Query 009222
Match_columns 540
No_of_seqs 166 out of 987
Neff 8.8
Searched_HMMs 46136
Date Thu Mar 28 21:55:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009222.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009222hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2167 Cullins [Cell cycle co 100.0 4.5E-96 1E-100 735.4 39.8 536 1-540 123-661 (661)
2 KOG2166 Cullins [Cell cycle co 100.0 1.3E-90 2.7E-95 744.1 51.1 525 5-538 190-725 (725)
3 COG5647 Cullin, a subunit of E 100.0 7.3E-91 1.6E-95 713.8 46.4 531 4-540 214-773 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 1.7E-86 3.8E-91 638.7 34.2 502 4-540 215-728 (728)
5 KOG2285 E3 ubiquitin ligase, C 100.0 2.2E-76 4.9E-81 573.9 44.2 535 4-540 192-777 (777)
6 PF00888 Cullin: Cullin family 100.0 1.3E-70 2.8E-75 603.0 45.6 433 4-442 148-588 (588)
7 smart00182 CULLIN Cullin. 100.0 1.2E-32 2.5E-37 244.6 17.6 141 222-363 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 1.7E-29 3.6E-34 259.6 41.4 310 216-537 442-762 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 3.1E-19 6.7E-24 136.2 4.2 65 470-534 2-68 (68)
10 TIGR01610 phage_O_Nterm phage 95.7 0.029 6.3E-07 45.8 5.9 66 369-442 20-93 (95)
11 PF09339 HTH_IclR: IclR helix- 94.3 0.071 1.5E-06 38.0 4.0 45 377-423 6-51 (52)
12 PF13412 HTH_24: Winged helix- 94.2 0.1 2.2E-06 36.4 4.6 46 373-420 2-47 (48)
13 PF02082 Rrf2: Transcriptional 94.0 0.12 2.6E-06 40.9 5.3 60 375-441 11-71 (83)
14 PF08220 HTH_DeoR: DeoR-like h 93.6 0.09 1.9E-06 38.4 3.5 47 376-424 2-48 (57)
15 PF12802 MarR_2: MarR family; 93.5 0.07 1.5E-06 39.4 2.9 51 372-424 3-55 (62)
16 smart00550 Zalpha Z-DNA-bindin 91.9 0.38 8.3E-06 36.5 5.1 49 374-424 6-56 (68)
17 PF01047 MarR: MarR family; I 91.5 0.16 3.5E-06 37.1 2.5 51 372-424 1-51 (59)
18 TIGR02337 HpaR homoprotocatech 91.1 0.36 7.9E-06 40.9 4.7 52 371-424 25-76 (118)
19 PF13463 HTH_27: Winged helix 90.7 0.53 1.2E-05 35.3 4.8 51 372-424 1-52 (68)
20 PF09012 FeoC: FeoC like trans 90.2 0.2 4.2E-06 38.2 2.0 45 481-531 5-49 (69)
21 PRK11512 DNA-binding transcrip 90.1 0.51 1.1E-05 41.6 4.9 52 371-424 37-88 (144)
22 PF01022 HTH_5: Bacterial regu 89.8 0.87 1.9E-05 31.6 4.9 45 374-421 2-46 (47)
23 TIGR02698 CopY_TcrY copper tra 89.1 1 2.2E-05 39.0 5.9 60 478-540 6-65 (130)
24 PF12840 HTH_20: Helix-turn-he 89.0 0.6 1.3E-05 34.4 3.8 49 373-423 9-57 (61)
25 COG3682 Predicted transcriptio 89.0 0.93 2E-05 38.4 5.2 62 476-540 6-67 (123)
26 smart00346 HTH_ICLR helix_turn 88.3 1.3 2.9E-05 35.3 5.8 45 377-423 8-53 (91)
27 PF08279 HTH_11: HTH domain; 88.1 1 2.2E-05 32.2 4.5 38 377-414 3-41 (55)
28 TIGR01889 Staph_reg_Sar staphy 87.1 1.3 2.9E-05 36.9 5.2 52 371-424 22-77 (109)
29 PRK10857 DNA-binding transcrip 87.0 1.7 3.6E-05 39.4 6.1 58 376-440 12-70 (164)
30 PRK11920 rirA iron-responsive 86.9 1.7 3.8E-05 38.7 6.2 57 377-440 13-69 (153)
31 PF01978 TrmB: Sugar-specific 86.9 0.43 9.2E-06 36.1 1.9 56 478-539 10-65 (68)
32 smart00420 HTH_DEOR helix_turn 86.2 1.2 2.7E-05 31.1 3.9 46 376-423 2-47 (53)
33 COG3355 Predicted transcriptio 86.0 1.9 4.2E-05 36.8 5.5 39 384-424 38-76 (126)
34 PF01978 TrmB: Sugar-specific 85.8 0.66 1.4E-05 35.0 2.5 51 372-424 6-56 (68)
35 PF04492 Phage_rep_O: Bacterio 85.7 2.2 4.7E-05 35.0 5.6 63 370-442 28-98 (100)
36 smart00550 Zalpha Z-DNA-bindin 85.6 1.8 3.8E-05 32.8 4.7 54 477-536 7-62 (68)
37 TIGR02010 IscR iron-sulfur clu 85.3 2.1 4.6E-05 37.3 5.8 57 377-440 13-70 (135)
38 PF04703 FaeA: FaeA-like prote 85.0 1.4 2.9E-05 32.7 3.7 56 379-438 5-61 (62)
39 PF08220 HTH_DeoR: DeoR-like h 84.8 0.98 2.1E-05 32.8 2.9 47 479-531 3-49 (57)
40 PRK15090 DNA-binding transcrip 84.6 2.2 4.7E-05 41.7 6.1 57 376-440 16-72 (257)
41 PRK13777 transcriptional regul 84.3 1.8 3.9E-05 39.9 5.0 53 370-424 41-93 (185)
42 smart00347 HTH_MARR helix_turn 84.1 1.7 3.6E-05 35.1 4.4 52 370-423 6-57 (101)
43 COG1959 Predicted transcriptio 83.9 2.4 5.2E-05 37.7 5.5 59 375-440 11-70 (150)
44 PF03965 Penicillinase_R: Peni 82.4 0.72 1.6E-05 39.0 1.5 60 478-540 5-64 (115)
45 PF13404 HTH_AsnC-type: AsnC-t 82.2 2.3 5E-05 28.8 3.6 36 377-412 6-41 (42)
46 PRK03573 transcriptional regul 81.7 2.4 5.3E-05 37.2 4.7 53 370-424 27-80 (144)
47 TIGR00738 rrf2_super rrf2 fami 80.7 3.5 7.5E-05 35.6 5.3 46 376-423 12-58 (132)
48 TIGR01884 cas_HTH CRISPR locus 79.5 4 8.7E-05 38.3 5.7 52 371-424 140-191 (203)
49 PF13463 HTH_27: Winged helix 79.3 4 8.7E-05 30.4 4.6 53 478-536 5-60 (68)
50 PHA00738 putative HTH transcri 79.1 4.1 8.9E-05 33.6 4.7 68 369-442 7-74 (108)
51 PF13601 HTH_34: Winged helix 79.0 1.7 3.7E-05 34.1 2.5 45 376-422 2-46 (80)
52 PF08280 HTH_Mga: M protein tr 78.9 2.7 5.9E-05 30.7 3.4 38 376-413 7-44 (59)
53 PF05584 Sulfolobus_pRN: Sulfo 78.6 4.4 9.5E-05 30.9 4.4 47 373-423 5-51 (72)
54 PF05732 RepL: Firmicute plasm 78.5 2.5 5.4E-05 38.2 3.7 47 389-444 76-122 (165)
55 PRK10870 transcriptional repre 78.3 4.4 9.6E-05 37.0 5.4 51 372-424 53-105 (176)
56 PF08784 RPA_C: Replication pr 78.1 3.7 8E-05 33.7 4.4 48 371-420 44-95 (102)
57 TIGR03879 near_KaiC_dom probab 77.4 3 6.6E-05 31.9 3.3 36 384-421 28-63 (73)
58 PRK04172 pheS phenylalanyl-tRN 77.3 20 0.00043 38.7 10.8 50 371-422 3-52 (489)
59 PRK10163 DNA-binding transcrip 77.3 5.4 0.00012 39.3 6.1 57 376-440 27-84 (271)
60 PRK11569 transcriptional repre 77.2 5 0.00011 39.6 5.9 47 376-424 30-77 (274)
61 COG1414 IclR Transcriptional r 77.0 5.5 0.00012 38.6 5.9 56 377-440 7-63 (246)
62 cd00090 HTH_ARSR Arsenical Res 76.7 4.6 9.9E-05 30.3 4.4 48 373-423 6-53 (78)
63 TIGR02944 suf_reg_Xantho FeS a 76.0 5.8 0.00013 34.1 5.3 55 378-439 13-69 (130)
64 smart00419 HTH_CRP helix_turn_ 75.7 5.6 0.00012 27.1 4.2 33 388-422 8-40 (48)
65 PF13412 HTH_24: Winged helix- 75.5 6.3 0.00014 27.2 4.4 45 477-527 4-48 (48)
66 smart00345 HTH_GNTR helix_turn 74.4 4.6 9.9E-05 29.0 3.6 40 383-424 14-54 (60)
67 smart00344 HTH_ASNC helix_turn 74.2 4.7 0.0001 33.3 4.1 45 375-421 4-48 (108)
68 PRK10141 DNA-binding transcrip 73.6 5.9 0.00013 33.5 4.5 62 373-440 15-76 (117)
69 PRK09834 DNA-binding transcrip 73.5 6.8 0.00015 38.3 5.7 55 377-439 14-69 (263)
70 PRK11014 transcriptional repre 73.2 9.1 0.0002 33.5 5.8 50 383-439 20-69 (141)
71 COG1846 MarR Transcriptional r 72.7 6.5 0.00014 32.9 4.7 51 372-424 20-70 (126)
72 PF09756 DDRGK: DDRGK domain; 72.6 2.5 5.5E-05 38.9 2.2 58 476-540 100-157 (188)
73 TIGR02431 pcaR_pcaU beta-ketoa 72.5 8.5 0.00018 37.3 6.0 44 377-422 12-56 (248)
74 smart00418 HTH_ARSR helix_turn 72.5 6.1 0.00013 28.5 4.0 46 481-533 2-47 (66)
75 PF01325 Fe_dep_repress: Iron 71.4 6.2 0.00013 29.0 3.6 45 378-424 12-56 (60)
76 PF10771 DUF2582: Protein of u 71.4 8.9 0.00019 28.7 4.4 37 378-414 12-48 (65)
77 PF09012 FeoC: FeoC like trans 71.4 4.5 9.7E-05 30.6 3.0 42 379-422 5-46 (69)
78 smart00418 HTH_ARSR helix_turn 71.1 7.2 0.00016 28.1 4.1 36 386-423 8-43 (66)
79 PF13730 HTH_36: Helix-turn-he 71.1 7.7 0.00017 27.6 4.1 25 390-414 27-51 (55)
80 COG2345 Predicted transcriptio 71.0 5.7 0.00012 37.5 4.1 43 378-422 15-57 (218)
81 PRK10434 srlR DNA-bindng trans 70.9 4.7 0.0001 39.3 3.8 48 375-424 6-53 (256)
82 cd00092 HTH_CRP helix_turn_hel 70.0 9.3 0.0002 28.2 4.5 35 387-423 24-58 (67)
