Confidence 77777666665543
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.78 E-value=6.4e-20 Score=147.14 Aligned_cols=67 Identities=55% Similarity=0.833 Sum_probs=61.9
Q ss_pred HhhhhhhhhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCc
Q 004725 661 EEDRKPQIEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRK 727 (733)
Q Consensus 661 ~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~ 727 (733)
.++|...|+|+||||||++|+++|++|+.+|.++++++|+|+..+||++||+||++|||+||++|+|
T Consensus 2 ~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 2 EQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred cchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 5789999999999999999999999999999999998999999999999999999999999999875
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.50 E-value=0.0032 Score=59.25 Aligned_cols=130 Identities=15% Similarity=0.281 Sum_probs=102.2
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCcHHHHHHHHh---hhccCCc-hHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 004725 25 AEKTWKILEHAIHEIYNHNASGLSFEELYRNAY---NMVLHKF-GEKLYSGLVTTMTFHLTEICKSIEAAQGGLFLEELN 100 (733)
Q Consensus 25 ~~~~W~~l~~~i~~I~~~~~~~~s~~~lY~~vy---~lc~~~~-~~~LY~~l~~~i~~~~~~i~~~l~~~~~~~~L~~~~ 100 (733)
.++.|..+..++-.+++++....+.+++-..|. +.|.++. ...+-+.+.+.+..-...+...+....++.+|..++
T Consensus 5 ~~~~W~~~~~~vl~lF~g~~l~~~iEdlN~lv~~~i~~~~~~~~~~~~~~dl~elL~tg~~~L~~~l~~~~~~~~l~rL~ 84 (158)
T PF08539_consen 5 SDDAWNSLCAKVLPLFQGERLRLPIEDLNELVRFHIKLCIQSFPPSYFLEDLEELLTTGMYILENQLNEVPDNRLLKRLV 84 (158)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHH
Confidence 678999999999999999988888888887774 5566654 345556777777777777777777777889999999
Q ss_pred HHHHHHH-HHHHHHHHHhhhhhhccccC-----------------CCCCcHHHHHHHHHHHHHhcchhhHHHHH
Q 004725 101 RKWADHN-KALQMIRDILMYMDRTFIPS-----------------THKTPVHELGLNLWRDVVIHSSKIQTRLQ 156 (733)
Q Consensus 101 ~~W~~~~-~~~~~l~~if~YLDr~yv~~-----------------~~~~~i~~~~l~~f~~~v~~~~~l~~~l~ 156 (733)
..|.-|. .-+-++..+|..|++.+-.. ....+|+.+++..||+.|+- +..+++.
T Consensus 85 eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvL--P~y~~l~ 156 (158)
T PF08539_consen 85 EIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVL--PYYQRLK 156 (158)
T ss_pred HHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhh--cchHhhh
Confidence 9999955 55689999999999644322 23479999999999999987 5655543
No 11
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=96.29 E-value=0.048 Score=60.26 Aligned_cols=279 Identities=12% Similarity=0.039 Sum_probs=152.8
Q ss_pred HHHHHHHHHHHHHHHHhhCCCC----CcHHHHHHHHhhhccCC--chHHHHHHHHHHHHHHHHH---HHHHHHhhh----
Q 004725 25 AEKTWKILEHAIHEIYNHNASG----LSFEELYRNAYNMVLHK--FGEKLYSGLVTTMTFHLTE---ICKSIEAAQ---- 91 (733)
Q Consensus 25 ~~~~W~~l~~~i~~I~~~~~~~----~s~~~lY~~vy~lc~~~--~~~~LY~~l~~~i~~~~~~---i~~~l~~~~---- 91 (733)
....|..|++++..|.+-.... ..|-.+++.+|+.|..+ +...+.+.++.......+. +...+...+
T Consensus 110 eAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l 189 (661)
T KOG2167|consen 110 EAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPL 189 (661)
T ss_pred chhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccch
Confidence 3567889999999888876543 34778888999999886 3445555555555554443 111111111
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCCCCCcHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHhcCCC
Q 004725 92 GGLFLEELNRKWADHNKALQMIRDILMYMDRTFIPSTHKTPVHELGLNLWRDVVIHSSKIQTRLQDTLLELVQRERSGEV 171 (733)
Q Consensus 92 ~~~~L~~~~~~W~~~~~~~~~l~~if~YLDr~yv~~~~~~~i~~~~l~~f~~~v~~~~~l~~~l~~~il~~I~~~R~g~~ 171 (733)
-..+...+...|-..... .++++-+|-.=+ .....+++++-..+....-.-++..+-+.+....++..++.++.
T Consensus 190 ~atV~~~LL~~hL~~IL~----kgl~~lvDm~q~--~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~kDk~ 263 (661)
T KOG2167|consen 190 IATVERCLLSRHLDLILT----KGLDSLVDMRQT--SDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEKDKD 263 (661)
T ss_pred HHHHHHHHHHHHHHHHHh----cchHHhhhhhhc--cchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchhhHH
Confidence 134555566666555332 334555554311 23455666666665332222225666677777777777776664
Q ss_pred CC--hHHHHHHHHHHHHhCcccchhhhhHhHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH--HHHHhhccChhh
Q 004725 172 IN--RGLMRNITKMLMDLGSFVYQDDFEKHFLEVSADFYRLESQEFIESCDCGDYLKKAERRLNEE--MERVSHYLDARS 247 (733)
Q Consensus 172 i~--~~~lk~ii~~l~~lg~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~~~~~l~~E--~~r~~~~l~~~t 247 (733)
.. .-..|+-++++.... +..+.-.+|+..++++|...++ .+...+.+||.+.....-.+ ++-+..-|. .+
T Consensus 264 mVqELL~FK~k~Dii~~~s---F~~~v~e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~gnk~~~d~~l~-~~ 337 (661)
T KOG2167|consen 264 MVQELLDFKKKVDIIVDES---FLKYVAEKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRAGNKETSDEELE-FV 337 (661)
T ss_pred HHHHHHHHHHHhhHHHHHH---HHHhhHHHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHhccccccchhHH-HH
Confidence 33 234577777777652 2222227899999999999998 45566889998877655444 222211110 01
Q ss_pred HHHHH---------HHHHHHHHHHHHHHHHhcch----hhhHHhHccCcHhHHHHHHHhhccCCCChHHHHHHHHHHHHH
Q 004725 248 EAKIT---------NVVEKEMIESHMNRLVHMEN----SGLVNMLVDDKYEDLGRMYCLFRRVPSGLILIRDVMTSYIRD 314 (733)
Q Consensus 248 ~~~l~---------~~~~~~Li~~~~~~ll~~~~----~~~~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~ 314 (733)
..+++ ++.+.-+-++-..+|+...+ .|+.-+-+-......+..|+|.+-+++ .+...+..+.|...
T Consensus 338 ~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfkd-me~sk~i~~~f~~~ 416 (661)
T KOG2167|consen 338 LDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFKD-MELSKEINRAFKQS 416 (661)
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhhh-HHHHHHHHHHHHHH
Confidence 11111 11122222233344443211 122222223345678889999887754 34445555555544
Q ss_pred HH
Q 004725 315 TG 316 (733)
Q Consensus 315 ~g 316 (733)
.|
T Consensus 417 ~~ 418 (661)
T KOG2167|consen 417 KG 418 (661)
T ss_pred HH
Confidence 33
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=94.89 E-value=0.089 Score=45.26 Aligned_cols=66 Identities=17% Similarity=0.208 Sum_probs=54.2
Q ss_pred EEEeeHHHHHHHHHHh--------CCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecc
Q 004725 558 ELNVSTYQMCVLMLFN--------SIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFND 629 (733)
Q Consensus 558 ~l~~s~~Qa~iLl~Fn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~ 629 (733)
...+++-|+.+|+..- ....+|-.||++.+|++...+.++|..|...+ +|.... ....|.+|.
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~G---lI~r~~------~~~~~~~n~ 90 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRR---IIFRQG------MMGIVGVNT 90 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCC---Ceeeec------CCceeecCC
Confidence 3457888999888655 46789999999999999999999999999888 887642 247899998
Q ss_pred cCc
Q 004725 630 KFT 632 (733)
Q Consensus 630 ~f~ 632 (733)
+++
T Consensus 91 ~~~ 93 (95)
T TIGR01610 91 PLS 93 (95)
T ss_pred Ccc
Confidence 865
No 13
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.17 E-value=0.12 Score=38.16 Aligned_cols=44 Identities=20% Similarity=0.240 Sum_probs=37.3
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
+..+..||....+++.+|..+|++.+|++...+.+.|..|...+
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g 45 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKG 45 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCc
Confidence 45677888888888899999999999999999999999999877
No 14
>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=93.98 E-value=0.094 Score=39.47 Aligned_cols=45 Identities=22% Similarity=0.352 Sum_probs=37.9
Q ss_pred HHHHHHHhCCCC-cCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 566 MCVLMLFNSIDR-LSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 566 a~iLl~Fn~~~~-~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
+.||..|.+.+. +|+.||++.+|+|...+.+.|..|...+ ++.++
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g---~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEG---YVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTT---SEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCc---CeecC
Confidence 457888887654 8999999999999999999999999887 77765
No 15
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=93.11 E-value=0.15 Score=39.77 Aligned_cols=51 Identities=20% Similarity=0.274 Sum_probs=43.9
Q ss_pred eeHHHHHHHHHHhCCCC--cCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 561 VSTYQMCVLMLFNSIDR--LSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|...+ ++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G---lv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG---LVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT---SEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEeC
Confidence 47789999988877666 9999999999999999999999999988 777654
No 16
>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=92.92 E-value=0.32 Score=40.58 Aligned_cols=59 Identities=15% Similarity=0.212 Sum_probs=42.9
Q ss_pred HHHHHHHHHhCCCC-cCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeeccc
Q 004725 564 YQMCVLMLFNSIDR-LSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDK 630 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~-~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~ 630 (733)
+++.+.+..+..+. +|.++|++.+|+|+..+.+.++.|...+ ++...+. +++-|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~G---li~s~~G-----~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAG---LIESSRG-----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTT---SEEEETS-----TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCC---eeEecCC-----CCCceeecCC
Confidence 34445554444443 9999999999999999999999999888 8865431 3577877764
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=92.09 E-value=0.28 Score=37.75 Aligned_cols=46 Identities=20% Similarity=0.325 Sum_probs=40.6
Q ss_pred HHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 565 QMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 565 Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
|..|+...++++.+|+++|++.+|+++..+.+-|..|...+ ++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g---~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQG---LIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEE
Confidence 45678888889999999999999999999999999999877 77664
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=91.54 E-value=0.37 Score=38.25 Aligned_cols=51 Identities=18% Similarity=0.215 Sum_probs=40.4
Q ss_pred eeHHHHHHHHHHh-CCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 561 VSTYQMCVLMLFN-SIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+|..|..||.... ..+.++..+|++.++++...+-+.|+.|...+ ++.+.+
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~g---lv~~~~ 52 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKG---LVEKER 52 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTT---SEEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEecC
Confidence 3678999998888 77889999999999999999999999999988 886653
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=91.39 E-value=0.19 Score=38.79 Aligned_cols=50 Identities=14% Similarity=0.254 Sum_probs=44.0
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
|..|+.+|....+.++++..+|++.++++...+.+.+..|...+ ++.+.+
T Consensus 2 t~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g---~I~r~~ 51 (59)
T PF01047_consen 2 TPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKG---LIERER 51 (59)
T ss_dssp THHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTT---SEEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCC---CEEecc
Confidence 67899999888888889999999999999999999999999988 777654
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=90.29 E-value=0.49 Score=36.85 Aligned_cols=49 Identities=16% Similarity=0.244 Sum_probs=41.4
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
++.-..||.++...+++|+.+|++.+|++...+..+|.-|...+ ++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aG---li~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAG---LIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTT---SEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC---CeEEe
Confidence 45667788888777899999999999999999999999999988 77654
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=89.36 E-value=0.83 Score=40.90 Aligned_cols=52 Identities=13% Similarity=0.228 Sum_probs=46.5
Q ss_pred EeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 560 NVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 560 ~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.++..|+.||.....++.+|..+|++.+|++...+.+.+..|...+ ++.+.+
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~G---lI~r~~ 76 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDG---LVTRLK 76 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCC---CEEecc
Confidence 4588999999988888899999999999999999999999999887 887754
No 22
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=89.20 E-value=0.99 Score=33.04 Aligned_cols=44 Identities=14% Similarity=0.276 Sum_probs=35.9
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceee
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLR 611 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~ 611 (733)
...-||.++-+ ++.++.||++.+|++...+.++|..|...+ ++.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~g---lV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAG---LVE 46 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT---SEE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCc---Cee
Confidence 34567766666 679999999999999999999999998877 654
No 23
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.02 E-value=1 Score=35.93 Aligned_cols=47 Identities=17% Similarity=0.218 Sum_probs=39.7
Q ss_pred HHHHHHHHHhCCCC--cCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 564 YQMCVLMLFNSIDR--LSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
..-.||.++.+.+. +|..+|++.+|++...+.++|..|...+ ++.+.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G---~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG---KVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEec
Confidence 44567777777655 9999999999999999999999999877 77664
No 24
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=87.55 E-value=1.2 Score=37.55 Aligned_cols=56 Identities=14% Similarity=0.247 Sum_probs=43.7
Q ss_pred HHHHHHHhCC-CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeeccc
Q 004725 566 MCVLMLFNSI-DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDK 630 (733)
Q Consensus 566 a~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~ 630 (733)
..||..+... +.+|+.+|++.+|++...+.+.|..|...+ +|...+. ++.|.+...
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g---~l~~~~~------~~~y~l~~~ 64 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELG---YVEQDGQ------NGRYRLGPK 64 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC---CeeecCC------CCceeecHH
Confidence 4466677765 689999999999999999999999999877 8876532 345655443
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=87.41 E-value=1.7 Score=37.58 Aligned_cols=62 Identities=21% Similarity=0.373 Sum_probs=48.4
Q ss_pred EeeHHHHHHHHH-------HhC-CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccC
Q 004725 560 NVSTYQMCVLML-------FNS-IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKF 631 (733)
Q Consensus 560 ~~s~~Qa~iLl~-------Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f 631 (733)
.++.-|.-|++. ||. .+.+|..++++.||++...+.+++..|+..+ +|... +..+-+|.+.
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~---vI~~~--------g~~~G~N~~i 97 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRG---VIIRD--------GKRIGVNKNI 97 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEeC--------CcEEeeeccc
Confidence 456667776665 554 4679999999999999999999999999988 88764 4566667655
Q ss_pred c
Q 004725 632 T 632 (733)
Q Consensus 632 ~ 632 (733)
+
T Consensus 98 ~ 98 (100)
T PF04492_consen 98 S 98 (100)
T ss_pred c
Confidence 3
No 26
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=87.36 E-value=1.3 Score=41.26 Aligned_cols=52 Identities=19% Similarity=0.315 Sum_probs=46.0
Q ss_pred EeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 560 NVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 560 ~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.+|..|+.||......+++|..+|++.+|++...+.+.+..|...+ ++.+.+
T Consensus 37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~G---lI~R~~ 88 (144)
T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKG---WVERLP 88 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEecc
Confidence 4688999999887777789999999999999999999999999888 887764
No 27
>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=86.64 E-value=0.53 Score=37.55 Aligned_cols=50 Identities=20% Similarity=0.206 Sum_probs=41.4
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
|-.++-|+..+-..+..|..+|++.+|++...+.+.|..|...+ ++...+
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~G---lV~~~~ 56 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKG---LVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTT---SEEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEEc
Confidence 45666677665566789999999999999999999999999988 776653
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=85.51 E-value=2.2 Score=37.55 Aligned_cols=52 Identities=25% Similarity=0.314 Sum_probs=44.8
Q ss_pred EeeHHHHHHHHHHh----CCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 560 NVSTYQMCVLMLFN----SIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 560 ~~s~~Qa~iLl~Fn----~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.+|..|..||.... ..+.+|..+|++.++++...+.+.+..|...+ ++.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg---~I~r~~ 77 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKG---YLSKER 77 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCC---CEeccC
Confidence 45888998886665 55779999999999999999999999999988 888764
No 29
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=84.15 E-value=2.4 Score=31.27 Aligned_cols=45 Identities=18% Similarity=0.261 Sum_probs=36.8
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
-.|+..+..+..++..+|++.+|++...+.+.|..|...+ ++...