83 COG1349 GlpR Transcriptional r 68.7 5.8 0.00013 38.6 3.9 49 376-426 7-55 (253)
84 PF01726 LexA_DNA_bind: LexA D 68.5 12 0.00026 28.0 4.7 57 472-533 6-63 (65)
85 cd07153 Fur_like Ferric uptake 67.8 13 0.00028 31.1 5.4 58 480-538 5-63 (116)
86 smart00420 HTH_DEOR helix_turn 66.9 7.6 0.00016 26.9 3.3 45 481-531 5-49 (53)
87 PF08221 HTH_9: RNA polymerase 66.6 8.8 0.00019 28.4 3.6 41 379-421 18-58 (62)
88 PF01047 MarR: MarR family; I 64.2 2.7 5.8E-05 30.4 0.4 47 478-530 5-51 (59)
89 PRK11179 DNA-binding transcrip 62.7 13 0.00028 33.0 4.7 48 372-421 7-54 (153)
90 PRK13509 transcriptional repre 62.6 11 0.00023 36.8 4.4 50 375-426 6-55 (251)
91 PRK11169 leucine-responsive tr 62.3 10 0.00022 34.2 3.9 48 372-421 12-59 (164)
92 PF12395 DUF3658: Protein of u 61.8 22 0.00049 29.7 5.7 62 476-538 48-109 (111)
93 PF02186 TFIIE_beta: TFIIE bet 61.7 12 0.00026 28.1 3.5 55 477-540 6-61 (65)
94 TIGR02702 SufR_cyano iron-sulf 61.0 17 0.00037 34.0 5.4 45 377-423 4-48 (203)
95 TIGR02844 spore_III_D sporulat 60.8 15 0.00033 28.7 4.1 35 375-410 7-41 (80)
96 smart00344 HTH_ASNC helix_turn 60.4 11 0.00023 31.1 3.5 46 477-528 4-49 (108)
97 PF01726 LexA_DNA_bind: LexA D 60.3 11 0.00024 28.2 3.1 51 372-424 4-60 (65)
98 PF02002 TFIIE_alpha: TFIIE al 59.8 8 0.00017 31.9 2.6 45 375-421 14-58 (105)
99 PRK06266 transcription initiat 59.6 14 0.0003 33.9 4.3 45 375-421 23-67 (178)
100 PF08784 RPA_C: Replication pr 58.8 11 0.00024 30.8 3.3 45 476-526 47-95 (102)
101 PF12324 HTH_15: Helix-turn-he 58.8 24 0.00053 27.3 4.8 39 375-413 25-63 (77)
102 PF11994 DUF3489: Protein of u 58.6 20 0.00044 27.3 4.2 49 373-421 9-57 (72)
103 PF04545 Sigma70_r4: Sigma-70, 58.5 24 0.00053 24.4 4.6 30 379-410 13-42 (50)
104 PRK10906 DNA-binding transcrip 58.0 13 0.00027 36.3 4.0 50 375-426 6-55 (252)
105 COG4189 Predicted transcriptio 57.8 15 0.00032 34.7 4.1 50 372-423 21-70 (308)
106 TIGR00373 conserved hypothetic 57.7 19 0.00041 32.3 4.8 44 376-421 16-59 (158)
107 PF12802 MarR_2: MarR family; 57.6 7.2 0.00016 28.3 1.8 48 478-531 7-56 (62)
108 PF02796 HTH_7: Helix-turn-hel 57.3 16 0.00035 24.9 3.4 32 378-411 13-44 (45)
109 PF04967 HTH_10: HTH DNA bindi 57.1 29 0.00062 24.8 4.6 30 383-412 18-47 (53)
110 PRK09802 DNA-binding transcrip 57.0 13 0.00028 36.6 3.9 49 374-424 17-65 (269)
111 PF06784 UPF0240: Uncharacteri 56.9 19 0.00042 32.9 4.8 63 346-413 97-161 (179)
112 COG3355 Predicted transcriptio 56.5 22 0.00047 30.5 4.6 40 484-529 36-75 (126)
113 PF00325 Crp: Bacterial regula 56.1 9.2 0.0002 24.2 1.8 26 388-413 2-27 (32)
114 COG1522 Lrp Transcriptional re 55.2 18 0.00039 31.9 4.3 49 372-422 6-54 (154)
115 PRK04424 fatty acid biosynthes 54.7 12 0.00027 34.4 3.2 47 375-423 8-54 (185)
116 PRK00215 LexA repressor; Valid 54.3 21 0.00046 33.3 4.8 52 372-425 2-59 (205)
117 PHA02943 hypothetical protein; 54.2 20 0.00044 31.5 4.1 55 379-440 16-70 (165)
118 PF00392 GntR: Bacterial regul 53.6 19 0.00041 26.6 3.5 46 484-536 17-63 (64)
119 PF05158 RNA_pol_Rpc34: RNA po 53.5 14 0.0003 37.5 3.6 145 370-532 80-260 (327)
120 PF09339 HTH_IclR: IclR helix- 53.1 23 0.00049 24.9 3.7 44 481-530 8-52 (52)
121 PF08281 Sigma70_r4_2: Sigma-7 52.6 27 0.0006 24.5 4.1 24 387-410 25-48 (54)
122 PF00196 GerE: Bacterial regul 52.4 18 0.00038 26.1 3.1 41 372-414 4-44 (58)
123 PRK00135 scpB segregation and 52.2 2E+02 0.0042 26.6 11.2 34 381-414 12-46 (188)
124 PRK14999 histidine utilization 51.5 24 0.00053 33.9 4.9 54 477-537 21-76 (241)
125 smart00421 HTH_LUXR helix_turn 51.2 32 0.00069 23.9 4.4 39 373-413 5-43 (58)
126 cd07377 WHTH_GntR Winged helix 50.9 35 0.00075 24.7 4.6 32 390-423 27-58 (66)
127 cd06170 LuxR_C_like C-terminal 50.2 34 0.00073 23.8 4.4 39 373-413 2-40 (57)
128 smart00526 H15 Domain in histo 50.2 68 0.0015 23.8 6.1 53 476-529 10-64 (66)
129 TIGR00498 lexA SOS regulatory 50.1 16 0.00034 34.1 3.2 51 372-424 4-60 (199)
130 KOG3054 Uncharacterized conser 49.8 18 0.0004 34.2 3.4 57 478-540 202-258 (299)
131 PRK10411 DNA-binding transcrip 49.5 23 0.00049 34.2 4.2 47 375-423 5-51 (240)
132 PF08672 APC2: Anaphase promot 49.5 25 0.00054 25.8 3.4 50 481-531 2-56 (60)
133 TIGR01889 Staph_reg_Sar staphy 49.2 30 0.00065 28.7 4.4 37 487-529 40-76 (109)
134 PF01853 MOZ_SAS: MOZ/SAS fami 49.2 18 0.00038 33.3 3.2 26 387-412 149-174 (188)
135 PF14394 DUF4423: Domain of un 49.1 38 0.00083 30.7 5.4 55 368-424 18-75 (171)
136 PF06163 DUF977: Bacterial pro 49.0 33 0.00072 29.2 4.5 52 474-531 10-61 (127)
137 PF01638 HxlR: HxlR-like helix 48.5 31 0.00068 27.4 4.3 45 376-423 7-52 (90)
138 PRK10681 DNA-binding transcrip 47.9 26 0.00056 34.1 4.4 39 375-413 8-46 (252)
139 PF09681 Phage_rep_org_N: N-te 47.9 24 0.00051 30.1 3.6 49 372-422 27-85 (121)
140 COG1349 GlpR Transcriptional r 47.7 16 0.00035 35.6 2.9 45 479-529 8-52 (253)
141 smart00345 HTH_GNTR helix_turn 47.6 38 0.00083 23.9 4.3 41 485-531 14-55 (60)
142 COG1654 BirA Biotin operon rep 47.5 58 0.0013 25.4 5.4 42 380-421 11-52 (79)
143 COG1522 Lrp Transcriptional re 47.3 30 0.00065 30.4 4.4 50 475-530 7-56 (154)
144 COG4742 Predicted transcriptio 47.1 30 0.00066 33.6 4.6 43 378-423 17-59 (260)
145 PF00538 Linker_histone: linke 47.0 63 0.0014 24.9 5.6 54 476-530 8-65 (77)
146 PRK10434 srlR DNA-bindng trans 46.9 17 0.00038 35.3 3.1 46 478-529 7-52 (256)
147 smart00347 HTH_MARR helix_turn 46.8 32 0.0007 27.3 4.2 47 478-530 12-58 (101)
148 PRK09334 30S ribosomal protein 46.3 33 0.00072 27.2 3.9 49 486-540 37-85 (86)
149 PF09107 SelB-wing_3: Elongati 46.3 31 0.00067 24.3 3.4 41 381-423 3-43 (50)
150 PRK11512 DNA-binding transcrip 45.4 31 0.00067 30.2 4.2 47 478-530 42-88 (144)
151 PRK11169 leucine-responsive tr 45.4 42 0.00091 30.2 5.1 48 475-528 13-60 (164)
152 PRK10906 DNA-binding transcrip 44.7 21 0.00045 34.8 3.2 46 478-529 7-52 (252)
153 smart00762 Cog4 COG4 transport 44.5 3.5E+02 0.0076 27.3 14.9 83 82-164 10-110 (324)
154 PF08318 COG4: COG4 transport 43.8 3.6E+02 0.0078 27.3 15.8 156 83-245 11-213 (331)
155 PLN03238 probable histone acet 43.5 46 0.001 32.7 5.2 39 374-412 208-247 (290)
156 PF04182 B-block_TFIIIC: B-blo 42.9 33 0.00071 26.3 3.4 50 373-424 1-52 (75)
157 PF10007 DUF2250: Uncharacteri 42.7 49 0.0011 26.7 4.4 53 370-424 3-55 (92)
158 smart00346 HTH_ICLR helix_turn 42.7 45 0.00097 26.2 4.4 45 481-531 10-55 (91)
159 PF13384 HTH_23: Homeodomain-l 42.6 31 0.00068 23.7 3.1 33 379-413 10-42 (50)
160 PRK10079 phosphonate metabolis 42.5 42 0.00092 32.2 5.0 54 477-537 21-75 (241)
161 smart00531 TFIIE Transcription 42.2 30 0.00064 30.6 3.5 36 379-414 6-41 (147)
162 TIGR01714 phage_rep_org_N phag 42.0 30 0.00064 29.4 3.2 49 372-422 27-83 (119)
163 PF09904 HTH_43: Winged helix- 41.2 53 0.0011 26.2 4.3 33 381-414 15-47 (90)
164 TIGR02337 HpaR homoprotocatech 41.0 42 0.00091 28.1 4.2 47 478-530 30-76 (118)
165 PRK13239 alkylmercury lyase; P 40.9 49 0.0011 31.0 4.8 39 375-413 23-61 (206)
166 COG4190 Predicted transcriptio 40.8 99 0.0021 26.6 6.1 52 373-426 63-114 (144)
167 PF08461 HTH_12: Ribonuclease 40.8 53 0.0011 24.6 4.2 50 480-530 2-52 (66)
168 PRK11179 DNA-binding transcrip 40.8 46 0.00099 29.5 4.6 47 476-528 9-55 (153)
169 PF00165 HTH_AraC: Bacterial r 40.6 38 0.00083 22.4 3.1 27 386-412 6-32 (42)
170 PF06163 DUF977: Bacterial pro 40.4 64 0.0014 27.5 4.9 48 374-423 12-59 (127)
171 cd07977 TFIIE_beta_winged_heli 40.2 54 0.0012 25.3 4.2 58 475-540 8-70 (75)
172 PRK11050 manganese transport r 40.1 41 0.00089 29.9 4.1 43 378-422 41-83 (152)
173 TIGR02404 trehalos_R_Bsub treh 40.0 28 0.0006 33.2 3.2 47 484-537 17-64 (233)
174 PRK03902 manganese transport t 40.0 41 0.00089 29.3 4.1 43 378-422 12-54 (142)
175 PF03444 HrcA_DNA-bdg: Winged 39.2 70 0.0015 24.9 4.6 48 375-424 10-57 (78)
176 TIGR01610 phage_O_Nterm phage 39.1 42 0.0009 27.1 3.7 38 487-530 44-81 (95)
177 PF01638 HxlR: HxlR-like helix 38.9 40 0.00087 26.8 3.5 54 479-538 8-63 (90)
178 cd06171 Sigma70_r4 Sigma70, re 38.9 69 0.0015 21.6 4.5 40 372-412 11-50 (55)
179 PF00392 GntR: Bacterial regul 38.4 39 0.00083 24.9 3.1 37 386-424 21-58 (64)
180 PF05491 RuvB_C: Holliday junc 38.4 22 0.00048 27.4 1.8 40 386-426 23-62 (76)
181 PRK09462 fur ferric uptake reg 38.4 77 0.0017 27.9 5.6 51 479-530 20-72 (148)
182 COG2865 Predicted transcriptio 38.3 43 0.00093 35.6 4.5 57 477-539 403-459 (467)
183 TIGR02325 C_P_lyase_phnF phosp 38.1 55 0.0012 31.2 5.0 47 484-537 25-72 (238)
184 PRK09764 DNA-binding transcrip 38.0 56 0.0012 31.3 5.1 47 484-537 22-69 (240)
185 TIGR02018 his_ut_repres histid 37.8 55 0.0012 31.1 4.9 47 484-537 18-65 (230)
186 KOG2905 Transcription initiati 37.7 43 0.00092 31.9 3.8 58 375-442 187-244 (254)
187 PRK06474 hypothetical protein; 37.4 77 0.0017 29.0 5.6 53 370-424 7-61 (178)
188 COG1321 TroR Mn-dependent tran 37.3 55 0.0012 29.2 4.4 45 378-424 14-58 (154)
189 KOG2747 Histone acetyltransfer 37.0 42 0.00092 34.5 4.0 64 347-412 281-353 (396)
190 PF13542 HTH_Tnp_ISL3: Helix-t 36.9 77 0.0017 21.9 4.4 35 375-411 16-50 (52)
191 PF13601 HTH_34: Winged helix 36.7 22 0.00047 27.8 1.5 46 478-529 2-47 (80)
192 PRK11402 DNA-binding transcrip 36.4 34 0.00073 32.8 3.2 47 484-537 26-73 (241)
193 COG1510 Predicted transcriptio 36.4 34 0.00074 30.8 2.9 58 380-442 34-91 (177)
194 PF14947 HTH_45: Winged helix- 36.3 70 0.0015 24.6 4.4 44 376-422 8-51 (77)
195 cd00090 HTH_ARSR Arsenical Res 36.3 53 0.0012 24.1 3.8 45 481-532 12-56 (78)
196 PRK00135 scpB segregation and 35.0 2.4E+02 0.0052 26.1 8.4 111 325-442 34-153 (188)
197 cd07377 WHTH_GntR Winged helix 34.5 1E+02 0.0023 22.0 5.0 49 477-531 10-60 (66)
198 PHA03103 double-strand RNA-bin 34.2 81 0.0017 29.0 5.0 44 378-423 17-60 (183)
199 PHA02591 hypothetical protein; 34.1 50 0.0011 25.5 3.0 25 387-411 58-82 (83)
200 TIGR00122 birA_repr_reg BirA b 33.2 1.9E+02 0.0042 21.3 6.3 39 379-420 5-43 (69)
201 PF02270 TFIIF_beta: Transcrip 33.1 61 0.0013 31.9 4.5 58 374-441 216-273 (275)
202 PLN02853 Probable phenylalanyl 32.7 3E+02 0.0065 29.5 9.6 45 375-421 4-49 (492)
203 PF09763 Sec3_C: Exocyst compl 32.7 6.3E+02 0.014 28.6 13.0 129 16-162 552-701 (701)
204 PRK03573 transcriptional regul 32.6 69 0.0015 27.8 4.3 36 489-530 45-80 (144)
205 PF01475 FUR: Ferric uptake re 32.4 65 0.0014 27.0 4.0 60 478-538 10-70 (120)
206 PF10668 Phage_terminase: Phag 32.3 67 0.0014 23.6 3.4 23 384-406 18-40 (60)
207 PRK13719 conjugal transfer tra 32.0 69 0.0015 30.2 4.3 46 371-419 143-188 (217)
208 PF09114 MotA_activ: Transcrip 32.0 49 0.0011 26.3 2.7 46 377-424 19-66 (96)
209 PF00356 LacI: Bacterial regul 31.8 58 0.0013 22.4 2.9 21 390-410 1-21 (46)
210 PF07106 TBPIP: Tat binding pr 31.8 96 0.0021 27.9 5.2 59 376-440 3-64 (169)
211 PF13936 HTH_38: Helix-turn-he 31.6 80 0.0017 21.3 3.5 31 379-410 12-42 (44)
212 PLN03239 histone acetyltransfe 31.1 78 0.0017 32.1 4.7 45 373-422 265-313 (351)
213 TIGR02698 CopY_TcrY copper tra 31.0 1.1E+02 0.0023 26.4 5.1 50 372-423 2-55 (130)
214 PF14947 HTH_45: Winged helix- 30.9 1E+02 0.0023 23.6 4.6 44 480-530 10-53 (77)
215 PRK14165 winged helix-turn-hel 30.8 75 0.0016 30.1 4.4 46 376-423 9-54 (217)
216 COG2188 PhnF Transcriptional r 29.8 48 0.001 31.8 3.0 47 484-537 24-71 (236)
217 PRK10840 transcriptional regul 29.8 78 0.0017 29.4 4.5 44 372-418 151-194 (216)
218 PRK09802 DNA-binding transcrip 29.8 47 0.001 32.6 3.0 47 478-530 19-65 (269)
219 PRK04214 rbn ribonuclease BN/u 29.6 1.2E+02 0.0027 31.8 6.3 38 383-422 305-342 (412)
220 PF13545 HTH_Crp_2: Crp-like h 29.3 65 0.0014 24.3 3.2 33 388-422 28-60 (76)
221 PRK15201 fimbriae regulatory p 29.1 90 0.002 28.5 4.3 41 372-414 134-174 (198)
222 TIGR02989 Sig-70_gvs1 RNA poly 28.9 89 0.0019 27.3 4.5 38 372-411 112-150 (159)
223 COG0735 Fur Fe2+/Zn2+ uptake r 28.8 1.3E+02 0.0029 26.3 5.5 60 478-538 23-83 (145)
224 TIGR00281 segregation and cond 28.8 4.7E+02 0.01 24.1 10.7 32 381-412 9-42 (186)
225 TIGR01884 cas_HTH CRISPR locus 28.7 82 0.0018 29.4 4.4 46 480-531 147-192 (203)
226 COG2197 CitB Response regulato 28.6 81 0.0018 29.6 4.3 42 371-414 148-189 (211)
227 PF05186 Dpy-30: Dpy-30 motif; 28.5 1E+02 0.0022 20.8 3.5 30 166-195 10-39 (42)
228 PF04760 IF2_N: Translation in 28.4 34 0.00073 24.3 1.3 23 388-410 3-25 (54)
229 COG2771 CsgD DNA-binding HTH d 28.2 1.4E+02 0.0031 21.3 4.8 41 371-413 4-44 (65)
230 PF11784 DUF3320: Protein of u 28.0 1.1E+02 0.0024 21.7 3.8 37 471-507 7-43 (52)
231 PRK15411 rcsA colanic acid cap 27.9 82 0.0018 29.4 4.2 42 371-414 137-178 (207)
232 TIGR02716 C20_methyl_CrtF C-20 27.5 90 0.0019 31.1 4.7 41 380-423 16-56 (306)
233 PF02334 RTP: Replication term 27.5 66 0.0014 26.7 2.9 53 475-528 17-72 (122)
234 PRK11475 DNA-binding transcrip 27.0 92 0.002 29.2 4.4 45 371-418 134-178 (207)
235 PRK14165 winged helix-turn-hel 26.9 91 0.002 29.5 4.3 53 480-538 11-63 (217)
236 PHA02701 ORF020 dsRNA-binding 26.6 1.5E+02 0.0032 27.2 5.3 45 377-423 7-52 (183)
237 TIGR00721 tfx DNA-binding prot 26.6 1.2E+02 0.0025 26.5 4.5 39 372-412 7-45 (137)
238 PF01399 PCI: PCI domain; Int 26.5 1.1E+02 0.0024 24.4 4.3 44 375-420 47-90 (105)
239 PF08221 HTH_9: RNA polymerase 26.4 83 0.0018 23.2 3.1 51 472-528 9-59 (62)
240 PRK04217 hypothetical protein; 26.4 1.2E+02 0.0025 25.5 4.3 41 371-412 42-82 (110)
241 PF04539 Sigma70_r3: Sigma-70 26.3 67 0.0015 24.5 2.8 26 387-412 19-44 (78)
242 COG3413 Predicted DNA binding 26.3 1E+02 0.0022 29.0 4.6 42 371-412 155-202 (215)
243 PRK10430 DNA-binding transcrip 26.2 1.1E+02 0.0023 29.1 4.8 49 372-422 159-210 (239)
244 TIGR03433 padR_acidobact trans 26.0 2.3E+02 0.005 22.9 6.0 51 477-528 5-57 (100)
245 COG1777 Predicted transcriptio 25.9 5.6E+02 0.012 24.1 10.0 41 379-422 20-60 (217)
246 cd00073 H15 linker histone 1 a 25.8 2.2E+02 0.0047 22.5 5.7 54 476-530 10-65 (88)
247 smart00088 PINT motif in prote 25.7 77 0.0017 24.7 3.1 34 385-420 21-54 (88)
248 smart00753 PAM PCI/PINT associ 25.7 77 0.0017 24.7 3.1 34 385-420 21-54 (88)
249 COG3398 Uncharacterized protei 25.7 1.3E+02 0.0029 28.4 4.9 60 376-441 176-235 (240)
250 PRK15431 ferrous iron transpor 25.2 99 0.0021 24.1 3.3 32 383-414 11-42 (78)
251 COG5090 TFG2 Transcription ini 25.1 92 0.002 29.4 3.8 55 378-442 199-253 (297)
252 PRK03902 manganese transport t 24.6 99 0.0021 26.9 3.9 48 477-530 9-56 (142)
253 PF01418 HTH_6: Helix-turn-hel 24.1 69 0.0015 24.6 2.4 32 381-412 27-58 (77)
254 PRK13509 transcriptional repre 23.9 81 0.0018 30.6 3.5 45 479-529 8-52 (251)