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g---~i~~~ 47 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQG---LLTRV 47 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEEe
Confidence 3456666666779999999999999999999999998876 66543
No 30
>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=84.09 E-value=1.5 Score=40.15 Aligned_cols=60 Identities=20% Similarity=0.250 Sum_probs=45.2
Q ss_pred hhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 669 EAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 669 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
+..|++++-..+.++..+++.. +.....+....|...|..|.+||||+|..+.+ .|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~----l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr-~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRI----LAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGR-KFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHH----HhhccCCcHHHHHHHHHHHHHCCceeeecCCC-cEEEEe
Confidence 4457777767777877766644 44346678899999999999999999986544 688864
No 31
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=84.06 E-value=2.3 Score=36.33 Aligned_cols=53 Identities=21% Similarity=0.300 Sum_probs=46.5
Q ss_pred EEEeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 558 ELNVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 558 ~l~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
+..++..+..||......+.+|..+|++.++++...+.++|..|...+ ++...
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g---~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKG---LIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCC---CeEec
Confidence 345688899999888887789999999999999999999999999887 78654
No 32
>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=83.83 E-value=3 Score=31.43 Aligned_cols=39 Identities=18% Similarity=0.288 Sum_probs=30.9
Q ss_pred HHHHHH-hCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 567 CVLMLF-NSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 567 ~iLl~F-n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.||..+ +..+.+|.++|++.+|++...+.+.|..|-..+
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 344444 666669999999999999999999999987655
No 33
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=83.07 E-value=3.1 Score=37.43 Aligned_cols=38 Identities=18% Similarity=0.236 Sum_probs=34.6
Q ss_pred CCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 574 SIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 574 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.++.+|+++|++.++.+...+.++|+.|+..| ++.+..
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~~~G---lV~Rek 76 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLLEAG---LVEREK 76 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcC---Ceeeee
Confidence 67889999999999999999999999999988 887653
No 34
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=82.77 E-value=2.7 Score=43.31 Aligned_cols=46 Identities=15% Similarity=0.252 Sum_probs=41.1
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+.||.+|.....+|+.||++.+|+|...+.+.|..|+..+ .|.+.+
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G---~l~~~~ 62 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLG---YVAQEG 62 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEcC
Confidence 4688889887789999999999999999999999999988 887754
No 35
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=82.51 E-value=1.6 Score=38.93 Aligned_cols=62 Identities=19% Similarity=0.291 Sum_probs=52.2
Q ss_pred hhhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 667 QIEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 667 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
..++.||+||=.++..+.+|++.++... +.++...|+--|..|..||.|.+.-++ ..|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~----~ews~sTV~TLl~RL~KKg~l~~~kdg-r~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD----REWSYSTVKTLLNRLVKKGLLTRKKDG-RAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc----ccccHHHHHHHHHHHHhccchhhhhcC-Ceeeeec
Confidence 4577899999999999999998776654 788999999999999999999998655 4677744
No 36
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=81.74 E-value=4.5 Score=38.58 Aligned_cols=45 Identities=13% Similarity=0.143 Sum_probs=37.0
Q ss_pred HHHHHHHHhCC-CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 565 QMCVLMLFNSI-DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 565 Qa~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
.+.+.+.|+.. ..+|.++|++.+|+|...+.+.|+.|..++ |+..
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aG---Lv~s 57 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNG---LVSS 57 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEe
Confidence 34444556654 579999999999999999999999999888 8874
No 37
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=81.71 E-value=4.3 Score=38.20 Aligned_cols=56 Identities=16% Similarity=0.062 Sum_probs=41.5
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecc
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFND 629 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~ 629 (733)
+.+.|..+..+.+|..+|++..|+|...|.+.|+.|..++ ++..... .++-|.++.
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aG---lv~S~rG-----~~GGy~La~ 68 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAG---LVETVRG-----RNGGVRLGR 68 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEeecC-----CCCCeeecC
Confidence 3344555555668999999999999999999999999888 7765431 245555554
No 38
>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=81.32 E-value=2 Score=41.04 Aligned_cols=47 Identities=26% Similarity=0.437 Sum_probs=41.2
Q ss_pred cCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCcCC
Q 004725 578 LSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFTSK 634 (733)
Q Consensus 578 ~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~~~ 634 (733)
+|..+|++.+|++...+.+++..|...+ +|.+.. .+.|.+|++|.-+
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~~---iI~k~~-------~G~Y~iNP~~~~k 122 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEKN---IIKKIR-------NGAYMINPNFFFK 122 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhCC---cEEEcc-------CCeEEECcHHhee
Confidence 5889999999999999999999999988 888753 5789999997654
No 39
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=80.08 E-value=4 Score=29.47 Aligned_cols=34 Identities=21% Similarity=0.318 Sum_probs=30.4
Q ss_pred CcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 577 RLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 577 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.+|..+|++.+|++...+.+.|..|...+ ++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g---~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEG---LISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEEe
Confidence 47899999999999999999999999887 88654
No 40
>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=80.06 E-value=3.3 Score=35.96 Aligned_cols=46 Identities=22% Similarity=0.250 Sum_probs=39.5
Q ss_pred EeeHHHHHHHHHHhC----CCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 560 NVSTYQMCVLMLFNS----IDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 560 ~~s~~Qa~iLl~Fn~----~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.++..|-.||-.+.+ .+.+++++|++.++++..+++.+|..|+..+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG 93 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEG 93 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTT
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 578899999988887 5679999999999999999999999999876
No 41
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=80.02 E-value=4.5 Score=31.61 Aligned_cols=45 Identities=18% Similarity=0.254 Sum_probs=35.1
Q ss_pred HHHHHhC-CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCC
Q 004725 568 VLMLFNS-IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPM 615 (733)
Q Consensus 568 iLl~Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~ 615 (733)
||..++. +..++..||++.+|++...+...|..|.+.+ .+.+.|.
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG---~V~~~~~ 50 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEG---KVERSPV 50 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT---SEEEES-
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC---CEEEecC
Confidence 4555666 7789999999999999999999999999877 6666554
No 42
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=79.81 E-value=1.9 Score=35.64 Aligned_cols=44 Identities=14% Similarity=0.311 Sum_probs=35.0
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
..||...+..+++++.+|.+.+|+++..+-++|..|...+ .+..
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~G---yV~~ 46 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAG---YVEV 46 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTT---SEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCC---CEEE
Confidence 4566666667789999999999999999999999999888 5543
No 43
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=79.52 E-value=4.3 Score=39.49 Aligned_cols=53 Identities=11% Similarity=0.044 Sum_probs=46.8
Q ss_pred EEeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 559 LNVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 559 l~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+.+|..|..||.....++++|..+|++.++++...+.+.+..|...+ ++.+.+
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kG---lI~R~~ 93 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERG---YLTFSK 93 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCC---CEEecC
Confidence 34688999999999888899999999999999999999999999887 887654
No 44
>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=79.26 E-value=4.3 Score=43.35 Aligned_cols=146 Identities=15% Similarity=0.137 Sum_probs=43.3
Q ss_pred EEeeHHHHHHHHHHhC--CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCcCCcc
Q 004725 559 LNVSTYQMCVLMLFNS--IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFTSKFV 636 (733)
Q Consensus 559 l~~s~~Qa~iLl~Fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~~~~~ 636 (733)
-.++..+..|+-+..+ ..++-..+|..+||++...+.++|.+|...+ +++... +...+++
T Consensus 80 ~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~---lIK~vk---------------sv~~~~r 141 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKK---LIKSVK---------------SVKNPNR 141 (327)
T ss_dssp -SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTT---SEEEE-----------------SS-SS-
T ss_pred cCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCC---CEEEec---------------CcCCCCe
Confidence 3457788888877765 5678899999999999999999999998877 665432 1223344
Q ss_pred eEEeccccccCCCchhhH----HHHHHHHhhhhhhhhhheehhcccCCC-----------------------------CC
Q 004725 637 KVKIGTVVAQRESEPENQ----ETRQRVEEDRKPQIEAAIVRIMKARRV-----------------------------LD 683 (733)
Q Consensus 637 ki~i~~~~~~~~~~~e~~----~~~~~~~~~r~~~i~A~IVRimK~~k~-----------------------------l~ 683 (733)
|+-+..-..| ..+-. -+..+.+.+-...+...|.+.+.++.. .+
T Consensus 142 K~Yml~~l~P---s~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T 218 (327)
T PF05158_consen 142 KVYMLYDLEP---SEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPT 218 (327)
T ss_dssp -EEEESSS------------------------------------------------------------------------
T ss_pred EEEEEccCCc---CcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCC
Confidence 4444321111 00000 012233444445555666666666544 34
Q ss_pred hHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCC
Q 004725 684 HNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVD 725 (733)
Q Consensus 684 ~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~ 725 (733)
.+++..-+.+.=-..-..+.++|...++-|+=.|-|++-...
T Consensus 219 ~~eI~~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~ 260 (327)
T PF05158_consen 219 LEEIAEFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSG 260 (327)
T ss_dssp ------------------------------------------
T ss_pred HHHHHHHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEecc
Confidence 444444443321112445788999999999999988886544
No 45
>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=79.08 E-value=5.7 Score=36.51 Aligned_cols=44 Identities=11% Similarity=0.194 Sum_probs=35.7
Q ss_pred HHHHHHHhCC-CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 566 MCVLMLFNSI-DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 566 a~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
+.+.+.++.. ..+|..+|++.+++|...+.+.|..|..++ ++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~g---lv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAG---LVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC---ceEE
Confidence 3444555543 469999999999999999999999999888 8764
No 46
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=78.38 E-value=4.7 Score=37.37 Aligned_cols=53 Identities=19% Similarity=0.283 Sum_probs=45.2
Q ss_pred EEeeHHHHHHHHHHhCC-CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 559 LNVSTYQMCVLMLFNSI-DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 559 l~~s~~Qa~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+.+|..|..+|...... +.+|..+|++.+|++...+.+.+..|...+ ++.+.+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~G---lV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKG---LISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCC---CEeeec
Confidence 34688899998887754 568999999999999999999999999988 887764
No 47
>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=78.04 E-value=5.4 Score=31.63 Aligned_cols=48 Identities=15% Similarity=0.230 Sum_probs=40.1
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
+..+..|+..+...+ ++..+|++.+|++...+.+.|..|...+ ++...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g---~i~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAG---LVESR 53 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCC---CeEEE
Confidence 456777887777766 9999999999999999999999998877 77654
No 48
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=77.61 E-value=2.3 Score=37.87 Aligned_cols=60 Identities=22% Similarity=0.305 Sum_probs=43.6
Q ss_pred hhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 669 EAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 669 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
+..|++++=..+.++..+++. .+.....+....|...+..|.+||||.|...+ ..|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~----~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g-r~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHE----ALPEERSWAYSTVQTLLNRLVEKGFLTREKIG-RAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHH----HHCTTSS--HHHHHHHHHHHHHTTSEEEEEET-TCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHH----HHHhccccchhHHHHHHHHHHhCCceeEeecC-CceEEEe
Confidence 445666666677777777664 44444677899999999999999999998654 3688864
No 49
>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=77.59 E-value=0.75 Score=36.84 Aligned_cols=45 Identities=16% Similarity=0.359 Sum_probs=34.3
Q ss_pred eehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCC
Q 004725 672 IVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKV 724 (733)
Q Consensus 672 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~ 724 (733)
|-.+|+.++.++.++|- .+|..+++.+...|+.|+.+|||++.+.
T Consensus 5 i~~~l~~~~~~S~~eLa--------~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELA--------REFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHH--------HHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHH--------HHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 34567888888887764 3489999999999999999999998754
No 50
>PHA00738 putative HTH transcription regulator
Probab=76.01 E-value=6.9 Score=34.06 Aligned_cols=68 Identities=13% Similarity=0.015 Sum_probs=52.4
Q ss_pred EEEeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCc
Q 004725 558 ELNVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFT 632 (733)
Q Consensus 558 ~l~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~ 632 (733)
++...+.=-.||.++.+++.+++.+|++.++++...+-++|.-|-.++ |+.....|. .-.|++|.+..
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAG---LV~srK~Gr----~vyY~Ln~~~~ 74 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQG---YIELYKEGR----TLYAKIRENSK 74 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCC---ceEEEEECC----EEEEEECCCcc
Confidence 455566666677777777779999999999999999999999999988 887654432 23577777643
No 51
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=75.91 E-value=6.1 Score=40.47 Aligned_cols=47 Identities=23% Similarity=0.392 Sum_probs=40.6
Q ss_pred HHHHHHHhCCCC-cCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCC
Q 004725 566 MCVLMLFNSIDR-LSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPM 615 (733)
Q Consensus 566 a~iLl~Fn~~~~-~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~ 615 (733)
+.||.+|..... +++.||++.+|+|...+.+.|..|+..+ ++.+.+.
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G---~v~~d~~ 54 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELG---YVEQDPE 54 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCC---CEEEcCC
Confidence 457888887554 7899999999999999999999999988 8888753
No 52
>PRK10870 transcriptional repressor MprA; Provisional
Probab=74.93 E-value=7.5 Score=37.54 Aligned_cols=52 Identities=12% Similarity=0.108 Sum_probs=44.0
Q ss_pred EeeHHHHHHHHHHhC--CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 560 NVSTYQMCVLMLFNS--IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 560 ~~s~~Qa~iLl~Fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.+|..|..||..... ..++|..+|++.+|++...+.+.+..|...+ ++.+.+
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kG---lV~R~~ 105 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRG---WIERRE 105 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEecC
Confidence 356788888877764 4579999999999999999999999999988 887764
No 53
>PRK11569 transcriptional repressor IclR; Provisional
Probab=74.68 E-value=6.4 Score=41.02 Aligned_cols=47 Identities=15% Similarity=0.239 Sum_probs=40.5
Q ss_pred HHHHHHHHhCC-CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 565 QMCVLMLFNSI-DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 565 Qa~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
-..||.+|.+. ..+|+.||++.+|++...+.+.|.+|+..+ .|.+.+
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G---~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQG---FVRQVG 77 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEcC
Confidence 34578889874 579999999999999999999999999988 887654
No 54
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=74.50 E-value=6.9 Score=40.69 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=40.6
Q ss_pred HHHHHHHHhCC-CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 565 QMCVLMLFNSI-DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 565 Qa~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
-..||.+|... ..+|+.||++.+|+|...+.+.|..|+..+ .|.+.+
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G---~l~~~~ 74 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAAD---FVYQDS 74 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEcC
Confidence 34688889865 579999999999999999999999999988 887754
No 55
>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=74.40 E-value=8.5 Score=34.98 Aligned_cols=46 Identities=20% Similarity=0.234 Sum_probs=35.9
Q ss_pred HHHHHHHHhCC-CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 565 QMCVLMLFNSI-DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 565 Qa~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
++.+.+.-+.+ ..+|.++|++.+|+|...+.+.|..|...+ ++...