255 TIGR02983 SigE-fam_strep RNA p 23.8 1E+02 0.0022 27.1 3.9 40 372-412 111-150 (162)
256 PRK09954 putative kinase; Prov 23.7 86 0.0019 32.1 3.8 44 479-528 6-49 (362)
257 PLN00104 MYST -like histone ac 23.5 1.3E+02 0.0028 31.8 4.9 43 375-422 360-403 (450)
258 PF09862 DUF2089: Protein of u 23.5 1.7E+02 0.0036 24.6 4.7 56 357-414 20-75 (113)
259 PRK09954 putative kinase; Prov 23.5 1.4E+02 0.0031 30.5 5.4 42 377-420 6-47 (362)
260 PF13551 HTH_29: Winged helix- 23.5 1.4E+02 0.003 24.2 4.4 36 378-414 3-38 (112)
261 TIGR01764 excise DNA binding d 23.3 99 0.0021 20.6 2.9 21 389-409 2-22 (49)
262 PRK03975 tfx putative transcri 23.0 1.5E+02 0.0032 26.0 4.5 39 371-411 6-44 (141)
263 PRK12423 LexA repressor; Provi 22.9 1.2E+02 0.0027 28.2 4.4 54 372-427 4-63 (202)
264 COG2512 Predicted membrane-ass 22.8 1E+02 0.0022 30.1 3.8 51 372-424 193-244 (258)
265 TIGR02787 codY_Gpos GTP-sensin 22.6 1.4E+02 0.0031 28.7 4.6 45 378-424 187-232 (251)
266 PF05043 Mga: Mga helix-turn-h 22.5 1E+02 0.0023 24.0 3.3 29 385-413 27-55 (87)
267 PRK00118 putative DNA-binding 22.4 1.6E+02 0.0034 24.4 4.3 39 373-412 19-57 (104)
268 PF11372 DUF3173: Domain of un 22.3 1.2E+02 0.0025 22.3 3.1 35 489-528 2-38 (59)
269 KOG2167 Cullins [Cell cycle co 22.2 1.7E+02 0.0037 31.8 5.5 36 14-51 289-324 (661)
270 PRK12522 RNA polymerase sigma 22.1 1.2E+02 0.0026 27.1 4.1 24 387-410 134-157 (173)
271 PRK10870 transcriptional repre 21.9 1.5E+02 0.0032 27.0 4.6 38 488-531 69-106 (176)
272 PRK12547 RNA polymerase sigma 21.8 1.4E+02 0.003 26.5 4.3 40 372-412 113-152 (164)
273 PF10752 DUF2533: Protein of u 21.8 3.7E+02 0.0081 21.0 5.8 37 466-504 21-57 (84)
274 PRK13777 transcriptional regul 21.6 1.4E+02 0.0029 27.6 4.2 46 478-529 47-92 (185)
275 PRK10411 DNA-binding transcrip 21.4 1.1E+02 0.0023 29.6 3.7 45 480-530 8-52 (240)
276 PRK12514 RNA polymerase sigma 21.4 1.1E+02 0.0024 27.5 3.7 38 372-410 130-167 (179)
277 PRK09642 RNA polymerase sigma 21.3 1.3E+02 0.0029 26.3 4.1 37 372-410 107-144 (160)
278 PF12728 HTH_17: Helix-turn-he 21.2 1.1E+02 0.0024 21.0 2.9 21 389-409 2-22 (51)
279 PRK04424 fatty acid biosynthes 21.2 74 0.0016 29.3 2.5 46 478-529 9-54 (185)
280 PRK12529 RNA polymerase sigma 21.1 1.3E+02 0.0028 27.2 4.0 38 372-410 128-165 (178)
281 COG2996 Predicted RNA-bindinin 21.1 98 0.0021 30.2 3.2 34 388-423 246-279 (287)
282 PRK12525 RNA polymerase sigma 21.1 1.5E+02 0.0032 26.4 4.4 24 387-410 133-156 (168)
283 PF08766 DEK_C: DEK C terminal 21.0 2E+02 0.0044 20.3 4.2 46 476-523 4-51 (54)
284 PRK12536 RNA polymerase sigma 20.9 1.4E+02 0.0029 27.0 4.2 40 372-412 130-169 (181)
285 PRK08295 RNA polymerase factor 20.9 1.2E+02 0.0026 28.0 3.9 38 373-412 157-194 (208)
286 PRK09483 response regulator; P 20.9 1.5E+02 0.0032 27.1 4.6 42 371-414 148-189 (217)
287 PF10826 DUF2551: Protein of u 20.8 2.5E+02 0.0055 22.1 4.8 68 371-441 8-79 (83)
288 COG1378 Predicted transcriptio 20.8 1.7E+02 0.0038 28.3 5.0 50 371-422 13-62 (247)
289 TIGR02999 Sig-70_X6 RNA polyme 20.7 1.4E+02 0.003 26.8 4.2 38 372-410 135-172 (183)
290 COG1733 Predicted transcriptio 20.6 2.3E+02 0.005 24.0 5.1 45 376-423 25-70 (120)
291 TIGR02952 Sig70_famx2 RNA poly 20.5 1.6E+02 0.0034 26.1 4.4 39 372-411 123-161 (170)
292 PRK10046 dpiA two-component re 20.4 1.5E+02 0.0032 27.9 4.4 43 378-422 166-209 (225)
293 PRK09047 RNA polymerase factor 20.3 1.4E+02 0.003 26.1 4.0 38 372-410 107-144 (161)
294 KOG3852 Uncharacterized conser 20.2 5.4E+02 0.012 25.7 8.0 107 142-270 220-335 (426)
295 PRK09333 30S ribosomal protein 20.0 1.1E+02 0.0023 27.2 3.0 49 374-424 53-115 (150)
296 PRK12541 RNA polymerase sigma 20.0 1.5E+02 0.0032 26.1 4.2 38 372-410 113-150 (161)
No 1
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.5e-96 Score=735.39 Aligned_cols=536 Identities=68% Similarity=1.039 Sum_probs=518.9
Q ss_pred CccccccchHhhhHHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHchhcCCCChHHHHHHHHHHHHHHHH
Q 009222 1 MFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHI 80 (540)
Q Consensus 1 m~~~l~~Y~~~fE~~~l~~t~~yY~~~~~~~~~~~~~~~Yl~~v~~~l~~E~~~~~~~l~~~s~~~l~~~~~~~Li~~~~ 80 (540)
|+.++++|.+.|+..+++.+.++|........++..+++||+.++..+.+|..++..|++.++...+..++.+.|+..|+
T Consensus 123 MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL 202 (661)
T KOG2167|consen 123 MLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHL 202 (661)
T ss_pred HHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHH
Confidence 78899999999999999999999999999999999999999999999999999999999988877799999999999999
Q ss_pred HHHHHHHHHHHHccCChhhHHHHHHHhhhc-cchHHHHHHHHHHHHHHhhhhhcCchhhHHHHHHHHHHHHHHHHHHHHh
Q 009222 81 SAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQS 159 (540)
Q Consensus 81 ~~ll~~~~~~ll~~~~~~~l~~ly~l~~~~-~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~ 159 (540)
+.++..|+..+++.++..++.++|.+++++ .+...++..|++|+++.|.+++.+.+.+++++..++.++++.+-++..|
T Consensus 203 ~~IL~kgl~~lvDm~q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~kDk~mVqELL~FK~k~Dii~~~s 282 (661)
T KOG2167|consen 203 DLILTKGLDSLVDMRQTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEKDKDMVQELLDFKKKVDIIVDES 282 (661)
T ss_pred HHHHhcchHHhhhhhhccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchhhHHHHHHHHHHHHHhhHHHHHH
Confidence 999999999999999999999999999999 7999999999999999999999999999999999999999999999999
Q ss_pred cCCC--HHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhhhcccChhHHHHHHHHHH
Q 009222 160 FSKN--EAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDL 237 (540)
Q Consensus 160 F~~~--~~f~~~l~~~f~~~ln~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~l~~i~~l~~~l~~Kd~F~~~Y~~~L 237 (540)
|..+ ..|..++++||+.++|...+++++++|+|.|..|+.|.++.++++++..++.++.+|+|+..||+|+.+|.+-|
T Consensus 283 F~~~v~e~f~~~~~~afe~fink~~~rpAelIak~~dt~Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdL 362 (661)
T KOG2167|consen 283 FLKYVAEKFLNSMSKAFETFINKRRNRPAELIAKYVDTKLRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDL 362 (661)
T ss_pred HHHhhHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence 9988 99999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCCHHHHHHHHHHHHHhhcchhHHhHHHHHhhHHHhHHHHHHHHHhhhhccCCCCCccEEEEEeecCCCCCC
Q 009222 238 AKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTY 317 (540)
Q Consensus 238 ~~RLL~~~~~~~~~E~~~i~~L~~~~g~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VL~~~~WP~~ 317 (540)
|+|||.++|.+.+.|..|+.+|+.+||..+|++|++|++|+..|++++..|+++.+.+...+.++ +.+.|++.++||.+
T Consensus 363 akrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty 441 (661)
T KOG2167|consen 363 AKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTY 441 (661)
T ss_pred HHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCC
Confidence 99999999999999999999999999999999999999999999999999999865544444555 99999999999999
Q ss_pred CCCCCcCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCCCCccHHHHHHH
Q 009222 318 PPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDA 397 (540)
Q Consensus 318 ~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~ 397 (540)
++.++.||++|..+++.|.+||-.+|.||+|+|.+++|+|.+++.|+.|+.++.+|++|++||++||+.+.||++||.+.