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~g---li~~~ 58 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAG---LVESV 58 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC---cEEec
Confidence 34444443433 379999999999999999999999999888 87643
No 56
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=73.96 E-value=6.3 Score=34.42 Aligned_cols=45 Identities=13% Similarity=0.202 Sum_probs=39.4
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceee
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLR 611 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~ 611 (733)
..-.||..+..+...|+.+|++.+|++...+.+.+..|...+ ++.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g---~i~ 48 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEG---VIK 48 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC---Cee
Confidence 345678788887889999999999999999999999999887 775
No 57
>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=73.87 E-value=8.2 Score=29.93 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=36.1
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
|..+-.+...++..+|++.+|+++..+..++..|...+ ++...|
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~G---lV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKG---LVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTT---SEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCC---CEEecC
Confidence 44444577889999999999999999999999999888 877654
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=73.85 E-value=5.9 Score=39.23 Aligned_cols=52 Identities=17% Similarity=0.201 Sum_probs=46.2
Q ss_pred EeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 560 NVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 560 ~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.++..|..||..+.+++.++..+|++.+|++...+.+.|..|...+ ++.+.+
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~G---lI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKG---LVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEEc
Confidence 4678899999999887889999999999999999999999999877 887653
No 59
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=73.48 E-value=3.9 Score=33.07 Aligned_cols=33 Identities=9% Similarity=0.021 Sum_probs=27.5
Q ss_pred hCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 573 NSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 573 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
...+.+|+.||++.+|++...++..+..+...+
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~ 60 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGETKAG 60 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence 333578999999999999999999988776654
No 60
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=73.43 E-value=6.6 Score=29.72 Aligned_cols=40 Identities=18% Similarity=0.379 Sum_probs=33.6
Q ss_pred HhCCCCc-CHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 572 FNSIDRL-SYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 572 Fn~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+..++.+ |..+|++.+|++...+.++|..|...+ ++...+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g---~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEAEG---LVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEEec
Confidence 4445567 899999999999999999999999877 876553
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=73.07 E-value=10 Score=30.52 Aligned_cols=47 Identities=21% Similarity=0.277 Sum_probs=36.1
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
+..|.. |+..... +.|+++|.+.||++.+.+...|.-|...+ ++.+.
T Consensus 5 t~~~~I-L~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~G---iI~Rk 51 (72)
T PF05584_consen 5 TVTQKI-LIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRG---IIERK 51 (72)
T ss_pred hHHHHH-HHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCC---Ceeee
Confidence 334443 3344444 89999999999999999999999999877 77653
No 62
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=72.70 E-value=10 Score=35.61 Aligned_cols=59 Identities=12% Similarity=0.139 Sum_probs=43.4
Q ss_pred HHHHHHHHHhCCC-CcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeeccc
Q 004725 564 YQMCVLMLFNSID-RLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDK 630 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~ 630 (733)
+.+.+.|.-+..+ ..|.++|++..|+|+..|.+.+..|..++ ++...+. +++-|.++..
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaG---lV~S~rG-----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAG---LVKSVRG-----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcC---CEEeecC-----CCCCccCCCC
Confidence 3445555555554 57899999999999999999999999888 7765432 3556666654
No 63
>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=72.02 E-value=9.6 Score=34.63 Aligned_cols=44 Identities=23% Similarity=0.338 Sum_probs=35.4
Q ss_pred HHHHHHh--CCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 567 CVLMLFN--SIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 567 ~iLl~Fn--~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.+|..+. ..+.+|+.+|++.+|+|...+.+.|..|...+ ++...
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~G---li~~~ 58 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAG---IVTSK 58 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCC---cEEec
Confidence 3444443 34579999999999999999999999999988 88643
No 64
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=71.65 E-value=8.1 Score=39.95 Aligned_cols=47 Identities=19% Similarity=0.284 Sum_probs=40.0
Q ss_pred HHHHHHHhCCC-CcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCC
Q 004725 566 MCVLMLFNSID-RLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPM 615 (733)
Q Consensus 566 a~iLl~Fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~ 615 (733)
+.||..|.+.+ .+|..||++.+|++...+.+.|..|...+ +|.+.+.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g---~v~~~~~ 61 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEG---YVRRSAS 61 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEecC
Confidence 45778887654 59999999999999999999999999888 8877653
No 65
>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=71.64 E-value=8.8 Score=39.29 Aligned_cols=44 Identities=20% Similarity=0.364 Sum_probs=38.8
Q ss_pred HHHHHHHhC-CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 566 MCVLMLFNS-IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 566 a~iLl~Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
..||.+|.. ...+|+.||++.+|+|...+.+.|..|...+ .|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G---~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELG---YVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEe
Confidence 457888986 5679999999999999999999999999988 7765
No 66
>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=71.56 E-value=6.5 Score=28.05 Aligned_cols=36 Identities=22% Similarity=0.379 Sum_probs=27.2
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHh
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSL 601 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 601 (733)
-.||-.+..+...++.+|++.+|++...+.+-++.|
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 356767777788999999999999999998877654
No 67
>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=71.47 E-value=9.7 Score=29.69 Aligned_cols=35 Identities=17% Similarity=0.226 Sum_probs=31.8
Q ss_pred CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 576 DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 576 ~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
..+|..+|++.+|++...+.+.|..|...+ ++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g---~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEG---LISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEec
Confidence 468999999999999999999999999887 88765
No 68
>PF13730 HTH_36: Helix-turn-helix domain
Probab=70.69 E-value=10 Score=28.48 Aligned_cols=27 Identities=11% Similarity=0.207 Sum_probs=25.4
Q ss_pred CHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 579 SYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 579 t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
|.+.|++.+|++...+.+++..|...+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G 53 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKG 53 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCc
Confidence 899999999999999999999998766
No 69
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=70.04 E-value=10 Score=33.84 Aligned_cols=60 Identities=15% Similarity=0.199 Sum_probs=44.3
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeeccc
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDK 630 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~ 630 (733)
.=..||.+.-+.++.++.||++.+|++...+-++|.-|..++ ++.....|. .-.|.+|.+
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AG---LV~~~r~Gr----~~~Y~l~~~ 76 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESG---LLLDRKQGK----WVHYRLSPH 76 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC---ceEEEEEcC----EEEEEECch
Confidence 334555555445679999999999999999999999999888 887665431 234666653
No 70
>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=69.49 E-value=6.9 Score=30.19 Aligned_cols=39 Identities=21% Similarity=0.268 Sum_probs=30.5
Q ss_pred HHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhh
Q 004725 565 QMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLAC 603 (733)
Q Consensus 565 Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 603 (733)
|.-+|-++-+.+.+|+.+|++.+|++...++.-+.-|-.
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 556665554477899999999999999999998887753
No 71
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=69.25 E-value=10 Score=28.86 Aligned_cols=36 Identities=11% Similarity=0.161 Sum_probs=31.6
Q ss_pred CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 575 IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 575 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.+..|..+|++.+|++...+.+.|..|...+ ++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g---~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAG---LVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCC---Ceeee
Confidence 5678999999999999999999999999877 77643
No 72
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=67.72 E-value=8.1 Score=38.41 Aligned_cols=44 Identities=18% Similarity=0.251 Sum_probs=38.0
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
..||.+.+..+.+|.+||++.+|++..-++++|+.|...+ ++..
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~G---lv~~ 57 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEG---LVEV 57 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCc---ceee
Confidence 4567777888899999999999999999999999999877 5543
No 73
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=67.64 E-value=33 Score=39.00 Aligned_cols=50 Identities=12% Similarity=0.222 Sum_probs=44.9
Q ss_pred EeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 560 NVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 560 ~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
.+|..|..||......+.+|..+|++.+|++...+.+++.+|...+ ++..
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kG---lV~~ 52 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKG---LVKV 52 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCC---CEEE
Confidence 4688999999999988899999999999999999999999998876 6654
No 74
>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=67.31 E-value=2.9 Score=33.24 Aligned_cols=54 Identities=17% Similarity=0.252 Sum_probs=38.1
Q ss_pred heehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeec
Q 004725 671 AIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYL 732 (733)
Q Consensus 671 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yv 732 (733)
.|-..|-.++.++..+|.. . ...+...+-+.++.|.++|+++|.++++..|..+
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~----~----l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAE----E----LGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHH----H----HTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHcCCCCHHHHHH----H----HCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 3333333566667666543 2 2347789999999999999999999887555544
No 75
>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=65.84 E-value=7.7 Score=30.95 Aligned_cols=37 Identities=16% Similarity=0.164 Sum_probs=29.3
Q ss_pred HHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 569 LMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 569 Ll~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.-...+.+.+|+++|+..++++++.+...|..|+..+
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG 42 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKG 42 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCT
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3344567789999999999999999999999999876
No 76
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=65.55 E-value=13 Score=32.73 Aligned_cols=51 Identities=16% Similarity=0.227 Sum_probs=44.5
Q ss_pred eeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 561 VSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+++.|..+|......+..+..+|++.++++...+.+.+..|...+ ++.+.+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~g---lv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKG---LIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCC---CeeecC
Confidence 688999999888877766669999999999999999999999888 777654
No 77
>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=65.27 E-value=10 Score=29.61 Aligned_cols=32 Identities=28% Similarity=0.366 Sum_probs=26.4
Q ss_pred CCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 574 SIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 574 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
..+..|+.+|...|++|.+.++.+|..|+..+
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~ 55 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQHN 55 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHHTT
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence 34689999999999999999999999999876
No 78
>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=63.87 E-value=18 Score=28.62 Aligned_cols=51 Identities=22% Similarity=0.300 Sum_probs=36.9
Q ss_pred eeHHHHHHHHHHhC-----CCCcCHHHHHHHcCCC-hHHHHHHHHHhhhccCcceeeccC
Q 004725 561 VSTYQMCVLMLFNS-----IDRLSYKEIEQATEIP-APELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+|.-|.-||...-+ +-.-|+.||++.+|+. ...+..+|..|...+ .|.+.+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG---~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKG---YIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTT---SEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCc---CccCCC
Confidence 35667777755432 3456999999999996 889999999999887 887764
No 79
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=63.09 E-value=21 Score=32.98 Aligned_cols=40 Identities=8% Similarity=0.076 Sum_probs=33.9
Q ss_pred HhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 572 FNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 572 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+..+..++..+|++.+|+|...+.++|+.|...+ ++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~G---lv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAG---YVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCC---EEEEec
Confidence 3344568999999999999999999999999888 887654
No 80
>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=62.73 E-value=7 Score=34.09 Aligned_cols=45 Identities=11% Similarity=0.129 Sum_probs=32.7
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceee
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLR 611 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~ 611 (733)
-.+.|+..+..++.++-++|++.+|++..++.+.|..|...+ ++.
T Consensus 14 ~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~---lv~ 58 (105)
T PF02002_consen 14 EAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDG---LVS 58 (105)
T ss_dssp TTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHS---S-E
T ss_pred hHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC---CeE
Confidence 345667666666789999999999999999999999999888 664
No 81
>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=61.85 E-value=19 Score=35.52 Aligned_cols=44 Identities=16% Similarity=0.229 Sum_probs=36.7
Q ss_pred HHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 567 CVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 567 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.||......+.+|..+|++.+|++...+.++|..|...+ ++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~G---lV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEG---LIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC---CeEEe
Confidence 455555555679999999999999999999999999887 77654
No 82
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=61.69 E-value=15 Score=34.57 Aligned_cols=48 Identities=8% Similarity=0.194 Sum_probs=42.6
Q ss_pred eeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceee
Q 004725 561 VSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLR 611 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~ 611 (733)
++..--.||..+..+...|+.+|++.+|+++..+.+-++.|...| ++.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G---vI~ 54 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAG---IIT 54 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC---Cee
Confidence 455677788888888899999999999999999999999999988 775
No 83
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.48 E-value=16 Score=35.35 Aligned_cols=44 Identities=18% Similarity=0.184 Sum_probs=37.5
Q ss_pred HHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceee
Q 004725 565 QMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLR 611 (733)
Q Consensus 565 Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~ 611 (733)
...||.+.-.++.+|-++|+..+|++...++++|..|...+ ++.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~g---Lv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDAR---LAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC---CeE
Confidence 45566666666789999999999999999999999999887 776
No 84
>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=58.53 E-value=22 Score=28.57 Aligned_cols=46 Identities=20% Similarity=0.144 Sum_probs=41.2
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCc
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGK 607 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~ 607 (733)
.+=|+.++-++...+.-|+++|++.||-....+.-+|..++..|.+
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklG 54 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLG 54 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcC
Confidence 5679999999998889999999999999999999999999877655
No 85
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=57.48 E-value=17 Score=34.61 Aligned_cols=48 Identities=10% Similarity=0.125 Sum_probs=42.6
Q ss_pred eeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceee
Q 004725 561 VSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLR 611 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~ 611 (733)
+.-.-..||..+..+..+|+.+|++.+|++...+.+-++.|...| ++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G---vI~ 59 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQG---FIQ 59 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC---CeE
Confidence 355667788889999999999999999999999999999999888 775
No 86
>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=56.69 E-value=21 Score=27.52 Aligned_cols=38 Identities=18% Similarity=0.360 Sum_probs=31.3
Q ss_pred hCCCCc-CHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 573 NSIDRL-SYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 573 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.....+ |..+|++.+|++...+.++|..|...+ +|...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G---~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELEAEG---LVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEec
Confidence 333444 499999999999999999999999887 87654
No 87
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=56.26 E-value=19 Score=35.71 Aligned_cols=49 Identities=22% Similarity=0.387 Sum_probs=42.6
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
|..-..||-+......+.+.||++.+|+|...+..+++.|..++ |+..+
T Consensus 22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aG---lirT~ 70 (308)
T COG4189 22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAG---LIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcC---ceeee
Confidence 44556788888888899999999999999999999999999988 77654
No 88
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=55.97 E-value=16 Score=37.62 Aligned_cols=47 Identities=15% Similarity=0.195 Sum_probs=41.9
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
-|..|+.+.++++.+++.||++.+|++...+++-|..|-..+ +|.+.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g---~l~r~ 52 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAG---TVIRT 52 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEEE
Confidence 467889999999999999999999999999999999998876 77664
No 89
>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=55.73 E-value=21 Score=33.81 Aligned_cols=43 Identities=19% Similarity=0.163 Sum_probs=35.8
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceee
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLR 611 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~ 611 (733)
..|+...=.++.+|-+||+..+|++..++.+.|..|...+ ++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~---Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAG---LAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC---Cce
Confidence 4455544455689999999999999999999999999888 774
No 90
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=55.10 E-value=32 Score=33.05 Aligned_cols=55 Identities=20% Similarity=0.219 Sum_probs=42.8
Q ss_pred EEEEeeHHHHHHHHHHhCCCCc-CHHHHHHHc--CCChHHHHHHHHHhhhccCcceeeccC
Q 004725 557 HELNVSTYQMCVLMLFNSIDRL-SYKEIEQAT--EIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 557 ~~l~~s~~Qa~iLl~Fn~~~~~-t~~ei~~~t--~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+++--+.+..+|+.+..-.+.- +..+|++.+ +++.++++.+|..|...| +|.+..