T Consensus 442 ~~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~ 521 (661)
T KOG2167|consen 442 PPMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKES 521 (661)
T ss_pred CchhccCCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCCCCceeEEecccccccchhhhhhhhHHHHHhhHHhH
Q 009222 398 TGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQV 477 (540)
Q Consensus 398 ~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~~~~~~e~~~~~~~~~~~r~~~i 477 (540)
||+.+.++++.|++|.+++.++|.++|+|+++.+++.|.+|..|+.+..||+||.|+++++.+|++.+.++|.+||.+.|
T Consensus 522 t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~i 601 (661)
T KOG2167|consen 522 TGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQI 601 (661)
T ss_pred ccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
|||||||||.||+++|+.|+.++.++++||+.+ ++|++||+||+|||++||+ | +.|.|||
T Consensus 602 daaivrimk~rk~l~h~~l~~el~~qlkfpv~~-d~kkriesli~rey~erd~-n-~~y~yva 661 (661)
T KOG2167|consen 602 DAAIVRIMKMRKTLSHNLLVTELFNQLKFPVKP-DLKKRIESLIDREYLERDD-N-NIYNYVA 661 (661)
T ss_pred HHHHHHHHHHHHhhchhHHHHHHHHhcCCCCCh-hHHHHHHHHHhHHHhcccc-c-ccccccC
Confidence 999999999999999999999999999999988 9999999999999999994 4 8999998
No 2
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.3e-90 Score=744.13 Aligned_cols=525 Identities=42% Similarity=0.721 Sum_probs=487.7
Q ss_pred cccchHhhhHHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHchhcCCCChHHHHHHHHHHHHHHHHHHHH
Q 009222 5 LGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAIL 84 (540)
Q Consensus 5 l~~Y~~~fE~~~l~~t~~yY~~~~~~~~~~~~~~~Yl~~v~~~l~~E~~~~~~~l~~~s~~~l~~~~~~~Li~~~~~~ll 84 (540)
+.+|.++||++++..|..||...+.+|+...++.+|+..++.++.+|..|+..|++..+..++.+.+...++..+.+.++
T Consensus 190 ~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~~~~~le~~~~~~~~~~~~ 269 (725)
T KOG2166|consen 190 LSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEPKLVEVVEDELIVVFADDLE 269 (725)
T ss_pred hhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccchhhHHHHHHHHHHHHHHHH
Confidence 34899999999999999999999999999889999999999999999999998887777777777777777776666655
Q ss_pred ---HHHHHHHHccCChhhHHHHHHHhhhc-cchHHHHHHHHHHHHHHhhhhhcCc-----hhhHHHHHHHHHHHHHHHHH
Q 009222 85 ---DKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE-----EKDKDMVSSLLEFKASLDTI 155 (540)
Q Consensus 85 ---~~~~~~ll~~~~~~~l~~ly~l~~~~-~~~~~l~~~~~~~i~~~g~~~~~~~-----~~~~~~i~~l~~l~~~~~~l 155 (540)
.+|+..++.+++.++|.++|++++++ +|++.+++.+..|+..+|..++... .++..++..++.++++|..+
T Consensus 270 e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~~~~~~~~v~~~l~~~~~~~~~ 349 (725)
T KOG2166|consen 270 EMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETAATNPVEYVQGLLELHDKYKVL 349 (725)
T ss_pred HHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhcccchHHHHhccHHHHHHHHHH
Confidence 36999999999999999999999999 9999999999999999998777643 45679999999999999999
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhhhcccChhHHHHHHHH
Q 009222 156 WEQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKK 235 (540)
Q Consensus 156 ~~~~F~~~~~f~~~l~~~f~~~ln~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~l~~i~~l~~~l~~Kd~F~~~Y~~ 235 (540)
+..||.++..|.++++.||..++|.+....+|+||.|||.+++++.++.++++++..++.++.+|+|+.+||+|..+|++
T Consensus 350 ~~~~f~~d~~f~~~ld~a~~~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk 429 (725)
T KOG2166|consen 350 VKECFANDTLFKKALDAAFEEFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKK 429 (725)
T ss_pred HHHHhhccHHHHHHHHHHHHHHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHH
Confidence 99999999999999999999999998754569999999999999988899999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCCHHHHHHHHHHHHHhhcchhHHhHHHHHhhHHHhHHHHHHHHHhhhhccCCCCCccEEEEEeecCCCC
Q 009222 236 DLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWP 315 (540)
Q Consensus 236 ~L~~RLL~~~~~~~~~E~~~i~~L~~~~g~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VL~~~~WP 315 (540)
.||+|||+++|.|.+.|+.||.+|++.||..||.+|++|++|+..|+++...|.+... .....+++|.|.|||.|+||
T Consensus 430 ~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~~~--~~~~~~~df~v~VLt~g~WP 507 (725)
T KOG2166|consen 430 VLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADYAN--YSANLGIDFTVTVLTTGFWP 507 (725)
T ss_pred HHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhhhc--hhccCCCceeEEEeecCCcC
Confidence 9999999999999999999999999999999999999999999999999999997611 12235799999999999999
Q ss_pred CCCCCCCcCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCCCCccHHHHH
Q 009222 316 TYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIK 395 (540)
Q Consensus 316 ~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei~ 395 (540)
.+++.++.||++|..+++.|..||.++|+||+|.|.|++|.|+|.+++.+++++++||++||+||++||+.+.+|+++|.
T Consensus 508 ~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~ 587 (725)
T KOG2166|consen 508 SYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEIL 587 (725)
T ss_pred CccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHH
Confidence 98888899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCCCCceeEEecccccccchhhhhhhhHHHHHhhHH
Q 009222 396 DATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQY 475 (540)
Q Consensus 396 ~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~~~~~~e~~~~~~~~~~~r~~ 475 (540)
+.|+++.+++.++|.||++.|.+++.. |.++. .+++.|.+|.+|+++.+|++++.++.+ |.+.+.+.+++||+.
T Consensus 588 ~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~----e~~~~~~~ve~dRk~ 661 (725)
T KOG2166|consen 588 EQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMD----ERKKVVEDVDKDRKY 661 (725)
T ss_pred HHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCch----hHHHHHhhhhhHHHH
Confidence 999999999999999998877666665 66666 789999999999999999999876543 677788899999999
Q ss_pred hHHHHHHhhhcCCCCCChHHHHHHHHHHc--CCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q 009222 476 QVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 538 (540)
Q Consensus 476 ~i~a~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Y 538 (540)
.|+||||||||+||.+.|++|+.+|.+|+ +|.|++.+||+|||.|||||||+|+ +|+++|.|
T Consensus 662 ~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 662 AIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred HHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 99999999999999999999999999999 9999999999999999999999999 89999998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.3e-91 Score=713.75 Aligned_cols=531 Identities=39% Similarity=0.640 Sum_probs=483.8
Q ss_pred ccccchHhhhHHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHchhcCCCChHHHHHHHHHHHHHHHHHHH
Q 009222 4 ALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAI 83 (540)
Q Consensus 4 ~l~~Y~~~fE~~~l~~t~~yY~~~~~~~~~~~~~~~Yl~~v~~~l~~E~~~~~~~l~~~s~~~l~~~~~~~Li~~~~~~l 83 (540)
+|.+|.+.||+.||+.|.+||..++.+++..+++.+||..++.++++|..++..|++.++..++..+++++||..|.+.+
T Consensus 214 ~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~eyL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l 293 (773)
T COG5647 214 NLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDL 293 (773)
T ss_pred cchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHH
Confidence 34899999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHH--HHHHHHccCChhhHHHHHHHhhhc-cchHHHHHHHHHHHHHHh---hh----hhcC----------chhhHHHHH
Q 009222 84 LDK--GFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTG---HG----IVMD----------EEKDKDMVS 143 (540)
Q Consensus 84 l~~--~~~~ll~~~~~~~l~~ly~l~~~~-~~~~~l~~~~~~~i~~~g---~~----~~~~----------~~~~~~~i~ 143 (540)
.++ |+..+++..+.+.|+.+|++++++ .++..|.+.|..||+..| .. ++.. ...+..+++
T Consensus 294 ~~~~s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q 373 (773)
T COG5647 294 EEQGSGFREALDASNLEKLQVLYRLLSETKYGVQPLQEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQ 373 (773)
T ss_pred HhchHHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHH
Confidence 864 899999999999999999999999 779999999999999999 11 1111 123568999
Q ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcCC---CCcHHHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhh
Q 009222 144 SLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQ---NRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLF 220 (540)
Q Consensus 144 ~l~~l~~~~~~l~~~~F~~~~~f~~~l~~~f~~~ln~~~---~~~~e~La~y~d~~l~~~~~~~~~~~~~~~l~~i~~l~ 220 (540)
.++.++..+..++.+.|.+|..+.+++++||+.++|.+. +.++|+||+|+|.+++++.+......++..+.+++.||
T Consensus 374 ~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLf 453 (773)
T COG5647 374 KLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFINGNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLF 453 (773)
T ss_pred HHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhccccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999953 36899999999999998765544457888899999999
Q ss_pred hcccChhHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcchhHHhHHHHHhhHHHhHHHHHHHHHhhhhccCCCC
Q 009222 221 RFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPS 300 (540)
Q Consensus 221 ~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~L~~~~g~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~ 300 (540)
+|+.+||+|+.+|++.||+|||+++|.+.+.|..||++|++.||.+||+|+++|++|+..|.++...|++...+ ...
T Consensus 454 ryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s---~~~ 530 (773)
T COG5647 454 RYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQS---YNK 530 (773)
T ss_pred HHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchh---hcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999876421 224
Q ss_pred CccEEEEEeecCCCCCCCC-CCCcCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEE---EcHHH
Q 009222 301 GIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELA---VSLFQ 376 (540)
Q Consensus 301 ~~~~~~~VL~~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~---~s~~Q 376 (540)
.+++.|.||+..+||..++ ..+++|++|.+.++.|++||.++|+||+|.|.|+||+|+|++.|+.+++.+. ++++|
T Consensus 531 ~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q 610 (773)
T COG5647 531 YLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQ 610 (773)
T ss_pred ccchhHHHHHHhcCCCCccccccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHH
Confidence 6899999999999997766 6899999999999999999999999999999999999999999988754443 66899
Q ss_pred HHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCCCCceeEEecccccc
Q 009222 377 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMK 456 (540)
Q Consensus 377 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~~ 456 (540)
+.|+++||+++++|+++|.+.|+++.+++++.|+||++. +++..-++++..++++.|.+|.+|+++..+|+++.+...
T Consensus 611 ~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~a--k~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~ 688 (773)
T COG5647 611 LLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCA--KLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAES 688 (773)
T ss_pred HHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhh--heeeeccccccCCCCceEEEccccccccceeeecccccc
Confidence 999999999999999999999999999999999999764 455444557788999999999999999999999886654
Q ss_pred cchhhhhhhhHHHHHhhHHhHHHHHHhhhcCCCCCChHHHHHHHHHHc--CCCCChHHHHHHHHHhhhhccccccCCCCC
Q 009222 457 ETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQ 534 (540)
Q Consensus 457 ~~~~e~~~~~~~~~~~r~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~ 534 (540)
+..+++..+++.+.+||+..+|||||||||++|+|+|++|+++|+.+. ||.|++.+||++|+.|||||||+|.++| .
T Consensus 689 ~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~ 767 (773)
T COG5647 689 ECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-E 767 (773)
T ss_pred hhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-c
Confidence 444566777789999999999999999999999999999999999999 9999999999999999999999999888 8
Q ss_pred ceeecC
Q 009222 535 IYNYLA 540 (540)
Q Consensus 535 ~y~Yia 540 (540)
+|+|+|
T Consensus 768 iY~YLa 773 (773)
T COG5647 768 IYVYLA 773 (773)
T ss_pred eeeecC
Confidence 999997
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-86 Score=638.72 Aligned_cols=502 Identities=29% Similarity=0.515 Sum_probs=472.1
Q ss_pred ccccchHhhhHHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHchhcCCCChHHHHHHHHHHHHHHHHHHH
Q 009222 4 ALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAI 83 (540)
Q Consensus 4 ~l~~Y~~~fE~~~l~~t~~yY~~~~~~~~~~~~~~~Yl~~v~~~l~~E~~~~~~~l~~~s~~~l~~~~~~~Li~~~~~~l 83 (540)
.+.+|++.||+|+|.+|..||+..++..+.+.++++|+.+|...+++|+-||++||+++|..+++..|++.+|.+|.+.+
T Consensus 215 ~~~fyqe~fe~p~lt~t~~yy~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l 294 (728)
T KOG2284|consen 215 TTAFYQESFEKPLLTDTEQYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL 294 (728)
T ss_pred cHHHHHHHhccccccchHHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred HHHHHHHHHccCChhhHHHHHHHhhhc-cchHHHHHHHHHHHHHHhhhhhcCchh---hHHHHHHHHHHHHHHHHHHHHh
Q 009222 84 LDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDEEK---DKDMVSSLLEFKASLDTIWEQS 159 (540)
Q Consensus 84 l~~~~~~ll~~~~~~~l~~ly~l~~~~-~~~~~l~~~~~~~i~~~g~~~~~~~~~---~~~~i~~l~~l~~~~~~l~~~~ 159 (540)
. -.++.++.+++..+++-+|.|+..+ -|+..+...|++||.+.|.+.+++.+. +..||+.++.+|++|..++...
T Consensus 295 h-a~ch~~i~~e~~~d~~nmy~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v 373 (728)
T KOG2284|consen 295 H-AVCHDLITNEENKDLRNMYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAV 373 (728)
T ss_pred H-HHHHHHHhhhhhhhHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 6 4899999999999999999999999 999999999999999999999987654 4589999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHhhcCC-----CCcHHHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhhhcccChhHHHHHHH
Q 009222 160 FSKNEAFCNTIKDAFEYLINLRQ-----NRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYK 234 (540)
Q Consensus 160 F~~~~~f~~~l~~~f~~~ln~~~-----~~~~e~La~y~d~~l~~~~~~~~~~~~~~~l~~i~~l~~~l~~Kd~F~~~Y~ 234 (540)
|++|..|..+++.|+..++|... .+.+|.||+|||.+++++.+|+++.+++.+|+..+.+|+|++|||+|..+|.
T Consensus 374 ~~~d~~f~s~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys 453 (728)
T KOG2284|consen 374 FMDDGEFSSGLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYS 453 (728)
T ss_pred hcCchhhhHHHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHH
Confidence 99999999999999999999865 3689999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHhhcchhHHhHHHHHhhHHHhHHHHHHHHHhhhhccCCCCCccEEEEEeecCCC
Q 009222 235 KDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYW 314 (540)
Q Consensus 235 ~~L~~RLL~~~~~~~~~E~~~i~~L~~~~g~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VL~~~~W 314 (540)
++||+||+.+.|.+.|.|..||++|++.||.+||+++- +.|++.|.+++++|.+.+.+
T Consensus 454 ~mla~rli~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~n-------------------- 511 (728)
T KOG2284|consen 454 KMLANRLIASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIAN-------------------- 511 (728)
T ss_pred HHHHHHHHhhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHHh--------------------
Confidence 99999999999999999999999999999999999998 99999999999999876541
Q ss_pred CCCCCCCCcCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCCCCccHHHH
Q 009222 315 PTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDI 394 (540)
Q Consensus 315 P~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei 394 (540)
+.+|.+|+..++.|+.||..+|+||+|+|++.++++++++++-++.|.-.++++||++|++||..+.+++.+|
T Consensus 512 -------f~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i 584 (728)
T KOG2284|consen 512 -------FHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDI 584 (728)
T ss_pred -------ccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhh
Confidence 7899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCCCCceeEEeccccc-ccchhhhhhhhHHHHHhh
Q 009222 395 KDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQM-KETVEENTSTTERVFQDR 473 (540)
Q Consensus 395 ~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~-~~~~~e~~~~~~~~~~~r 473 (540)
.+.+|++.+.+.+.+.++.+ .++|.... ..+..+..|++|.+|+++..+.++..++. +.+..|.+.+...+.+||
T Consensus 585 ~~~~~~~~~~l~kti~tild--v~~~~~d~--~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~dr 660 (728)
T KOG2284|consen 585 GEEIGVSGDYLLKTIRTILD--VTLLTCDD--QNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDR 660 (728)
T ss_pred hhhhCccHHHHHHHHHHHHh--ceeecccc--cccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHH
Confidence 99999999999999999975 56776543 35677789999999999999999876443 345677788888999999
Q ss_pred HHhHHHHHHhhhcCCCCCChHHHHHHHHHHc--CCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 474 QYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 474 ~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
++.++|+||||||+||.+.|+.|+.+|+++. +|.|++.+||++||.||++.||+|.+.+ +.|.|+|
T Consensus 661 k~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 661 KYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 9999999999999999999999999999999 9999999999999999999999999866 9999998
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.2e-76 Score=573.92 Aligned_cols=535 Identities=31% Similarity=0.505 Sum_probs=480.1
Q ss_pred ccccchHhhhHHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHchhcCC--CChHHHHHHHHHHHHHHHHH
Q 009222 4 ALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDV--STRKPLIATAERQLLERHIS 81 (540)
Q Consensus 4 ~l~~Y~~~fE~~~l~~t~~yY~~~~~~~~~~~~~~~Yl~~v~~~l~~E~~~~~~~l~~--~s~~~l~~~~~~~Li~~~~~ 81 (540)
.|.+|++.||..||+.|.+||+..+..++++.++.+||+.+..-+++|+.|+.+||.+ .|..+++.++.++|+.++.+
T Consensus 192 kL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~ 271 (777)
T KOG2285|consen 192 KLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKRYLEMNSPSSGKLMEKAVNALVESFED 271 (777)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHH
Confidence 4679999999999999999999999999999999999999999999999999999977 67799999999999999999
Q ss_pred HHHHHHHHHHHccCChhhHHHHHHHhhhc-cchHHHHHHHHHHHHHHhhhhhcC-c----hhhHHHHHHHHHHHHHHHHH
Q 009222 82 AILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMD-E----EKDKDMVSSLLEFKASLDTI 155 (540)
Q Consensus 82 ~ll~~~~~~ll~~~~~~~l~~ly~l~~~~-~~~~~l~~~~~~~i~~~g~~~~~~-~----~~~~~~i~~l~~l~~~~~~l 155 (540)
.|+. +|..|+...+++.|.++|+|+.++ .|++.+...+..||...|..-+.. . ++...+|+.++.++++|..+
T Consensus 272 tIlA-EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~aaE~ittDsEkYVeqLL~lFnkFS~L 350 (777)
T KOG2285|consen 272 TILA-ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNAAENITTDSEKYVEQLLLLFNKFSSL 350 (777)
T ss_pred HHHH-HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhhhhhccCCHHHHHHHHHHHHHHHHHH
Confidence 9986 799999999999999999999999 999999999999999999875432 2 33568999999999999999
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHhhcCC--------------------CCcHHHHHHHHHHHHhcC--CCCCChHHHHHHH
Q 009222 156 WEQSFSKNEAFCNTIKDAFEYLINLRQ--------------------NRPAELIAKFLDEKLRAG--NKGTSEEELEGTL 213 (540)
Q Consensus 156 ~~~~F~~~~~f~~~l~~~f~~~ln~~~--------------------~~~~e~La~y~d~~l~~~--~~~~~~~~~~~~l 213 (540)
+.+.|+.|+.|..|-+.||+.++|... ++.+|+||.|||.++|+. ++..++++++.++
T Consensus 351 VreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL 430 (777)
T KOG2285|consen 351 VREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKL 430 (777)
T ss_pred HHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHH
Confidence 999999999999999999999999842 578999999999999985 4667889999999
Q ss_pred HhhhhhhhcccChhHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhc--chhHHhHHHHHhhHHHhHHHHHHHHHh
Q 009222 214 DKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECG--SQFTNKLEGMFKDIELSKEINESFKQS 291 (540)
Q Consensus 214 ~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~L~~~~g--~~~~~kl~~Ml~D~~~S~~l~~~f~~~ 291 (540)
++++.+++|+.+||+|+.+++.+|++||+...|.+.+.|..|++.|+ +|| .+|.+++..|++|++.|++++..|+..
T Consensus 431 ~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~ 509 (777)
T KOG2285|consen 431 NQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKA 509 (777)
T ss_pred HhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999998 577 679999999999999999999999998
Q ss_pred hhhccCCCCCccEEEEEeecCCCCCCCC-CCCcCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEE
Q 009222 292 SQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKEL 370 (540)
Q Consensus 292 ~~~~~~~~~~~~~~~~VL~~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l 370 (540)
....++....-.+++.||+.|.|...+. ..+.||.+|+..+...++||+++|.||+|+|.|+++.+++++.-+-|.|++
T Consensus 510 ~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDL 589 (777)
T KOG2285|consen 510 LTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDL 589 (777)
T ss_pred HhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccCccchhhhhhccCCeeEeeccccccee
Confidence 7754333334578899999999998876 679999999999999999999999999999999999999887655589999
Q ss_pred EEcHHHHHHHHHhcCC--CCccHHHHHHHhCCCHHHHHHHhhhhhc-C--CceeeecCCC----CCCCCCCCeEEEccCC
Q 009222 371 AVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLAC-G--KVRVLQKLPK----GRDVEDDDSFVFNEGF 441 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~--~~~t~~ei~~~~~i~~~~l~~~L~~L~~-~--k~~iL~~~~~----~~~~~~~~~~~~N~~f 441 (540)
.|+++||+||.+||+. +.+|++.+.-.|.+|+.++++.|-||+. + |..||..+|+ .+++.++..|.+|.+|
T Consensus 590 evTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF 669 (777)
T KOG2285|consen 590 EVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEF 669 (777)
T ss_pred eeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechh
Confidence 9999999999999986 7899999999999999999999999987 4 4778887775 2568888999999999
Q ss_pred CC-----CceeEEeccccccc--chhhhhhhhHHHHHhhHHhHHHHHHhhhcCCCCCChHHHHHHHHHHc--CCCCChHH
Q 009222 442 TA-----PLYRIKVNAIQMKE--TVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPAD 512 (540)
Q Consensus 442 ~~-----~~~~i~i~~~~~~~--~~~e~~~~~~~~~~~r~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ 512 (540)
.- ..+|.++|.+.--+ +....++..+.+.+-|-...|-+||+|||.+|+++..+|-.++.+.+ .|-|+..+
T Consensus 670 ~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKm 749 (777)
T KOG2285|consen 670 NVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKM 749 (777)
T ss_pred hhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHH
Confidence 72 23455555543211 22223344567889999999999999999999999999999999999 89999999
Q ss_pred HHHHHHHhhhhccccccCCCCCceeecC
Q 009222 513 LKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 513 ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
||++||+|||..|++||++|-++|+|+|
T Consensus 750 IKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 750 IKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHHHHhhhhhccchhhccceeeeC
Confidence 9999999999999999999999999997
No 6
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=1.3e-70 Score=603.03 Aligned_cols=433 Identities=45% Similarity=0.745 Sum_probs=386.4
Q ss_pred ccccchHhhhHHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHchhcCCCChHHHHHHHHHHHHHHHHHHH
Q 009222 4 ALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAI 83 (540)
Q Consensus 4 ~l~~Y~~~fE~~~l~~t~~yY~~~~~~~~~~~~~~~Yl~~v~~~l~~E~~~~~~~l~~~s~~~l~~~~~~~Li~~~~~~l 83 (540)
.+++|.+.||++||+.|.+||+.++ +++.++.+|+.+|+.++++|..|+..|+++++.+++.+++.++||.+|.+.+
T Consensus 148 ~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l 224 (588)
T PF00888_consen 148 SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDEL 224 (588)
T ss_dssp HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHH
T ss_pred hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999999999 5777999999999999999999999999999999999999999999999988
Q ss_pred HHHHHHHHHccCChhhHHHHHHHhhhc-cchHHHHHHHHHHHHHHhhhhhcCc---hhhHHHHHHHHHHHHHHHHHHHHh
Q 009222 84 LDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE---EKDKDMVSSLLEFKASLDTIWEQS 159 (540)
Q Consensus 84 l~~~~~~ll~~~~~~~l~~ly~l~~~~-~~~~~l~~~~~~~i~~~g~~~~~~~---~~~~~~i~~l~~l~~~~~~l~~~~ 159 (540)
.+|+..|+++++.++|+++|++++++ ++++.++++|++||.+.|..++... .++.++|+.++++|+++..++..|
T Consensus 225 -~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~ 303 (588)
T PF00888_consen 225 -SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLIQEC 303 (588)
T ss_dssp -HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHHHHT
T ss_pred -HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHHHHh
Confidence 67999999999999999999999998 9999999999999999999988763 567799999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhhhcccChhHHHHHHHHHHHH
Q 009222 160 FSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAK 239 (540)
Q Consensus 160 F~~~~~f~~~l~~~f~~~ln~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~l~~i~~l~~~l~~Kd~F~~~Y~~~L~~ 239 (540)
|++++.|..++++||+.++|.....++++||+|||.+++++.++.++++.+..++.++.+|+++++||+|+.+|+++||+
T Consensus 304 F~~~~~f~~~l~~af~~~~n~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~ 383 (588)
T PF00888_consen 304 FDNDSEFKKALDEAFEEFLNKNNNKIPELLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAK 383 (588)
T ss_dssp TTT-HHHHHHHHHHHHHHHHCSTSHHHHHHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHH
T ss_pred ccccHHHHHHHHHhHHHHHHcCCcchHHHHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHH
Confidence 99999999999999999999997789999999999999998777778889999999999999999999999999999999
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHhhcchhHHhHHHHHhhHHHhHHHHHHHHHhhhhccCCC-CCccEEEEEeecCCCCCCC
Q 009222 240 RLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLP-SGIEMSVHVLTTGYWPTYP 318 (540)
Q Consensus 240 RLL~~~~~~~~~E~~~i~~L~~~~g~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~-~~~~~~~~VL~~~~WP~~~ 318 (540)
|||.+++.+.+.|..+|++|+.+||.+++++|+.|++|+..|+++++.|++...+..... .+++|+|.||++++||..+
T Consensus 384 RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~ 463 (588)
T PF00888_consen 384 RLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWPKYP 463 (588)
T ss_dssp HHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-S-S
T ss_pred HHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCCCCC
Confidence 999999999999999999999999999999999999999999999999999876532111 2789999999999999999
Q ss_pred CCC-CcCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCCCCccHHHHHHH
Q 009222 319 PMD-VRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDA 397 (540)
Q Consensus 319 ~~~-~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~ 397 (540)
..+ +.+|++|+.+++.|++||+++|++|+|+|.|.+|+|+|++++++|+++++||++||+||++||+.+++|+++|++.