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~g---li~k~~ 75 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLG---LIKKDG 75 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCC---CeEECC
Confidence 3334455666777666654443 899999999 999999999999999888 998864
No 91
>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=54.89 E-value=17 Score=32.04 Aligned_cols=57 Identities=16% Similarity=0.191 Sum_probs=43.1
Q ss_pred eehhccc-CCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceee
Q 004725 672 IVRIMKA-RRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRY 731 (733)
Q Consensus 672 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Y 731 (733)
|..+|.. .+.++.++|...+.++ ...++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~---~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKK---GPSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhc---CCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4455554 5679999999888765 2467889999999999999999997544343444
No 92
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=54.31 E-value=19 Score=37.05 Aligned_cols=47 Identities=17% Similarity=0.234 Sum_probs=41.9
Q ss_pred HHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 565 QMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 565 Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
|-.|+-+.++++.++++||++.+|+++.+++|=|..|...+ +|.+..
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g---~l~R~h 53 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQG---LLLRVH 53 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCC---cEEEEe
Confidence 56788899999999999999999999999999999999877 777643
No 93
>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=54.30 E-value=21 Score=23.88 Aligned_cols=28 Identities=14% Similarity=0.232 Sum_probs=22.7
Q ss_pred cCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 578 LSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 578 ~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
+|-+||++.+|++.+.+-+.|..|-..+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQG 30 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcC
Confidence 6789999999999999999999887655
No 94
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=53.46 E-value=21 Score=28.45 Aligned_cols=54 Identities=9% Similarity=0.089 Sum_probs=40.8
Q ss_pred hhhheehhcccCCC--CChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcce
Q 004725 668 IEAAIVRIMKARRV--LDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLY 729 (733)
Q Consensus 668 i~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y 729 (733)
.+..|...|+.++. ++..+|-. + ...+...+.+.+..|.++|||.++++.|..|
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 34567778888766 88777653 3 3456779999999999999999987765554
No 95
>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=53.40 E-value=31 Score=25.30 Aligned_cols=33 Identities=18% Similarity=0.386 Sum_probs=24.3
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHH
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQS 600 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 600 (733)
.+|-+.| ..++|+.||++.+|++...+......
T Consensus 11 ~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 11 EVIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 3444566 45789999999999999988776543
No 96
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=52.64 E-value=25 Score=33.97 Aligned_cols=64 Identities=16% Similarity=0.158 Sum_probs=50.1
Q ss_pred ceeEeecCcceEEEEEeeCCCceEEEEeeHHHHHHHHHHhC--CCCcCHHHHHHHcCCChHHHHHHHHHhhh
Q 004725 534 RRLTWQTNMGTADLKGTFGKGQKHELNVSTYQMCVLMLFNS--IDRLSYKEIEQATEIPAPELKRCLQSLAC 603 (733)
Q Consensus 534 R~L~w~~~l~~~~i~~~~~~~~~~~l~~s~~Qa~iLl~Fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 603 (733)
|.-.|.+.+|..+++ +.+.| .||+.||.-|+.-.. -..||.+.||+..+++.+++...|..+..
T Consensus 97 r~~~~~~~fg~~ep~-~vPkG-----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~~ 162 (179)
T PF06784_consen 97 RDTIPDFEFGFYEPE-KVPKG-----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFKP 162 (179)
T ss_pred CCCcccccccccCcc-cCCCC-----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcCC
Confidence 344578889998886 45553 468899988776543 35799999999999999999999988754
No 97
>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=52.37 E-value=8.8 Score=29.35 Aligned_cols=47 Identities=13% Similarity=0.333 Sum_probs=39.4
Q ss_pred hheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCC
Q 004725 670 AAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKV 724 (733)
Q Consensus 670 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~ 724 (733)
..|+..++.++.++..+|.+ .|..+...|.+=+..|-++|.|+|.-+
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 35777888899999888763 388899999999999999999998643
No 98
>PRK00215 LexA repressor; Validated
Probab=52.01 E-value=33 Score=33.83 Aligned_cols=52 Identities=19% Similarity=0.243 Sum_probs=42.2
Q ss_pred eeHHHHHHHHHHhC-----CCCcCHHHHHHHcCC-ChHHHHHHHHHhhhccCcceeeccCC
Q 004725 561 VSTYQMCVLMLFNS-----IDRLSYKEIEQATEI-PAPELKRCLQSLACVKGKHVLRKEPM 615 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~-----~~~~t~~ei~~~t~i-~~~~l~~~L~~L~~~k~~~iL~~~~~ 615 (733)
++.-|..+|....+ ....|+.||++.+|+ +...+.+.|..|...+ ++.+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g---~i~~~~~ 59 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKG---FIRRDPG 59 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCC---CEEeCCC
Confidence 36678888866652 446899999999999 9999999999999887 7876653
No 99
>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=51.99 E-value=4.9e+02 Score=31.14 Aligned_cols=23 Identities=4% Similarity=0.329 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCC
Q 004725 331 DFVQRLLDLKDKYDKVINSAFNN 353 (733)
Q Consensus 331 ~~i~~ll~l~~~~~~l~~~~F~~ 353 (733)
.+-+.++..|.++..++..|++|
T Consensus 679 ~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 679 AMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCC
Confidence 34567888999999999999875
No 100
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=51.27 E-value=36 Score=25.68 Aligned_cols=29 Identities=17% Similarity=0.370 Sum_probs=24.6
Q ss_pred HhCCCCcCHHHHHHHcCCChHHHHHHHHH
Q 004725 572 FNSIDRLSYKEIEQATEIPAPELKRCLQS 600 (733)
Q Consensus 572 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 600 (733)
|+.-...|.+||++.+|++...+..+|..
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 55567899999999999999988877764
No 101
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=51.14 E-value=26 Score=35.91 Aligned_cols=48 Identities=15% Similarity=0.184 Sum_probs=41.8
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
-|..|+..+++++.+++.||++.+|++...+++-|..|...+ ++.+..
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g---~i~r~~ 53 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESG---KLKKVR 53 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEec
Confidence 466788899999999999999999999999999999998766 776644
No 102
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=50.48 E-value=26 Score=27.64 Aligned_cols=56 Identities=13% Similarity=0.283 Sum_probs=34.2
Q ss_pred hhhhhhhhheehhcccCC-CCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCC
Q 004725 663 DRKPQIEAAIVRIMKARR-VLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVD 725 (733)
Q Consensus 663 ~r~~~i~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~ 725 (733)
+|+..|=.+|...++.++ .-+..|| .+.+. +. +..-+...++.|.++|||+|+++.
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEI----a~~~g--~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREI----AEALG--LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHH----HHHHT--SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHH----HHHhC--CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 344445555555555543 3333333 34432 32 578899999999999999999764
No 103
>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=50.19 E-value=20 Score=25.81 Aligned_cols=31 Identities=19% Similarity=0.239 Sum_probs=22.2
Q ss_pred HHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHH
Q 004725 567 CVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQ 599 (733)
Q Consensus 567 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 599 (733)
.|+-++.++ +|+.+|++.+|++...+.+.|.
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 345556664 8999999999999999988775
No 104
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=48.84 E-value=38 Score=27.65 Aligned_cols=43 Identities=19% Similarity=0.254 Sum_probs=31.8
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
+.||.... .++.+..+|+..+|++...+.+.|..|...+ ++..
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~g---LI~~ 51 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKG---LIKK 51 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTT---SEEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCc---CeeC
Confidence 45666665 5678899999999999999999999999887 7744
No 105
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=48.27 E-value=18 Score=35.17 Aligned_cols=46 Identities=9% Similarity=0.075 Sum_probs=40.7
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
-+..|+...+.++.+++.+|++.+|++...+++-|..|...+ ++.+
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g---~~~r 53 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPE---LRER 53 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcch---HHHH
Confidence 567888899999999999999999999999999999998876 5554
No 106
>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=47.49 E-value=34 Score=27.79 Aligned_cols=49 Identities=14% Similarity=0.225 Sum_probs=41.5
Q ss_pred HHHHHHHHHHhC--CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 563 TYQMCVLMLFNS--IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 563 ~~Qa~iLl~Fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
..|.++|...-. ..+++-.++...+|++...+-..++.|...+ ++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~g---LI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKG---LIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCC---CEEEEE
Confidence 467888887765 4678999999999999999999999999888 887754
No 107
>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=46.92 E-value=37 Score=25.24 Aligned_cols=24 Identities=33% Similarity=0.506 Sum_probs=17.5
Q ss_pred CCcCHHHHHHHcCCChHHHHHHHH
Q 004725 576 DRLSYKEIEQATEIPAPELKRCLQ 599 (733)
Q Consensus 576 ~~~t~~ei~~~t~i~~~~l~~~L~ 599 (733)
+++|+.||++.+|++...+...+.
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 368999999999999999887764
No 108
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=46.17 E-value=39 Score=31.39 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=42.2
Q ss_pred eeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 561 VSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
+.-.-.-||..+..+...++.+|++.+|++...+.+-+..|...| ++..
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~G---iI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEG---VIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC---ceee
Confidence 344566788888888889999999999999999999999999888 7764
No 109
>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=46.11 E-value=38 Score=28.50 Aligned_cols=45 Identities=13% Similarity=0.275 Sum_probs=37.2
Q ss_pred HHHHHHHHhCCCCcCHHHHHHHc-CCChHHHHHHHHHhhhccCcceeecc
Q 004725 565 QMCVLMLFNSIDRLSYKEIEQAT-EIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 565 Qa~iLl~Fn~~~~~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
-+.||..... +...++||.+.+ |++...|...|..|...+ ++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~G---Lv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAG---LVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTT---SEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcc---hhhcc
Confidence 3566766666 688999999999 999999999999999988 88764
No 110
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=45.86 E-value=30 Score=35.90 Aligned_cols=50 Identities=6% Similarity=0.054 Sum_probs=42.8
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.--|..|+.+.+.++.+++.||++.+|++...++|-|..|-..+ ++.+..
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G---~l~r~~ 65 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQG---IAVRAY 65 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCC---CeEEEe
Confidence 34578889999999899999999999999999999999997766 666543
No 111
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=45.37 E-value=33 Score=35.26 Aligned_cols=48 Identities=15% Similarity=0.198 Sum_probs=41.7
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
-+..|+...++++.+++.||++.++++...+++-|..|...+ +|.+..
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g---~l~r~~ 53 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQN---KILRHH 53 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCC---CEEEec
Confidence 466788888999999999999999999999999999998877 776653
No 112
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=45.15 E-value=75 Score=28.79 Aligned_cols=68 Identities=18% Similarity=0.178 Sum_probs=50.1
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCC---CeEeecccCc
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAED---DAFFFNDKFT 632 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~---~~f~~N~~f~ 632 (733)
|+--..+|-+..+.+..|+.|+++.+|-+.+.+-+.|..|...+ |+..+.+|....|. +.+.++-.|.
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~G---lI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLG---LIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcC---eEEEecCCcccCceeeccccEEeeecC
Confidence 33444567778888899999999999999999999999999877 88776544433332 3445555554
No 113
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.19 E-value=47 Score=24.37 Aligned_cols=39 Identities=26% Similarity=0.328 Sum_probs=29.8
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhh
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLA 602 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 602 (733)
+.-+..++.++. .+++..+|++.+|++...+...+..+.
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 445555665553 357999999999999999988887654
No 114
>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=43.60 E-value=28 Score=34.16 Aligned_cols=51 Identities=22% Similarity=0.253 Sum_probs=41.9
Q ss_pred eeHHHHHHHHHHhC-----CCCcCHHHHHHHcCCC-hHHHHHHHHHhhhccCcceeeccC
Q 004725 561 VSTYQMCVLMLFNS-----IDRLSYKEIEQATEIP-APELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
++..|..||....+ ....|+.||++.+|++ ...+.++|..|...+ +|.+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g---~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKG---YIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCC---CEecCC
Confidence 46788888877653 2347899999999998 999999999999887 887653
No 115
>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=43.05 E-value=51 Score=24.26 Aligned_cols=39 Identities=23% Similarity=0.279 Sum_probs=28.7
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhh
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLA 602 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 602 (733)
+..|..++.++- +++|..+|++.+|++...+...+..+.
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344555554443 468999999999999999888877654
No 116
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=42.84 E-value=41 Score=34.23 Aligned_cols=47 Identities=13% Similarity=0.215 Sum_probs=39.5
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
-|..|+..+++++.++++||++.+|++...+++-|..|...+ .|.+.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~---~l~r~ 51 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQG---KILRN 51 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEe
Confidence 356688888888899999999999999999999999997754 55443
No 117
>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=42.68 E-value=14 Score=35.96 Aligned_cols=58 Identities=17% Similarity=0.292 Sum_probs=39.7
Q ss_pred hhhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 667 QIEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 667 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
.++ ..|...|.+|.+..++|- ..|...++++-.+|..|...|-|.---+|++.|+||.
T Consensus 100 lL~-~Fi~yIK~~Kvv~ledla--------~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQ-EFINYIKEHKVVNLEDLA--------AEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHH-HHHHHHHH-SEE-HHHHH--------HHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHH-HHHHHHHHcceeeHHHHH--------HHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 444 445888999999888773 2388899999999999999999988878899999984
No 118
>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=42.24 E-value=39 Score=26.72 Aligned_cols=37 Identities=27% Similarity=0.244 Sum_probs=30.9
Q ss_pred HHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhh
Q 004725 567 CVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLAC 603 (733)
Q Consensus 567 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 603 (733)
.|--+.++...+|+.+|++.||+++.++..+|-=|..
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar 48 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR 48 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4556778888999999999999999999999986654
No 119
>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=42.10 E-value=42 Score=27.74 Aligned_cols=35 Identities=3% Similarity=0.060 Sum_probs=30.7
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHH
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQ 599 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 599 (733)
-++.|+-...+ +.+|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 46778888888 899999999999999999988763
No 120
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=42.05 E-value=35 Score=26.55 Aligned_cols=38 Identities=21% Similarity=0.414 Sum_probs=31.6
Q ss_pred CCCCc-CHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 574 SIDRL-SYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 574 ~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.++.+ |..+|++.+|++...+.++|..|...+ ++...+
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g---~i~~~~ 58 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEAEG---LIERRP 58 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTT---SEEEET
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCC---cEEEEC
Confidence 35678 999999999999999999999999888 887654
No 121
>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=41.63 E-value=4.7e+02 Score=27.97 Aligned_cols=154 Identities=14% Similarity=0.247 Sum_probs=86.6
Q ss_pred hhHHhHccCcHhHHHHHHHhhccC---CCChHHHHHHHHHHHHHHHhHhhcCccc----CCCchHHHHHHHHHHHHHHH-
Q 004725 274 GLVNMLVDDKYEDLGRMYCLFRRV---PSGLILIRDVMTSYIRDTGKQLVSDPER----LKDPVDFVQRLLDLKDKYDK- 345 (733)
Q Consensus 274 ~~~~ll~~~~~~~L~~ly~l~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~----~~~~~~~i~~ll~l~~~~~~- 345 (733)
.|..-...++.+.+.|.++||--+ ++|++....-+.+.|.....+.++.... ...+.-|...|..+++.+-.