T Consensus 464 ~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~ 543 (588)
T PF00888_consen 464 SENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEK 543 (588)
T ss_dssp -SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHH
T ss_pred CCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHH
Confidence 866 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCHHHHHHHhhhhhcCCceeee--cCCCCCCCCCCCeEEEccCCC
Q 009222 398 TGIEDKELRRTLQSLACGKVRVLQ--KLPKGRDVEDDDSFVFNEGFT 442 (540)
Q Consensus 398 ~~i~~~~l~~~L~~L~~~k~~iL~--~~~~~~~~~~~~~~~~N~~f~ 442 (540)
||++++.++++|.+|++ .+++. +.++++++.+++.|.+|.+|+
T Consensus 544 ~~~~~~~l~~~L~~l~~--~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 544 TGISEEELKRALKSLVK--SKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp C---HHHHHHHHHCCCT--TTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HCcCHHHHHHHHHHHHh--CCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 99999999999999975 45554 677888899999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=1.2e-32 Score=244.57 Aligned_cols=141 Identities=55% Similarity=0.904 Sum_probs=132.0
Q ss_pred cccChhHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcchhHHhHHHHHhhHHHhHHHHHHHHHhhhhccCCCCC
Q 009222 222 FIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSG 301 (540)
Q Consensus 222 ~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~L~~~~g~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 301 (540)
|+++||+|+.+|+++||+|||..++++.+.|..+|++|+.+||.+++++|++|++|+..|++++++|++...+. ....+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~-~~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENN-SNKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999876542 12356
Q ss_pred ccEEEEEeecCCCCCCCC-CCCcCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEe
Q 009222 302 IEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEF 363 (540)
Q Consensus 302 ~~~~~~VL~~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~ 363 (540)
++|+|.|||+++||..+. .++.+|++|+.+++.|++||.++|++|+|+|.|++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999999988 78999999999999999999999999999999999999999864
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-29 Score=259.62 Aligned_cols=310 Identities=22% Similarity=0.304 Sum_probs=251.2
Q ss_pred hhhhhhcccChhHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcchhHHhHHHHHhhHHHhHHHHHHHHHhh-hh
Q 009222 216 VLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSS-QA 294 (540)
Q Consensus 216 i~~l~~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~L~~~~g~~~~~kl~~Ml~D~~~S~~l~~~f~~~~-~~ 294 (540)
+..+++.+++|+.|++.||.+||.||+....++.+.|.+-++.||-++|.+..+.|++|++|+..|++++++++... ..
T Consensus 442 ~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~ 521 (765)
T KOG2165|consen 442 FGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELS 521 (765)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhh
Confidence 34566778999999999999999999999999999999999999999999999999999999999999999999741 11
Q ss_pred c-cCCCCCccEEEEEeecCCCCCCCCCCCcCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEEEc
Q 009222 295 R-TKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVS 373 (540)
Q Consensus 295 ~-~~~~~~~~~~~~VL~~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s 373 (540)
+ ......+.+++.|||+.+||......+.+|..++..++.|.+.|.+.+++|+|.|.+++|.|++++++.+++.+++||
T Consensus 522 r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVs 601 (765)
T KOG2165|consen 522 RGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVS 601 (765)
T ss_pred cccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeC
Confidence 1 112235788999999999999988899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCCCCceeEEeccc
Q 009222 374 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAI 453 (540)
Q Consensus 374 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~ 453 (540)
+.||+|+++|.+.++||++++++.+|+|...+++.|..|+ +.|+|.++|. +++.++|+++++=.+..+- .+.+
T Consensus 602 p~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~d~~q~--~~~~ 674 (765)
T KOG2165|consen 602 PEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEMDFDQA--EGTV 674 (765)
T ss_pred HHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeecccccccccc--CCCc
Confidence 9999999999999999999999999999999999999996 4799988764 3567889998864322110 1111
Q ss_pred ccccchhhhhhh--hHHHHH--hhHHhHHHHHHhhhcCCCCCChHHHHHHHHHHc-----CCCCChHHHHHHHHHhhhhc
Q 009222 454 QMKETVEENTST--TERVFQ--DRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL-----KFPIKPADLKKRIESLIDRE 524 (540)
Q Consensus 454 ~~~~~~~e~~~~--~~~~~~--~r~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l-----~F~~~~~~ik~~Ie~Li~~e 524 (540)
.. +..++..+. ...+.+ .--..-...|+..+-.-+.|+.+.+.+ +.+.. ...+|-++++..+..++..|
T Consensus 675 ~~-e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHn-mLkmF~~~~~~~~~TlqeL~~fLq~kV~e~ 752 (765)
T KOG2165|consen 675 LL-EAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHN-MLKMFVPPDGSAEITLQELQGFLQRKVREG 752 (765)
T ss_pred cc-ccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHH-HHeeeecCCCCCcccHHHHHHHHHHHhhcc
Confidence 11 111111111 112222 112344568999888889999998765 55544 23467789999999999999
Q ss_pred cccccCCCCCcee
Q 009222 525 YLERDKNNPQIYN 537 (540)
Q Consensus 525 yi~r~~~~~~~y~ 537 (540)
-++-.++ .|.
T Consensus 753 kL~f~~G---~Y~ 762 (765)
T KOG2165|consen 753 KLEFIAG---SYR 762 (765)
T ss_pred ceEEecc---eee
Confidence 8888763 564
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.76 E-value=3.1e-19 Score=136.20 Aligned_cols=65 Identities=60% Similarity=0.958 Sum_probs=59.9
Q ss_pred HHhhHHhHHHHHHhhhcCCCCCChHHHHHHHHHHc--CCCCChHHHHHHHHHhhhhccccccCCCCC
Q 009222 470 FQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQ 534 (540)
Q Consensus 470 ~~~r~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~ 534 (540)
.++|...|+|+|||+||++|+++|++|+.+|.+.+ +|+|+..+||++||+||++|||+||++|+|
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 57899999999999999999999999999999999 899999999999999999999999999875
No 10
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=95.67 E-value=0.029 Score=45.76 Aligned_cols=66 Identities=17% Similarity=0.184 Sum_probs=54.6
Q ss_pred EEEEcHHHHHHHHHhc--------CCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 369 ELAVSLFQTVVLMLFN--------DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 369 ~l~~s~~Q~~iLl~Fn--------~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
...+++-|+.+|+..- ....+|-.||++.+|++.+.+.++|..|. +.++|.+.. ....|++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~ 91 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTP 91 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCC
Confidence 3457888999998766 46789999999999999999999999996 578987643 2478999988
Q ss_pred CC
Q 009222 441 FT 442 (540)
Q Consensus 441 f~ 442 (540)
++
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 65
No 11
>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=94.28 E-value=0.071 Score=38.04 Aligned_cols=45 Identities=20% Similarity=0.313 Sum_probs=37.7
Q ss_pred HHHHHHhcCCC-CccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 377 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 377 ~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
+.||.+|.+.+ .+|+.||++.+|+|...+.+.|..|.. .|++.++
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~--~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE--EGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CcCeecC
Confidence 46888888875 489999999999999999999999974 6888764
No 12
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.20 E-value=0.1 Score=36.44 Aligned_cols=46 Identities=15% Similarity=0.303 Sum_probs=37.8
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceee
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 420 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL 420 (540)
+..+..||..+.+++.+|..||++.+|++...+.+.|..|.. .|++
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~--~g~I 47 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE--KGLI 47 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH--TTSE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH--CcCc
Confidence 456788999999999999999999999999999999999964 4554
No 13
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=94.02 E-value=0.12 Score=40.89 Aligned_cols=60 Identities=17% Similarity=0.263 Sum_probs=43.1
Q ss_pred HHHHHHHHhcCCC-CccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCC
Q 009222 375 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 441 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 441 (540)
+++.+.+..+..+ .+|.++|++.+++|+..+.+.+..|. +.+++.... ..++-|.++.+.
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-----G~~GGy~L~~~~ 71 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-----GRGGGYRLARPP 71 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-----STTSEEEESS-C
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-----CCCCceeecCCH
Confidence 4444555544443 49999999999999999999999996 578887543 246778887763
No 14
>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=93.62 E-value=0.09 Score=38.36 Aligned_cols=47 Identities=23% Similarity=0.483 Sum_probs=40.9
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
|..|+..+++++.+|+++|++.+|+++..+++-|..|. +.+++.+..