T Consensus 15 ~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~LFe~ia~i 94 (331)
T PF08318_consen 15 KFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTKLFEHIATI 94 (331)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHHHHHHHHHH
Confidence 566777788899999999998644 4577766666666666666666655422 22445556666666655444
Q ss_pred ------HHHHhcCCcHH--HHHHHHHHH----HHhhcC---CCCc---hHHHHHHHHHHhhc--------C---------
Q 004725 346 ------VINSAFNNDKT--FQNALNSSF----EYFINL---NSRS---PEFISLFVDDKLRK--------G--------- 390 (733)
Q Consensus 346 ------l~~~~F~~~~~--f~~~l~~af----~~~ln~---~~~~---~e~La~y~D~~l~~--------~--------- 390 (733)
+|..+||.... +...+..-+ ..++.. .-++ ...+-.|-...+.+ +
T Consensus 95 i~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 174 (331)
T PF08318_consen 95 IEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSSRAASSSQS 174 (331)
T ss_pred HHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhcccccccccccccccccccc
Confidence 45568886532 111111111 112221 1111 12233333333322 0
Q ss_pred -CCCCChHHHHHHHHhHhhhhccccchHHHHHHHHHHHHhHhcCC
Q 004725 391 -LRGVSEEDVENVLDKVMMLFRFLQEKDVFEKYYKQHLAKRLLSG 434 (733)
Q Consensus 391 -~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~ 434 (733)
..+.+.-+++..|+++..+.+. -..|.++++.|.-..
T Consensus 175 ~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~ 212 (331)
T PF08318_consen 175 EDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEF 212 (331)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcc
Confidence 0112334678888888777753 358999999998774
No 122
>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=41.59 E-value=24 Score=34.22 Aligned_cols=26 Identities=35% Similarity=0.457 Sum_probs=22.5
Q ss_pred CcCHHHHHHHcCCChHHHHHHHHHhh
Q 004725 577 RLSYKEIEQATEIPAPELKRCLQSLA 602 (733)
Q Consensus 577 ~~t~~ei~~~t~i~~~~l~~~L~~L~ 602 (733)
.+|+++|++.||+..+++..+|+.|-
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 69999999999999999999999873
No 123
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=41.55 E-value=34 Score=25.84 Aligned_cols=45 Identities=9% Similarity=0.178 Sum_probs=31.7
Q ss_pred ehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCC
Q 004725 673 VRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDR 726 (733)
Q Consensus 673 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~ 726 (733)
++.+. .+.++..++.. . +..+...+.+.|+.|.++|++.+.....
T Consensus 3 l~~l~-~~~~~~~~i~~----~----l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 3 LKLLA-EGELCVCELAE----I----LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHhh-cCCccHHHHHH----H----HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 34444 55667666543 2 3457789999999999999999876443
No 124
>PRK06474 hypothetical protein; Provisional
Probab=39.58 E-value=82 Score=30.43 Aligned_cols=53 Identities=17% Similarity=0.225 Sum_probs=41.7
Q ss_pred EEeeHHHHHHHHHHhCCCC-cCHHHHHHHc-CCChHHHHHHHHHhhhccCcceeeccC
Q 004725 559 LNVSTYQMCVLMLFNSIDR-LSYKEIEQAT-EIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 559 l~~s~~Qa~iLl~Fn~~~~-~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+-.++.-..||..+-..++ +|..+|++.+ +++...+-++|..|...+ ++....
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~G---LI~~~~ 61 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSG---ILHVVK 61 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCC---CEEEee
Confidence 3446666777766655444 9999999999 799999999999999988 887643
No 125
>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=39.57 E-value=31 Score=26.93 Aligned_cols=46 Identities=13% Similarity=0.323 Sum_probs=30.4
Q ss_pred hhheehhcc-cCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhccccc
Q 004725 669 EAAIVRIMK-ARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERD 722 (733)
Q Consensus 669 ~A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd 722 (733)
+..|.+.+. ....++..+|.. .+..+...+-+.|+.|+++|||++.
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~--------~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAE--------RLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHH--------HTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHccCCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEec
Confidence 345555666 566777655542 3556778899999999999999765
No 126
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=39.49 E-value=90 Score=25.75 Aligned_cols=41 Identities=12% Similarity=0.088 Sum_probs=33.5
Q ss_pred HHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceee
Q 004725 570 MLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLR 611 (733)
Q Consensus 570 l~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~ 611 (733)
+..++.+.+|=++|++.+|++...+-++++.|-..++. |..
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~-I~s 52 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVD-IES 52 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCc-eEe
Confidence 34455667999999999999999999999999877755 543
No 127
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=39.25 E-value=71 Score=26.13 Aligned_cols=40 Identities=15% Similarity=0.212 Sum_probs=29.1
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhh
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLAC 603 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 603 (733)
+.-.+|-+.-....+|..+|+..+|.+.+++..+|..+-+
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p~ 64 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMPD 64 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-TT
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCCC
Confidence 3455667777889999999999999999999999987743
No 128
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=38.51 E-value=74 Score=28.62 Aligned_cols=43 Identities=19% Similarity=0.261 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 563 TYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 563 ~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.+.+-|+.+--+++.+|+.++...||++-..+.+.+.-|+..+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G 54 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARG 54 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence 4567788888889999999999999999999999999999876
No 129
>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=38.44 E-value=65 Score=25.72 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=30.2
Q ss_pred CcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 577 RLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 577 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.+|-++|++.+|++...+.+.|.-|...+ ++...
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g---~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEG---IIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTT---SEEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEEc
Confidence 47899999999999999999999998877 77654
No 130
>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=38.16 E-value=56 Score=27.79 Aligned_cols=42 Identities=19% Similarity=0.190 Sum_probs=34.2
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
....+.-.+.....+++++|++.++++.+++...+..++..|
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~ 88 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNG 88 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCC
Confidence 344455555678899999999999999999999999998876
No 131
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=38.14 E-value=68 Score=27.33 Aligned_cols=53 Identities=19% Similarity=0.271 Sum_probs=44.3
Q ss_pred EEeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 559 LNVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 559 l~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+..+.....||..+...+.=...-|+..+++|.+++...|..|...| +|.+..
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~G---Ller~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMG---LLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCC---CeEEec
Confidence 34567778889888877666778899999999999999999999988 887764
No 132
>PRK11050 manganese transport regulator MntR; Provisional
Probab=37.17 E-value=74 Score=29.82 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=36.7
Q ss_pred HHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 567 CVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 567 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.|+.++..++.++..+|++.++++...+.+.|..|...+ ++...
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~G---lI~r~ 84 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDG---LVEMR 84 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEEe
Confidence 444566677789999999999999999999999998876 77653
No 133
>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=36.76 E-value=1.1e+02 Score=25.12 Aligned_cols=48 Identities=10% Similarity=0.209 Sum_probs=38.4
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+++.|=+.-..+..+.-.+|++.++++...++..+..|-..+ +|...|
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lG---lve~~p 57 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELG---LVESQP 57 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCC---CccCCC
Confidence 445554555567789999999999999999999999998877 886543
No 134
>PHA02943 hypothetical protein; Provisional
Probab=35.99 E-value=72 Score=29.69 Aligned_cols=42 Identities=17% Similarity=0.103 Sum_probs=32.8
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
||-.+ ..++.|..||++.+|++...+.-+|.-|-.-| .+.+.
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG---~VkrV 57 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEG---MVLKV 57 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcC---ceEEE
Confidence 45555 66678999999999999999999998776655 55443
No 135
>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=35.97 E-value=72 Score=26.38 Aligned_cols=32 Identities=9% Similarity=0.225 Sum_probs=28.8
Q ss_pred CCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 574 SIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 574 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.+..+++++|++.++++.+++...+..++..+
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~ 52 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDG 52 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCC
Confidence 46789999999999999999999999998776
No 136
>smart00753 PAM PCI/PINT associated module.
Probab=35.97 E-value=72 Score=26.38 Aligned_cols=32 Identities=9% Similarity=0.225 Sum_probs=28.8
Q ss_pred CCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 574 SIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 574 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.+..+++++|++.++++.+++...+..++..+
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~ 52 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDG 52 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCC
Confidence 46789999999999999999999999998776
No 137
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=35.90 E-value=41 Score=24.47 Aligned_cols=35 Identities=14% Similarity=0.238 Sum_probs=22.0
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhc
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACV 604 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~ 604 (733)
++.++.+ +.|..+|++.+|++...+.+-+..+...
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~~~ 44 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYREE 44 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT-----
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcccc
Confidence 4445554 7899999999999999998887766543
No 138
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=35.41 E-value=69 Score=29.48 Aligned_cols=42 Identities=14% Similarity=0.195 Sum_probs=35.2
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
|..+.+.++..++.+|++.++++...+.+.|..|...+ ++..
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~G---li~~ 54 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDE---YLIY 54 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCC---CEEE
Confidence 44455667788999999999999999999999999877 7754
No 139
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=35.22 E-value=53 Score=33.68 Aligned_cols=40 Identities=15% Similarity=0.178 Sum_probs=36.5
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhh
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLAC 603 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 603 (733)
-|..|+.+.+.++.+++.+|++.+|+++..+++-|..|-.
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 4778999999999999999999999999999999998763
No 140
>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=35.12 E-value=19 Score=26.15 Aligned_cols=44 Identities=9% Similarity=0.280 Sum_probs=32.8
Q ss_pred hhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhccc
Q 004725 669 EAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLE 720 (733)
Q Consensus 669 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~ 720 (733)
+-.|+..+.....++..+|-.. +..+.+.+.+.|..|.++|||+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~--------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEK--------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHH--------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH--------hCCCHHHHHHHHHHHHHCcCcC
Confidence 4456777777888888777543 3458889999999999999985
No 141
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=35.05 E-value=53 Score=31.17 Aligned_cols=53 Identities=13% Similarity=0.171 Sum_probs=38.8
Q ss_pred cCCCceeEeecCcceEEEEEeeCCCceEEEEeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhc
Q 004725 530 THTGRRLTWQTNMGTADLKGTFGKGQKHELNVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACV 604 (733)
Q Consensus 530 ~~~~R~L~w~~~l~~~~i~~~~~~~~~~~l~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~ 604 (733)
+++.++|+|.++|- -|+-.+.- +.-..|+++|++.+|.++.+++++|+.=..+
T Consensus 36 ~~~~~~lTWvdSLa---------------------vAAga~ar-ekag~Ti~EIAeelG~TeqTir~hlkgetkA 88 (182)
T COG1318 36 KDPYERLTWVDSLA---------------------VAAGALAR-EKAGMTISEIAEELGRTEQTVRNHLKGETKA 88 (182)
T ss_pred hCcccccchhhHHH---------------------HHHHHHHH-HHccCcHHHHHHHhCCCHHHHHHHHhcchhh
Confidence 35788999987543 23323333 4457899999999999999999999865554
No 142
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=34.78 E-value=1.5e+02 Score=28.84 Aligned_cols=112 Identities=16% Similarity=0.183 Sum_probs=63.7
Q ss_pred cHHHHHHHHHHHHHHhccCCCceeEeecCcceEEEEEe--eCC------CceEEEEeeHHHHHHHHHHhCCCCcCHHHHH
Q 004725 513 PAEIMGICEKFRSYYLGTHTGRRLTWQTNMGTADLKGT--FGK------GQKHELNVSTYQMCVLMLFNSIDRLSYKEIE 584 (733)
Q Consensus 513 P~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~--~~~------~~~~~l~~s~~Qa~iLl~Fn~~~~~t~~ei~ 584 (733)
|.++..+++....-|.... |-+.-...-|...+..+ |.. +....-..|...+-+|-..--+..+|-.+|.
T Consensus 34 ~~~v~~~l~~L~~~y~~~~--~gi~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~ 111 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGDD--RGLKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEID 111 (188)
T ss_pred HHHHHHHHHHHHHHHhhCC--CCEEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHH
Confidence 3578899999999998653 33333322222222211 100 0112223455555555444445689999999
Q ss_pred HHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCc
Q 004725 585 QATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFT 632 (733)
Q Consensus 585 ~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~ 632 (733)
+.+|++. ..++..|...+ ++...+..........|.++..|-
T Consensus 112 ~irGv~~---~~ii~~L~~~g---LI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNS---DGALQTLLAKG---LIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCH---HHHHHHHHHCC---CeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999986 46677777767 776433211111345677777774
No 143
>PF05261 Tra_M: TraM protein, DNA-binding; InterPro: IPR007925 The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus [].; GO: 0003677 DNA binding, 0000746 conjugation; PDB: 3ON0_A 3OMY_B 1DP3_A 2G9E_A 3D8A_B 2G7O_A.
Probab=34.62 E-value=3.5e+02 Score=24.40 Aligned_cols=56 Identities=21% Similarity=0.459 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHHHHHhcCCCCC-hHHHHHHHHHHHHhCcccchh------------hhhHhHHHHHHH
Q 004725 151 IQTRLQDTLLELVQRERSGEVIN-RGLMRNITKMLMDLGSFVYQD------------DFEKHFLEVSAD 206 (733)
Q Consensus 151 l~~~l~~~il~~I~~~R~g~~i~-~~~lk~ii~~l~~lg~~~Y~~------------~FE~~~L~~t~~ 206 (733)
+++.+.+.|-+++...|..++-+ .--+.++..||.+||+-+|.. .|-+.+|+.+..
T Consensus 8 ~s~~v~~~I~~iVe~r~qeGA~~~dvs~SSv~smLlELGLrVY~~Q~E~k~s~Fnq~eFnk~lLe~v~k 76 (127)
T PF05261_consen 8 VSNKVLEEINDIVEERRQEGATEKDVSFSSVSSMLLELGLRVYEAQMERKESGFNQEEFNKVLLENVSK 76 (127)
T ss_dssp --HCHHHHHHHHHHHHHCCT-TTTT--HHHHHHHHHHCCCCHHHHCCHHCSSS--HHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHhHHHHHHHHhhccCCCCHHHHHHHHHHHHHH
Confidence 34567778888888888766533 234678899999999655553 455666665543
No 144
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=34.57 E-value=4.5e+02 Score=25.74 Aligned_cols=54 Identities=9% Similarity=0.244 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHHH-hcCCcHHHHHHHHHHHHHhhcCCCCchHHHHHHHHHHhhcC
Q 004725 331 DFVQRLLDLKDKYDKVINS-AFNNDKTFQNALNSSFEYFINLNSRSPEFISLFVDDKLRKG 390 (733)
Q Consensus 331 ~~i~~ll~l~~~~~~l~~~-~F~~~~~f~~~l~~af~~~ln~~~~~~e~La~y~D~~l~~~ 390 (733)
..|+.|-.-.+..+.++.. ||..+..+ +.+++| +..+-.+|.|-+|.|++=+.+
T Consensus 88 ~~IQqLqk~LK~aE~iLtta~fqA~qKL-ksi~~A-----~krpvsSEelIKyAHrIS~~N 142 (272)
T KOG4552|consen 88 EVIQQLQKNLKSAEVILTTACFQANQKL-KSIKEA-----EKRPVSSEELIKYAHRISKHN 142 (272)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH-----hcCCCCHHHHHHHHHHhhhcc
Confidence 3345554444444444444 66654443 333433 335667799999999987653
No 145
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=34.55 E-value=45 Score=24.17 Aligned_cols=45 Identities=13% Similarity=0.249 Sum_probs=32.9
Q ss_pred eehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCC
Q 004725 672 IVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKV 724 (733)
Q Consensus 672 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~ 724 (733)
|.+.+..+..++..+|... |..+...+.+.|..|.++|+|.+..+
T Consensus 5 il~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 5 ILELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 3444455566777666543 46688999999999999999998753
No 146
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=34.45 E-value=94 Score=31.23 Aligned_cols=49 Identities=16% Similarity=0.186 Sum_probs=37.2
Q ss_pred eeHHHHHHHHHH---hCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 561 VSTYQMCVLMLF---NSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 561 ~s~~Qa~iLl~F---n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
.+.-+.-+++.+ +...++|.++|++.+|+++..++.++..|++.+ ++..
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~---~~~~ 210 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCH---ILFT 210 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC---EEEE
Confidence 344554444332 335789999999999999999999999999877 7743
No 147
>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=34.33 E-value=62 Score=28.54 Aligned_cols=63 Identities=16% Similarity=0.169 Sum_probs=44.6
Q ss_pred hhhhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceee
Q 004725 666 PQIEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRY 731 (733)
Q Consensus 666 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Y 731 (733)
..+|+.|.+ -....-.....++.+|+.++. ..++...+--||+.||+.|.++-.++-.++-+|
T Consensus 47 d~yD~~Il~-~~~~~~~~~arvIg~vl~~~~--~~i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 47 DYYDDFILE-QAPDEFQKAARVIGEVLGHSD--QGIGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HHhhHHHHh-cCCccccHHHHHHHHHHHhcC--cCCChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 345555555 122344566788999998874 336778999999999999999998765555444
No 148
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=34.15 E-value=42 Score=29.11 Aligned_cols=46 Identities=13% Similarity=0.278 Sum_probs=38.0
Q ss_pred hhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccc
Q 004725 668 IEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLER 721 (733)
Q Consensus 668 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r 721 (733)
+|-.|++.+.....++..+|-.. +..+...+.+++..|.++|+|+|
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 45678888888888888777543 46688999999999999999995
No 149
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=33.14 E-value=72 Score=32.73 Aligned_cols=42 Identities=14% Similarity=0.279 Sum_probs=35.2
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
||++.-+ +..|++||.+.++++...+..+|.-|.+.+ ++.++
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~~~~---LV~~~ 59 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLKDKG---LVVQE 59 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHhhCC---CEEec
Confidence 4444544 678999999999999999999999999877 77765
No 150
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=32.94 E-value=51 Score=35.72 Aligned_cols=66 Identities=23% Similarity=0.278 Sum_probs=40.8
Q ss_pred eEeecCcceEEEEEeeCCCceE-EEE----eeHHHHHHHHHHhC-CC-CcCHHHHHHHcCCChHHHHHHHHHhh
Q 004725 536 LTWQTNMGTADLKGTFGKGQKH-ELN----VSTYQMCVLMLFNS-ID-RLSYKEIEQATEIPAPELKRCLQSLA 602 (733)
Q Consensus 536 L~w~~~l~~~~i~~~~~~~~~~-~l~----~s~~Qa~iLl~Fn~-~~-~~t~~ei~~~t~i~~~~l~~~L~~L~ 602 (733)
+.+.+.||..|=++--+. +.. +|- -+-+-..||-.+-+ .+ .+|+++|++.|||..+++...|++|-
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 477788887776433222 211 000 02233344433333 22 39999999999999999999999884
No 151
>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=32.76 E-value=1.2e+02 Score=27.65 Aligned_cols=50 Identities=16% Similarity=0.181 Sum_probs=39.6
Q ss_pred eeHHHHHHHHHHhCCCCcCHHHHHHHc----CCChHHHHHHHHHhhhccCcceeecc
Q 004725 561 VSTYQMCVLMLFNSIDRLSYKEIEQAT----EIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~~~~~t~~ei~~~t----~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
+|..+..|+..+=+.+..|+.+|.+.+ |++...+...|..|...| ++...
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG---~v~~~ 55 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKG---CLTTE 55 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCC---ceeee
Confidence 466788888777666789999977665 788899999999999877 77643
No 152
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=32.56 E-value=63 Score=32.36 Aligned_cols=58 Identities=17% Similarity=0.286 Sum_probs=43.8
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCc
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFT 632 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~ 632 (733)
+-..++-+|.++..||+.+|.+.|+=|+..|+.+|..++ ++.+.++ ...+|.+-+.|.
T Consensus 187 vld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic------v~NkKg~-----~k~tyeLKPEYK 244 (254)
T KOG2905|consen 187 VLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC------VLNKKGP-----YKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH------HHhccCc-----ccCceecCHHHh
Confidence 334566788899999999999999999999999999887 4544321 245677666653
No 153
>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=32.51 E-value=24 Score=26.94 Aligned_cols=47 Identities=9% Similarity=0.214 Sum_probs=30.8
Q ss_pred hheehhcccCCC--CChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCC
Q 004725 670 AAIVRIMKARRV--LDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKV 724 (733)
Q Consensus 670 A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~ 724 (733)
..|...+..... ++..+|.. . +..+...+.+.|..|.++|||+|..+
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~----~----l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAE----R----LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHH----H----HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHCCCCCcCHHHHHH----H----HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 334444444444 56655543 2 34577899999999999999999754
No 154
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=32.15 E-value=91 Score=29.34 Aligned_cols=45 Identities=18% Similarity=0.327 Sum_probs=37.2
Q ss_pred HHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 567 CVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 567 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+|..+..+.......+|++.+|+++..+..+++-|...+ ++...|
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~G---lV~~~~ 58 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLG---LVEYEP 58 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCC---CeEEec
Confidence 344455567789999999999999999999999998877 776654
No 155
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=32.14 E-value=30 Score=34.91 Aligned_cols=35 Identities=11% Similarity=0.223 Sum_probs=29.0
Q ss_pred hccCCCCChHHHHHHHHHhhhhhcccccCCCCccee
Q 004725 695 LQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYR 730 (733)
Q Consensus 695 l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~ 730 (733)
|..+|..+...|+++|+.|++.|+|.|..+ +++|+
T Consensus 30 La~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 30 LMDQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 334599999999999999999999999864 55654
No 156
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=32.12 E-value=20 Score=27.18 Aligned_cols=45 Identities=16% Similarity=0.352 Sum_probs=31.0
Q ss_pred heehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccC
Q 004725 671 AIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDK 723 (733)
Q Consensus 671 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~ 723 (733)
.+..++-....++..+|-. .+..+...+-+.+..|.++|||+|..
T Consensus 7 ~iL~~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 7 RILRILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 3444444555666665532 24558889999999999999999964
No 157
>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=32.03 E-value=86 Score=23.73 Aligned_cols=40 Identities=23% Similarity=0.262 Sum_probs=32.0
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhh
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLAC 603 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 603 (733)
|.-+..||.++.. +.+..+|++.+|+++..+..++..+..
T Consensus 5 T~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 5 TERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp -HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 5667778877776 468999999999999999999888765
No 158
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=31.77 E-value=83 Score=31.29 Aligned_cols=44 Identities=23% Similarity=0.243 Sum_probs=35.8
Q ss_pred HHHHHHhCC-CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 567 CVLMLFNSI-DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 567 ~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.||.++-++ .+.|.+||++.+|+++..++.++..|...+ ++...
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~---~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRH---LIIAE 210 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCC---eEEEE
Confidence 566666553 268999999999999999999999999887 66543
No 159
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=31.76 E-value=1.1e+02 Score=22.44 Aligned_cols=34 Identities=15% Similarity=0.345 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHH
Q 004725 565 QMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQS 600 (733)
Q Consensus 565 Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 600 (733)
.+.|+.+.-+. .|+.+++..+|++...+.+.+..
T Consensus 17 ~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 17 EQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 34444443332 69999999999999999988764
No 160
>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=31.49 E-value=35 Score=26.98 Aligned_cols=54 Identities=22% Similarity=0.197 Sum_probs=32.0
Q ss_pred hhheehhcccC-CCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 669 EAAIVRIMKAR-RVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 669 ~A~IVRimK~~-k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
=|.||..||++ +.++.+||..++. +..+ .+.++.|-+.+=|+-|+++ +.|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l~------~d~~----~~~~~~Lk~npKI~~d~~~-~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYLS------LDIG----KKLKQWLKNNPKIEYDPDG-NTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHHT------SSS-----HHHHHHHHH-TTEEEE-TT--CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHc------CCCC----HHHHHHHHcCCCEEEecCC-CEEEecc
Confidence 36789999996 6788887775543 4333 2344556688889998643 6899976
No 161
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=30.97 E-value=36 Score=25.51 Aligned_cols=28 Identities=7% Similarity=0.175 Sum_probs=24.4
Q ss_pred cCCCCChHHHHHHHHHhhhhhcccccCC
Q 004725 697 SRFLPNPVVIKKRIESLIEREFLERDKV 724 (733)
Q Consensus 697 ~~F~~~~~~ik~~Ie~LIereyi~rd~~ 724 (733)
..|..+...+.+.+..|.+.|+|.+..+
T Consensus 28 ~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 28 AQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3578899999999999999999988754
No 162
>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=30.54 E-value=1e+02 Score=21.92 Aligned_cols=39 Identities=23% Similarity=0.323 Sum_probs=28.0
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHh
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSL 601 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 601 (733)
+..+..++.++-- ++++..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4455555544432 45899999999999999988877643
No 163
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=30.03 E-value=34 Score=34.74 Aligned_cols=34 Identities=18% Similarity=0.262 Sum_probs=28.4
Q ss_pred ccCCCCChHHHHHHHHHhhhhhcccccCCCCccee
Q 004725 696 QSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYR 730 (733)
Q Consensus 696 ~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~ 730 (733)
...|..+...++++|+.|++.|+|.|..+ +++|+
T Consensus 40 a~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 40 CTQYNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 34588999999999999999999999854 56654
No 164
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=29.58 E-value=1.3e+02 Score=23.65 Aligned_cols=37 Identities=16% Similarity=0.175 Sum_probs=29.8
Q ss_pred HHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccC
Q 004725 569 LMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKG 606 (733)
Q Consensus 569 Ll~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~ 606 (733)
+-.+.+. ..+..+|++.+|++...+.+.+..|-..+.
T Consensus 6 l~~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~ 42 (69)
T TIGR00122 6 LALLADN-PFSGEKLGEALGMSRTAVNKHIQTLREWGV 42 (69)
T ss_pred HHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 3344443 478999999999999999999999977663
No 165
>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=29.51 E-value=74 Score=28.62 Aligned_cols=50 Identities=8% Similarity=0.127 Sum_probs=38.4
Q ss_pred eeHHHHHHHHH--Hh--------CCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 561 VSTYQMCVLML--FN--------SIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 561 ~s~~Qa~iLl~--Fn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
+..+.-.+++. .| ..-..|.++||..++-+.+.++.+|..|.+.+ ++...
T Consensus 27 ~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~k~g---lIe~~ 86 (121)
T PF09681_consen 27 TVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQKLG---LIEID 86 (121)
T ss_pred HHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEEe
Confidence 34455555555 44 44578999999999999999999999998766 77654
No 166
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=29.45 E-value=82 Score=32.68 Aligned_cols=39 Identities=26% Similarity=0.331 Sum_probs=30.7
Q ss_pred HHHHHHHHHhC-CCCcCHHHHHHHcCCChHHHHHHHHHhh
Q 004725 564 YQMCVLMLFNS-IDRLSYKEIEQATEIPAPELKRCLQSLA 602 (733)
Q Consensus 564 ~Qa~iLl~Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 602 (733)
+...|+-.+.+ ...+|+++|+..|||..+++..+|++|-
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 44555544443 5789999999999999999999999773
No 167
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=29.36 E-value=5e+02 Score=24.61 Aligned_cols=59 Identities=19% Similarity=0.298 Sum_probs=42.7
Q ss_pred HHHHHHHHhC-CCCcCHHHHHHHc--CCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeeccc
Q 004725 565 QMCVLMLFNS-IDRLSYKEIEQAT--EIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDK 630 (733)
Q Consensus 565 Qa~iLl~Fn~-~~~~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~ 630 (733)
...|+-.|.. +.++|+.+|...+ +++...+.++|..|+..| . |..+. +...-+|..|.+
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g-~-i~~K~-----~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEG-K-IVEKE-----YGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCC-C-eeeee-----ecceEEEeeCcc
Confidence 3567766665 5689999999988 588999999999999875 2 55443 223456766654
No 168
>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=29.16 E-value=1.2e+02 Score=26.49 Aligned_cols=57 Identities=18% Similarity=0.233 Sum_probs=40.8
Q ss_pred HHHHHHhC-CCCcCHHHHHHHc-----CCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecc
Q 004725 567 CVLMLFNS-IDRLSYKEIEQAT-----EIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFND 629 (733)
Q Consensus 567 ~iLl~Fn~-~~~~t~~ei~~~t-----~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~ 629 (733)
.||..+.+ ...+|.+||.+.+ +++...+-++|..|...+ ++.+...+. ....|.++.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~G---li~~~~~~~---~~~~y~~~~ 67 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAG---LVREIELGD---GKARYELNT 67 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCC---CEEEEEeCC---CceEEEeCC
Confidence 45555544 4569999999988 689999999999999988 887653211 124566654
No 169
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=28.96 E-value=1e+02 Score=30.84 Aligned_cols=45 Identities=18% Similarity=0.206 Sum_probs=36.9
Q ss_pred HHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 566 MCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
.+.+-..++...+|..+|++.++++...+.+.|..|...+ ++.+.
T Consensus 10 iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~G---lI~R~ 54 (217)
T PRK14165 10 LALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEG---YITRT 54 (217)
T ss_pred HHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEE
Confidence 3344445556679999999999999999999999999887 88765
No 170
>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=28.43 E-value=50 Score=26.93 Aligned_cols=27 Identities=30% Similarity=0.274 Sum_probs=20.7
Q ss_pred hhhhhheehhcccCC--CCChHHHHHHHH
Q 004725 666 PQIEAAIVRIMKARR--VLDHNNIVTEVT 692 (733)
Q Consensus 666 ~~i~A~IVRimK~~k--~l~~~~L~~~v~ 692 (733)
...=|.||..||++. .++.+|+..++.
T Consensus 8 ~t~l~~aV~ymK~r~~~Plt~~EIl~~ls 36 (75)
T cd07977 8 FTQLAKIVDYMKKRHQHPLTLDEILDYLS 36 (75)
T ss_pred hhhHHHHHHHHHhcCCCCccHHHHHHHHh
Confidence 344578999999975 888888887664
No 171
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=28.41 E-value=39 Score=34.32 Aligned_cols=55 Identities=18% Similarity=0.359 Sum_probs=38.9
Q ss_pred hhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCccee
Q 004725 668 IEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYR 730 (733)
Q Consensus 668 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~ 730 (733)
|...|...++....|.-+ .+|...|..+...|+++|+.|++.|+|.|..+ +++|+
T Consensus 21 L~~~I~~~~~~G~~LPsE-------~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 21 LEQELRQHYRCGDYLPAE-------QQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred HHHHHhcccCCCCcCCCH-------HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 444444456666666542 23334599999999999999999999999864 45554
No 172
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=28.29 E-value=1.5e+02 Score=22.10 Aligned_cols=41 Identities=12% Similarity=0.092 Sum_probs=33.2
Q ss_pred HHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 570 MLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 570 l~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
-+|++++.+|+++..+.+|++-+.....|..|=..+ +..+.
T Consensus 3 ~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g---~T~R~ 43 (50)
T PF09107_consen 3 ELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLDREG---ITRRV 43 (50)
T ss_dssp HHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTT---SEEEE
T ss_pred HHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHhccC---CEEEe
Confidence 467788999999999999999999999998886555 55554
No 173
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.69 E-value=75 Score=29.58 Aligned_cols=32 Identities=16% Similarity=0.141 Sum_probs=28.9
Q ss_pred CCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 574 SIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 574 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.++.+|-++|++.+|++...+.+.|..|-..+
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~ 43 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDEK 43 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhh
Confidence 34579999999999999999999999998866
No 174
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=27.59 E-value=39 Score=34.04 Aligned_cols=33 Identities=27% Similarity=0.469 Sum_probs=28.0
Q ss_pred cCCCCChHHHHHHHHHhhhhhcccccCCCCccee
Q 004725 697 SRFLPNPVVIKKRIESLIEREFLERDKVDRKLYR 730 (733)
Q Consensus 697 ~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~ 730 (733)
.+|..+...++++|+.|.+.|+|.|..+ +++|+
T Consensus 40 ~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 40 ERFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 3599999999999999999999999854 45554
No 175
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=27.08 E-value=3e+02 Score=26.47 Aligned_cols=23 Identities=13% Similarity=0.297 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhh
Q 004725 98 ELNRKWADHNKALQMIRDILMYM 120 (733)
Q Consensus 98 ~~~~~W~~~~~~~~~l~~if~YL 120 (733)
...+.|.-|..-+.-|.+|+.+|
T Consensus 167 ~~~eae~yY~~Tv~slddVl~~l 189 (190)
T PLN02999 167 KVYESYLYYEKTLKSIDNVVELL 189 (190)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHh
Confidence 35578999999999999999887
No 176
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=26.67 E-value=83 Score=21.99 Aligned_cols=28 Identities=11% Similarity=0.270 Sum_probs=20.4
Q ss_pred CCCcCHHHHHHHcCCChHHHHHHHHHhh
Q 004725 575 IDRLSYKEIEQATEIPAPELKRCLQSLA 602 (733)
Q Consensus 575 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 602 (733)
...+++++|++..|++...+.+..+...
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 4579999999999999998888877554
No 177
>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=26.63 E-value=93 Score=32.39 Aligned_cols=59 Identities=24% Similarity=0.349 Sum_probs=33.2
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccC
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKF 631 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f 631 (733)
+-+--.|.-+|..+..|++.+|.+.|+-|+..|+.+|..++ ++.+.++ ....|.|=+.|
T Consensus 215 ~eL~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa------~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 215 NELLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA------VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH--------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH------HHhccCC-----cCCcEecchHH
Confidence 33455677889999999999999999999999999999886 5655532 13556655544
No 178
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=26.47 E-value=1.2e+02 Score=26.03 Aligned_cols=53 Identities=9% Similarity=0.158 Sum_probs=43.8
Q ss_pred hhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccc
Q 004725 668 IEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLER 721 (733)
Q Consensus 668 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r 721 (733)
++-+|..++. .+.++=-+|.+.+.+.....+.++...+=..+..|-++|+|++
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 4556666776 4678889999998877655678899999999999999999998
No 179
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=26.09 E-value=93 Score=30.90 Aligned_cols=55 Identities=18% Similarity=0.271 Sum_probs=42.1
Q ss_pred HHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCCCCCCCCCCeEeecccCc
Q 004725 567 CVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPMSKDIAEDDAFFFNDKFT 632 (733)
Q Consensus 567 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~~~~~~~~~~f~~N~~f~ 632 (733)
.++-+|.+.+.||+..|++-+|=|+..|+.+|.+.+ +|.+.++ -...|.+-+.|.
T Consensus 199 ~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~ia------vLnKkgp-----ya~kY~LrPEYK 253 (297)
T COG5090 199 MLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIA------VLNKKGP-----YANKYELRPEYK 253 (297)
T ss_pred HHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHH------hhhccCc-----ccceeecCHHHH
Confidence 355678999999999999999999999999998876 5655432 134566666664
No 180
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=26.03 E-value=39 Score=28.30 Aligned_cols=39 Identities=26% Similarity=0.250 Sum_probs=33.2
Q ss_pred hccCCCCChHHHHHHHHHhhhhhcccccCCCCcceeecC
Q 004725 695 LQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRYLA 733 (733)
Q Consensus 695 l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Yva 733 (733)
+..++....+.-+++|..|.++|.|+.-..+...-.|.|
T Consensus 47 lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 47 LASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 334678888999999999999999988877778888876
No 181
>PRK13239 alkylmercury lyase; Provisional
Probab=25.74 E-value=1.2e+02 Score=30.03 Aligned_cols=39 Identities=18% Similarity=0.243 Sum_probs=34.4
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhh
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLA 602 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 602 (733)
+...||.++-++...|+++|+..+|.+.+.+...|+.|-
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 556677778889999999999999999999999999874
No 182
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.58 E-value=47 Score=24.74 Aligned_cols=21 Identities=14% Similarity=0.279 Sum_probs=18.3
Q ss_pred CCCChHHHHHHHHHhhhhhcc
Q 004725 699 FLPNPVVIKKRIESLIEREFL 719 (733)
Q Consensus 699 F~~~~~~ik~~Ie~LIereyi 719 (733)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 345788999999999999987
No 183
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=25.27 E-value=5.9e+02 Score=25.23 Aligned_cols=41 Identities=15% Similarity=0.201 Sum_probs=32.0
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeec
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRK 612 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~ 612 (733)
||.+..... .=+.+|+..+|++.+-+..+|.-|-.++ |+..
T Consensus 20 Il~lLt~~p-~yvsEiS~~lgvsqkAVl~HL~~LE~AG---lveS 60 (217)
T COG1777 20 ILQLLTRRP-CYVSEISRELGVSQKAVLKHLRILERAG---LVES 60 (217)
T ss_pred HHHHHhcCc-hHHHHHHhhcCcCHHHHHHHHHHHHHcC---Cchh
Confidence 344444433 4578999999999999999999999888 7764
No 184
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=25.19 E-value=76 Score=30.22 Aligned_cols=41 Identities=17% Similarity=0.224 Sum_probs=31.9
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
-|..-++.++. +++|++||++.||++...+-..+.-|...+
T Consensus 29 G~iYgilyls~-~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~ 69 (177)
T COG1510 29 GQIYGILYLSR-KPLTLDEIAEALGMSKSNVSMGLKKLQDWN 69 (177)
T ss_pred HHHhhhheecC-CCccHHHHHHHHCCCcchHHHHHHHHHhcc
Confidence 34444455555 689999999999999999888888887766
No 185
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=25.00 E-value=1.8e+02 Score=32.25 Aligned_cols=39 Identities=26% Similarity=0.243 Sum_probs=34.7
Q ss_pred HhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 572 FNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 572 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
+.....+|.++|++.++++...+.+.|..|...+ ++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~ag---LI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELARIG---LLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCC---CeEec
Confidence 5667789999999999999999999999999888 88753
No 186
>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=24.98 E-value=1.7e+02 Score=24.75 Aligned_cols=35 Identities=20% Similarity=0.357 Sum_probs=24.8
Q ss_pred HHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 570 MLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 570 l~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.+..+... ++..|.+.||||...++.+|.+|-..+
T Consensus 15 ~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~~ 49 (90)
T PF09904_consen 15 YLIDSGER-NVPALMEATGMPRRTIQDTIKALPELG 49 (90)
T ss_dssp HHHHHS-B--HHHHHHHH---HHHHHHHHHGGGGGT
T ss_pred HHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcCC
Confidence 34455555 999999999999999999999998665
No 187
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=24.83 E-value=1.6e+02 Score=29.21 Aligned_cols=65 Identities=22% Similarity=0.179 Sum_probs=45.2
Q ss_pred EEeeHHHHHHHHHHh-CCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccCC-CCCCCCCCeEee
Q 004725 559 LNVSTYQMCVLMLFN-SIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEPM-SKDIAEDDAFFF 627 (733)
Q Consensus 559 l~~s~~Qa~iLl~Fn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~~-~~~~~~~~~f~~ 627 (733)
|.-.|+|...- .|. ...++|.+|+++.+|++-...++-|..|++.+ +|.-+-. |+...|.-.|.+
T Consensus 155 i~~~Tl~~i~~-~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~---~l~a~i~yG~vGRP~r~Y~~ 221 (224)
T COG4565 155 LDELTLQKVRE-ALKEPDQELTAEELAQALGISRVTARRYLEYLVSNG---ILEAEIHYGKVGRPERRYRL 221 (224)
T ss_pred cCHHHHHHHHH-HHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcC---eeeEEeeccccCCcceeeec
Confidence 55567776544 343 35689999999999999999999999999887 7754321 333334444443
No 188
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=24.63 E-value=1.2e+02 Score=28.11 Aligned_cols=52 Identities=21% Similarity=0.256 Sum_probs=42.2
Q ss_pred EEeeHHHHHHHHHHhC-CCCcCHHHHHHHc-----CCChHHHHHHHHHhhhccCcceeecc
Q 004725 559 LNVSTYQMCVLMLFNS-IDRLSYKEIEQAT-----EIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 559 l~~s~~Qa~iLl~Fn~-~~~~t~~ei~~~t-----~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
+.+|.-...||-.+.+ .+.+|.++|-..+ +++...+-++|..|...| ++.+-
T Consensus 17 lr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~G---lv~~~ 74 (145)
T COG0735 17 LRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAG---LVHRL 74 (145)
T ss_pred CCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCC---CEEEE
Confidence 5678899999977775 4569999887765 488899999999999988 77653
No 189
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=24.46 E-value=1.1e+02 Score=31.16 Aligned_cols=47 Identities=26% Similarity=0.422 Sum_probs=40.3
Q ss_pred EEeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 559 LNVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 559 l~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
|-.|-++|-+-+..=..+..|..||++.+|+|..-+-..|.+|.+.|
T Consensus 12 lGlt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG 58 (247)
T COG1378 12 LGLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKG 58 (247)
T ss_pred cCCCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCC
Confidence 44577788777666666789999999999999999999999999877
No 190
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=24.26 E-value=60 Score=28.38 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=28.7
Q ss_pred cCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccC
Q 004725 678 ARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDK 723 (733)
Q Consensus 678 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~ 723 (733)
..+.++..+|.. ....+...+-+.|..|.++|||.|..
T Consensus 40 ~~~~~t~~eL~~--------~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 40 NEGKLTLKEIIK--------EILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred cCCcCcHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 446677776653 23457789999999999999999743
No 191
>PRK14999 histidine utilization repressor; Provisional
Probab=24.01 E-value=48 Score=33.60 Aligned_cols=47 Identities=11% Similarity=0.237 Sum_probs=35.2
Q ss_pred hcccCCCC-ChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCccee
Q 004725 675 IMKARRVL-DHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYR 730 (733)
Q Consensus 675 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~ 730 (733)
.++....| +-.+|. ..|..+...|+++|+.|.+.|+|.|..+ +++|+
T Consensus 29 ~~~~G~~LPsE~eLa--------~~~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSEAELV--------AQYGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCHHHHH--------HHHCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 55665566 444443 3488999999999999999999999864 56664
No 192
>PRK09462 fur ferric uptake regulator; Provisional
Probab=23.95 E-value=1.1e+02 Score=28.32 Aligned_cols=50 Identities=4% Similarity=0.121 Sum_probs=39.6
Q ss_pred heehhccc--CCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccC
Q 004725 671 AIVRIMKA--RRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDK 723 (733)
Q Consensus 671 ~IVRimK~--~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~ 723 (733)
+|.+++.. .+-++.++|...+.+.- ..++...|=+.|+.|.+.|.|.+-.
T Consensus 21 ~Il~~l~~~~~~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 21 KILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 44555554 36999999998887652 5568899999999999999998864
No 193
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=23.85 E-value=1.5e+02 Score=24.87 Aligned_cols=46 Identities=13% Similarity=0.187 Sum_probs=34.5
Q ss_pred HHHHHHHhCCCCcCHHHHHHHc--CCChHHHHHHHHHhhhccCcceeeccC
Q 004725 566 MCVLMLFNSIDRLSYKEIEQAT--EIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 566 a~iLl~Fn~~~~~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
+.||-..-+++-+|..++++.+ .++...+.+++.-|++.+ ++.+++
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkg---lIEKSG 66 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLIKKG---LIEKSG 66 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTT---SEEEET
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcC---cccccC
Confidence 4455556667778999999976 788889999999999887 888774
No 194
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=23.40 E-value=1.4e+02 Score=27.46 Aligned_cols=39 Identities=23% Similarity=0.182 Sum_probs=31.2
Q ss_pred eeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHh
Q 004725 561 VSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSL 601 (733)
Q Consensus 561 ~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 601 (733)
+|.-|..|+.++ ..++|.+||++.+|++...+...+...
T Consensus 7 Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 7 LTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 477788888886 367999999999999998887655443
No 195
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=23.26 E-value=65 Score=29.87 Aligned_cols=51 Identities=18% Similarity=0.344 Sum_probs=42.0
Q ss_pred hhhhhhheehhcccCCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccC
Q 004725 665 KPQIEAAIVRIMKARRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDK 723 (733)
Q Consensus 665 ~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~ 723 (733)
-..+|..|.+++.....++..+|-..+- .+...+.++|+.|.++|.|++-.
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lg--------lS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVG--------LSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCceeeEE
Confidence 3457788999999998999988865442 57889999999999999998853
No 196
>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=23.24 E-value=1.1e+02 Score=27.45 Aligned_cols=49 Identities=12% Similarity=0.228 Sum_probs=37.7
Q ss_pred eHHHHHHHHHHhC--------CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 562 STYQMCVLMLFNS--------IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 562 s~~Qa~iLl~Fn~--------~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
..+.-..|+..|. .-..+.+.||..++-+.+.++.+|..|.+-+ ++...
T Consensus 28 ~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~g---lIe~~ 84 (119)
T TIGR01714 28 IIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESLG---LIEKK 84 (119)
T ss_pred HHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEEe
Confidence 3455555555554 3467999999999999999999999998766 77653
No 197
>PLN03239 histone acetyltransferase; Provisional
Probab=23.03 E-value=1.2e+02 Score=32.50 Aligned_cols=38 Identities=21% Similarity=0.275 Sum_probs=29.3
Q ss_pred HHHHHHHHHhCC----CCcCHHHHHHHcCCChHHHHHHHHHh
Q 004725 564 YQMCVLMLFNSI----DRLSYKEIEQATEIPAPELKRCLQSL 601 (733)
Q Consensus 564 ~Qa~iLl~Fn~~----~~~t~~ei~~~t~i~~~~l~~~L~~L 601 (733)
+...|+-.+-+. ..+|+++|+..|||..+++..+|+.|
T Consensus 267 W~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 267 WGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred HHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 445555444222 46999999999999999999999887
No 198
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=22.69 E-value=1.1e+02 Score=32.15 Aligned_cols=35 Identities=20% Similarity=0.271 Sum_probs=32.0
Q ss_pred CCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 576 DRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 576 ~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
...|.++|++.+|+++.-+.+-|..|+..+ +|.+.
T Consensus 22 gp~t~~eLA~~~~~~~~~~~~lL~~L~~lg---ll~~~ 56 (306)
T TIGR02716 22 GPKDLATLAADTGSVPPRLEMLLETLRQMR---VINLE 56 (306)
T ss_pred CCCCHHHHHHHcCCChHHHHHHHHHHHhCC---CeEec
Confidence 578999999999999999999999999888 89764
No 199
>PF14493 HTH_40: Helix-turn-helix domain
Probab=22.69 E-value=1.8e+02 Score=24.48 Aligned_cols=36 Identities=22% Similarity=0.241 Sum_probs=30.7
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.+-+|++ ++|+++|++.-|++...+..+|..++..+
T Consensus 6 T~~l~~~--G~si~eIA~~R~L~~sTI~~HL~~~~~~g 41 (91)
T PF14493_consen 6 TYELFQK--GLSIEEIAKIRGLKESTIYGHLAELIESG 41 (91)
T ss_pred HHHHHHc--CCCHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence 4567875 58999999999999999999998887654
No 200
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=22.64 E-value=2e+02 Score=29.90 Aligned_cols=34 Identities=21% Similarity=0.268 Sum_probs=30.0
Q ss_pred cCHHHHHHHcC--CChHHHHHHHHHhhhccCcceeeccC
Q 004725 578 LSYKEIEQATE--IPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 578 ~t~~ei~~~t~--i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
.+..+|++.++ |+.++++.+|..|...| +|.+..
T Consensus 138 ~~~~~ia~~l~p~is~~ev~~sL~~L~~~g---likk~~ 173 (271)
T TIGR02147 138 DDPEELAKRCFPKISAEQVKESLDLLERLG---LIKKNE 173 (271)
T ss_pred CCHHHHHHHhCCCCCHHHHHHHHHHHHHCC---CeeECC
Confidence 36789999999 89999999999999888 998864
No 201
>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=22.64 E-value=49 Score=25.71 Aligned_cols=29 Identities=14% Similarity=0.264 Sum_probs=24.4
Q ss_pred ccCCCCChHHHHHHHHHhhhhhcccccCC
Q 004725 696 QSRFLPNPVVIKKRIESLIEREFLERDKV 724 (733)
Q Consensus 696 ~~~F~~~~~~ik~~Ie~LIereyi~rd~~ 724 (733)
..+|..+...+.+++..|.+.|+|.+.++
T Consensus 31 a~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 31 AERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 34588899999999999999999998764
No 202
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=22.60 E-value=1.2e+02 Score=28.23 Aligned_cols=50 Identities=14% Similarity=0.112 Sum_probs=41.0
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHcCC-------ChHH-------HHHHHHHhhhccCcceeeccCCC
Q 004725 564 YQMCVLMLFNSIDRLSYKEIEQATEI-------PAPE-------LKRCLQSLACVKGKHVLRKEPMS 616 (733)
Q Consensus 564 ~Qa~iLl~Fn~~~~~t~~ei~~~t~i-------~~~~-------l~~~L~~L~~~k~~~iL~~~~~~ 616 (733)
-.|+||-.+-....+.+..++..+|. |... ++.+|+.|-..+ ++.+.+.|
T Consensus 54 R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~g---lVek~~~G 117 (150)
T PRK09333 54 RAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAG---LVEKTKKG 117 (150)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCC---CeeeCCCC
Confidence 46888888777778999999999999 6655 899999999888 88776543
No 203
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=22.29 E-value=1.9e+02 Score=28.09 Aligned_cols=43 Identities=14% Similarity=0.102 Sum_probs=35.7
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeecc
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
++.-.+.++..|..+|+..+|++..++.++|-.|...+ .+...
T Consensus 18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~---~v~~~ 60 (183)
T PHA03103 18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREG---MVYMS 60 (183)
T ss_pred HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcC---ceecC
Confidence 45556677889999999999999999999999998776 55544
No 204
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=22.26 E-value=55 Score=33.18 Aligned_cols=36 Identities=17% Similarity=0.398 Sum_probs=29.5
Q ss_pred HhccCCCCChHHHHHHHHHhhhhhcccccCCCCccee
Q 004725 694 QLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYR 730 (733)
Q Consensus 694 ~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~ 730 (733)
+|...|.++...++++|..|.+.|+|.|-.+ +++|+
T Consensus 36 eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 36 ELAEQFGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred HHHHHHCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 3444699999999999999999999999854 45654
No 205
>PHA02591 hypothetical protein; Provisional
Probab=22.16 E-value=1e+02 Score=25.21 Aligned_cols=25 Identities=16% Similarity=0.344 Sum_probs=22.1
Q ss_pred CCcCHHHHHHHcCCChHHHHHHHHH
Q 004725 576 DRLSYKEIEQATEIPAPELKRCLQS 600 (733)
Q Consensus 576 ~~~t~~ei~~~t~i~~~~l~~~L~~ 600 (733)
.++|.++||+.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 4789999999999999999888765
No 206
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=22.14 E-value=1.6e+02 Score=29.81 Aligned_cols=44 Identities=14% Similarity=0.197 Sum_probs=37.1
Q ss_pred HHHHHhC-CCCcCHHHHHHHcCCChHHHHHHHHHhhhccCcceeeccC
Q 004725 568 VLMLFNS-IDRLSYKEIEQATEIPAPELKRCLQSLACVKGKHVLRKEP 614 (733)
Q Consensus 568 iLl~Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~~iL~~~~ 614 (733)
||-.++. ...++..+|++.+|++...+.+++..|...+ ++...|
T Consensus 188 IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aG---vIe~r~ 232 (251)
T TIGR02787 188 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAG---VIESRS 232 (251)
T ss_pred HHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEecc
Confidence 5555666 3679999999999999999999999999988 887654
No 207
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=22.07 E-value=53 Score=24.61 Aligned_cols=22 Identities=18% Similarity=0.448 Sum_probs=19.0
Q ss_pred CcCHHHHHHHcCCChHHHHHHH
Q 004725 577 RLSYKEIEQATEIPAPELKRCL 598 (733)
Q Consensus 577 ~~t~~ei~~~t~i~~~~l~~~L 598 (733)
.+++.||++.+|++..++...|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999988887
No 208
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=21.76 E-value=69 Score=24.45 Aligned_cols=28 Identities=11% Similarity=0.217 Sum_probs=23.9
Q ss_pred ccCCCCChHHHHHHHHHhhhhhcccccC
Q 004725 696 QSRFLPNPVVIKKRIESLIEREFLERDK 723 (733)
Q Consensus 696 ~~~F~~~~~~ik~~Ie~LIereyi~rd~ 723 (733)
...|..+...+.+.+..|.++|+|.+.+
T Consensus 32 a~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 32 AEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 3346778999999999999999998875
No 209
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=21.54 E-value=1.4e+02 Score=27.49 Aligned_cols=37 Identities=14% Similarity=0.199 Sum_probs=28.1
Q ss_pred eeHHHHHHHHH-HhCCCCcCHHHHHHHcCCChHHHHHHHH
Q 004725 561 VSTYQMCVLML-FNSIDRLSYKEIEQATEIPAPELKRCLQ 599 (733)
Q Consensus 561 ~s~~Qa~iLl~-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 599 (733)
+|+-|..|+.+ |- +++++.||++.+|+|...+...+.
T Consensus 112 L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 112 LPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 35566666655 43 468999999999999998887764
No 210
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=21.09 E-value=2.3e+02 Score=21.37 Aligned_cols=42 Identities=21% Similarity=0.207 Sum_probs=35.5
Q ss_pred EeeHHHHHHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhh
Q 004725 560 NVSTYQMCVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLAC 603 (733)
Q Consensus 560 ~~s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 603 (733)
.+|.-+..++.++-.+ .+..+|+...|++...+..++.....
T Consensus 4 ~Lt~rE~~v~~l~~~G--~s~~eia~~l~is~~tV~~h~~~i~~ 45 (65)
T COG2771 4 DLTPREREILRLVAQG--KSNKEIARILGISEETVKTHLRNIYR 45 (65)
T ss_pred cCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3577888899888876 79999999999999999998887643
No 211
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=20.94 E-value=1.4e+02 Score=33.27 Aligned_cols=37 Identities=30% Similarity=0.349 Sum_probs=29.3
Q ss_pred HHHHHHH-HhCCCCcCHHHHHHHcCCChHHHHHHHHHh
Q 004725 565 QMCVLML-FNSIDRLSYKEIEQATEIPAPELKRCLQSL 601 (733)
Q Consensus 565 Qa~iLl~-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 601 (733)
-..||-. .+....+|+++|+..|||..+++..+|++|
T Consensus 361 ~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l 398 (450)
T PLN00104 361 TRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL 398 (450)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 3344433 344468999999999999999999999987
No 212
>KOG4481 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.82 E-value=1.3e+02 Score=28.52 Aligned_cols=64 Identities=13% Similarity=0.210 Sum_probs=51.1
Q ss_pred CceeEeecCcceEEEEEeeCCCceEEEEeeHHHHHHHHHHhC--CCCcCHHHHHHHcCCChHHHHHHHHHhh
Q 004725 533 GRRLTWQTNMGTADLKGTFGKGQKHELNVSTYQMCVLMLFNS--IDRLSYKEIEQATEIPAPELKRCLQSLA 602 (733)
Q Consensus 533 ~R~L~w~~~l~~~~i~~~~~~~~~~~l~~s~~Qa~iLl~Fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 602 (733)
.+++-|-++++...++ ..++| .|+..||.-++-|.+ .++|+.+-|++...+..+++...+..+.
T Consensus 95 e~r~p~~~~f~~~~i~-rIpkg-----kit~~eAL~~ln~hkL~petw~AekIA~ey~l~~~~v~~il~YF~ 160 (194)
T KOG4481|consen 95 EFRLPKDYHFDEINIK-RIPKG-----KITIVEALTFLNNHKLLPETWTAEKIAQEYHLEQEDVNDILKYFV 160 (194)
T ss_pred hcCCcccccCCCcCcc-cCCCC-----ceeHHHHHHHHhhhhcChhhhHHHHHHHHHhhchhhHHHHHHHhc
Confidence 4578999999998887 56663 358899999888865 4689999999999998888877777664
No 213
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=20.79 E-value=95 Score=27.54 Aligned_cols=58 Identities=17% Similarity=0.241 Sum_probs=41.5
Q ss_pred heehhccc-CCCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCCCCcceee
Q 004725 671 AIVRIMKA-RRVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKVDRKLYRY 731 (733)
Q Consensus 671 ~IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~Y 731 (733)
+|..+|+. .+.++.++|...+.+. ...++...|=+.|+.|.+.|.|.+-..+.+...|
T Consensus 12 ~Il~~l~~~~~~~ta~ei~~~l~~~---~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 12 AILELLKESPEHLTAEEIYDKLRKK---GPRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp HHHHHHHHHSSSEEHHHHHHHHHHT---TTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHhhhc---cCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 34445555 4689999999877743 3567889999999999999999997655444444
No 214
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=20.69 E-value=63 Score=32.44 Aligned_cols=33 Identities=12% Similarity=0.272 Sum_probs=28.0
Q ss_pred cCCCCChHHHHHHHHHhhhhhcccccCCCCccee
Q 004725 697 SRFLPNPVVIKKRIESLIEREFLERDKVDRKLYR 730 (733)
Q Consensus 697 ~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~ 730 (733)
..|..+...|+++|+.|.+.|+|.|..+ +++|+
T Consensus 33 ~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 65 (230)
T TIGR02018 33 AQYGCSRMTVNRALRELTDAGLLERRQG-VGTFV 65 (230)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 3599999999999999999999999864 45553
No 215
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.53 E-value=1.8e+02 Score=24.89 Aligned_cols=38 Identities=18% Similarity=0.143 Sum_probs=29.9
Q ss_pred HHHHHHhCCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 567 CVLMLFNSIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 567 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.+++++.++.. |..+++..+|++...+.+.+..+...+
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 45666666543 799999999999999999998876544
No 216
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=20.29 E-value=1.4e+02 Score=23.27 Aligned_cols=22 Identities=14% Similarity=0.357 Sum_probs=18.7
Q ss_pred CCCCcCHHHHHHHcCCChHHHH
Q 004725 574 SIDRLSYKEIEQATEIPAPELK 595 (733)
Q Consensus 574 ~~~~~t~~ei~~~t~i~~~~l~ 595 (733)
.++.++..+||+.+|+++..+.
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHH
Confidence 4568999999999999997654
No 217
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=20.27 E-value=68 Score=32.51 Aligned_cols=33 Identities=21% Similarity=0.366 Sum_probs=27.8
Q ss_pred cCCCCChHHHHHHHHHhhhhhcccccCCCCccee
Q 004725 697 SRFLPNPVVIKKRIESLIEREFLERDKVDRKLYR 730 (733)
Q Consensus 697 ~~F~~~~~~ik~~Ie~LIereyi~rd~~~~~~y~ 730 (733)
..|..+...|+++|+.|.+.|+|.|..+ +++|+
T Consensus 37 ~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 69 (240)
T PRK09764 37 TEFGVSRVTVRQALRQLVEQQILESIQG-SGTYV 69 (240)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 3589999999999999999999999865 45553
No 218
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=20.26 E-value=1.8e+02 Score=20.81 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=18.8
Q ss_pred HHHHHhCCCCcCHHHHHHHcCCChHHHHHHHH
Q 004725 568 VLMLFNSIDRLSYKEIEQATEIPAPELKRCLQ 599 (733)
Q Consensus 568 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 599 (733)
.+..+-+ .++|..+|+..+|.+...+.+.|.
T Consensus 12 ~I~~l~~-~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 12 QIEALLE-QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHHHHC-S---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHH-cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 3333333 458999999999999998877664
No 219
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=20.10 E-value=1.3e+02 Score=24.74 Aligned_cols=32 Identities=25% Similarity=0.371 Sum_probs=28.7
Q ss_pred CCCCcCHHHHHHHcCCChHHHHHHHHHhhhcc
Q 004725 574 SIDRLSYKEIEQATEIPAPELKRCLQSLACVK 605 (733)
Q Consensus 574 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 605 (733)
.++..+..+|+..+++|.+.+...|.-|+..+
T Consensus 13 ~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kG 44 (78)
T PRK15431 13 LRGRMEAAQISQTLNTPQPMINAMLQQLESMG 44 (78)
T ss_pred HcCcccHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 45678999999999999999999999999764
No 220
>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=20.06 E-value=1.3e+02 Score=26.57 Aligned_cols=49 Identities=16% Similarity=0.202 Sum_probs=38.9
Q ss_pred eHHHHHHHHHHhCCCCcCHHHHHHHcCCC----hHHHHHHHHHhhhccCcceeecc
Q 004725 562 STYQMCVLMLFNSIDRLSYKEIEQATEIP----APELKRCLQSLACVKGKHVLRKE 613 (733)
Q Consensus 562 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~i~----~~~l~~~L~~L~~~k~~~iL~~~ 613 (733)
|..+..|+..+=+.+.+|+.||.+.++=+ ...+...|..|+..+ +|...
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg---~l~~~ 54 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKG---FLTRE 54 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTT---SEEEE
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCC---ceeEe
Confidence 55677788777666679999999988644 888999999999887 88765
No 221
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=20.04 E-value=1.3e+02 Score=24.90 Aligned_cols=44 Identities=14% Similarity=0.205 Sum_probs=33.3
Q ss_pred ehhcccC-CCCChHHHHHHHHHHhccCCCCChHHHHHHHHHhhhhhcccccCC
Q 004725 673 VRIMKAR-RVLDHNNIVTEVTKQLQSRFLPNPVVIKKRIESLIEREFLERDKV 724 (733)
Q Consensus 673 VRimK~~-k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~rd~~ 724 (733)
...+... ..++..+|..++ ..+...+.+.+..|.+.|||.+++.
T Consensus 11 l~~l~~~~~~~t~~~ia~~l--------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 11 LRALAEEPGGLTLAELAERL--------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHhCCCCcCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 3444444 678888877544 4577899999999999999999753
Done!