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~~ 48 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 45688889999999999999999999999999999996 467777654
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=93.52 E-value=0.07 Score=39.40 Aligned_cols=51 Identities=20% Similarity=0.292 Sum_probs=44.0
Q ss_pred EcHHHHHHHHHhcCCCC--ccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~--~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~--~~Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLE--KKGLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEeC
Confidence 57889999999888877 9999999999999999999999996 468887654
No 16
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.95 E-value=0.38 Score=36.46 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=40.8
Q ss_pred HHHHHHHHHhcCCCC--ccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 374 LFQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 374 ~~Q~~iLl~Fn~~~~--~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
...-.||.++.+.+. +|..||++.+|++...+.++|..|. +.+++.+.+
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~--~~G~V~~~~ 56 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE--KKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 345578888888766 9999999999999999999999995 468887643
No 17
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=91.47 E-value=0.16 Score=37.07 Aligned_cols=51 Identities=14% Similarity=0.289 Sum_probs=44.2
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+|..|+.+|....+.+++|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~~ 51 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERER 51 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEecc
Confidence 367899999999999999999999999999999999999996 468887654
No 18
>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=91.05 E-value=0.36 Score=40.93 Aligned_cols=52 Identities=15% Similarity=0.257 Sum_probs=46.4
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
.++..|+.||..+..++.+|..+|++.+|++...+-+.+..|. +.|++.+.+
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le--~~GlI~r~~ 76 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLE--RDGLVTRLK 76 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHH--HCCCEEecc
Confidence 3688899999999888999999999999999999999999996 578888754
No 19
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=90.68 E-value=0.53 Score=35.30 Aligned_cols=51 Identities=18% Similarity=0.225 Sum_probs=39.8
Q ss_pred EcHHHHHHHHHhc-CCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVLMLFN-DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn-~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+|..|..||..+. ..+.+|..+|++.++++...+-+.+..|.. .+++.+.+
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~--~glv~~~~ 52 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEE--KGLVEKER 52 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHH--TTSEEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEecC
Confidence 4678999999998 778999999999999999999999999974 68886653
No 20
>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=90.18 E-value=0.2 Score=38.16 Aligned_cols=45 Identities=24% Similarity=0.409 Sum_probs=37.2
Q ss_pred HHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 481 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 481 IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
|-.+|+.++.++.++|-. +|..+++.+..-|+.|+.+|||++.+.
T Consensus 5 i~~~l~~~~~~S~~eLa~------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAR------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHHH------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHHH------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 556788999999999887 789999999999999999999998653
No 21
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=90.11 E-value=0.51 Score=41.62 Aligned_cols=52 Identities=21% Similarity=0.233 Sum_probs=46.2
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
.+|..|+.||......+++|..+|++.++++...+-+.+..|. +.|++.+.+
T Consensus 37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 4788899999888777889999999999999999999999995 578998765
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=89.83 E-value=0.87 Score=31.58 Aligned_cols=45 Identities=13% Similarity=0.316 Sum_probs=36.4
Q ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 374 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 374 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
+....||.++-+ ++.++.||++.+|++...+..+|..|.. .|++.
T Consensus 2 ~~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~--~glV~ 46 (47)
T PF01022_consen 2 PTRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLRE--AGLVE 46 (47)
T ss_dssp HHHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHH--CcCee
Confidence 345677877777 7899999999999999999999999963 66664
No 23
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=89.08 E-value=1 Score=39.02 Aligned_cols=60 Identities=20% Similarity=0.271 Sum_probs=46.2
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
+..|++++-..+.++..+++....+ ...+...-+...|+.|.+||+|+|..++ ..|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~--~~~~~~tTv~T~L~rL~~KG~v~~~k~g-r~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAE--KKDWSDSTIKTLLGRLVDKGCLTTEKEG-RKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhh--ccCCcHHHHHHHHHHHHHCCceeeecCC-CcEEEEe
Confidence 4567888877888888887765443 3457788899999999999999998544 4788854
No 24
>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=89.01 E-value=0.6 Score=34.40 Aligned_cols=49 Identities=12% Similarity=0.231 Sum_probs=40.9
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
++.-..||..+...++.|+.+|++.+|++...+..+|..|.. .+++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~--aGli~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE--AGLIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEEe
Confidence 456678888887778999999999999999999999999964 7888653
No 25
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=88.95 E-value=0.93 Score=38.41 Aligned_cols=62 Identities=18% Similarity=0.283 Sum_probs=52.8
Q ss_pred hHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 476 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 476 ~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
..++-|+++|=.++..+.+|++.++.+ .+.++..-|+--|..|..||.|.+.-++ ..|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~--~~ews~sTV~TLl~RL~KKg~l~~~kdg-r~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPA--DREWSYSTVKTLLNRLVKKGLLTRKKDG-RAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhh--cccccHHHHHHHHHHHHhccchhhhhcC-Ceeeeec
Confidence 357889999999999999999988877 4778899999999999999999998643 5777743
No 26
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=88.28 E-value=1.3 Score=35.27 Aligned_cols=45 Identities=16% Similarity=0.293 Sum_probs=38.6
Q ss_pred HHHHHHhcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 377 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 377 ~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
..||..+.+. +.+|+.||++.+|++...+.+.|..|.. .+++.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeec
Confidence 4577777776 6899999999999999999999999964 7888764
No 27
>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=88.15 E-value=1 Score=32.23 Aligned_cols=38 Identities=16% Similarity=0.454 Sum_probs=30.5
Q ss_pred HHHHHHh-cCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 377 TVVLMLF-NDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 377 ~~iLl~F-n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
..||..+ +..+.+|.++|++.+|++...+.+.|..|..
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3455555 6666799999999999999999999999964
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=87.11 E-value=1.3 Score=36.94 Aligned_cols=52 Identities=23% Similarity=0.333 Sum_probs=44.7
Q ss_pred EEcHHHHHHHHHhc----CCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 371 AVSLFQTVVLMLFN----DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn----~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
.+|..|..||..+. ..+.+|..+|++.++++...+-+.+..|. +.|++.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~ 77 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKER 77 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccC
Confidence 46888999997766 55789999999999999999999999996 578998765
No 29
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=86.96 E-value=1.7 Score=39.36 Aligned_cols=58 Identities=14% Similarity=0.281 Sum_probs=43.5
Q ss_pred HHHHHHHhcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 376 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 376 Q~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
.+.+.+.|+.. ..+|.++|++.+|+|...+.+.|..|. +.||+.... ..++-|.+..+
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s~r-----G~~GGy~Lar~ 70 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSSVR-----GPGGGYLLGKD 70 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeCC-----CCCCCeeccCC
Confidence 34445556654 589999999999999999999999995 588997542 23445776655
No 30
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=86.91 E-value=1.7 Score=38.73 Aligned_cols=57 Identities=16% Similarity=0.236 Sum_probs=43.2
Q ss_pred HHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 377 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 377 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
+.+.+..+..+.+|..+|++..|+|...|.+.|..|. +.+++.... ..++-|.++.+
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-----G~~GGy~La~~ 69 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-----GRNGGVRLGRP 69 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-----CCCCCeeecCC
Confidence 3444555555678999999999999999999999995 689987654 23456766655
No 31
>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=86.87 E-value=0.43 Score=36.07 Aligned_cols=56 Identities=18% Similarity=0.354 Sum_probs=42.9
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeec
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYL 539 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yi 539 (540)
++.|-..|-.++.++..+|...+ ..+...+-+.++.|.++|+|++.++++..|..+
T Consensus 10 E~~vy~~Ll~~~~~t~~eIa~~l------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 10 EAKVYLALLKNGPATAEEIAEEL------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHCHEEHHHHHHHH------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 44445555577888888877644 477899999999999999999998776666554
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=86.17 E-value=1.2 Score=31.11 Aligned_cols=46 Identities=24% Similarity=0.457 Sum_probs=37.3
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
|-.|+..+.+...+|..+|++.+|++...+.+.|..|.. .+++.+.
T Consensus 2 ~~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~~ 47 (53)
T smart00420 2 QQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTRV 47 (53)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 345666677777899999999999999999999999964 5676653
No 33
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=86.00 E-value=1.9 Score=36.78 Aligned_cols=39 Identities=13% Similarity=0.250 Sum_probs=34.8
Q ss_pred cCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 384 NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 384 n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+.+++.|+++|++.++.+...+.++|+.|.. .|++.++.
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Rek 76 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVEREK 76 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeeee
Confidence 3678999999999999999999999999974 79998764
No 34
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=85.84 E-value=0.66 Score=35.00 Aligned_cols=51 Identities=18% Similarity=0.232 Sum_probs=41.7
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+|-.++.|+..+-..+..|..+|++.+|++...+.+.|..|.. .|++.+.+
T Consensus 6 Ls~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~--~GlV~~~~ 56 (68)
T PF01978_consen 6 LSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEE--KGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHH--TTSEEEEE
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEEc
Confidence 3455677776666778899999999999999999999999974 68887653
No 35
>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=85.72 E-value=2.2 Score=35.05 Aligned_cols=63 Identities=19% Similarity=0.306 Sum_probs=48.7
Q ss_pred EEEcHHHHHHHHH-------hcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCC
Q 009222 370 LAVSLFQTVVLML-------FNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 441 (540)
Q Consensus 370 l~~s~~Q~~iLl~-------Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 441 (540)
..++.-|..|++. ||.. +.+|..++++.+|++...+.++++.|+ +.++|... +..+.+|.+.
T Consensus 28 ~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i 97 (100)
T PF04492_consen 28 ADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNI 97 (100)
T ss_pred ccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeeccc
Confidence 3466777777766 4543 689999999999999999999999996 57899753 3566677665
Q ss_pred C
Q 009222 442 T 442 (540)
Q Consensus 442 ~ 442 (540)
+
T Consensus 98 ~ 98 (100)
T PF04492_consen 98 S 98 (100)
T ss_pred c
Confidence 3
No 36
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=85.60 E-value=1.8 Score=32.78 Aligned_cols=54 Identities=11% Similarity=0.258 Sum_probs=43.5
Q ss_pred HHHHHHhhhcCCCC--CChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCce
Q 009222 477 VDAAIVRIMKTRKV--LSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIY 536 (540)
Q Consensus 477 i~a~IVRimK~~k~--l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y 536 (540)
.+..|...|+.++. ++..+|-.++ ..+...+.+.|..|.++|||.+++..|..|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l------gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL------GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH------CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 45567888999877 9988887644 466789999999999999999988765554
No 37
>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=85.28 E-value=2.1 Score=37.26 Aligned_cols=57 Identities=14% Similarity=0.282 Sum_probs=41.1
Q ss_pred HHHHHHhcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 377 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 377 ~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
+.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++.... ..++-|.+..+
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s~~-----G~~Ggy~l~~~ 70 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKSVR-----GPGGGYQLGRP 70 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEe-----CCCCCEeccCC
Confidence 3444555543 479999999999999999999999995 578886532 12345665554
No 38
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=85.03 E-value=1.4 Score=32.72 Aligned_cols=56 Identities=23% Similarity=0.328 Sum_probs=39.1
Q ss_pred HHHHhcC-CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEc
Q 009222 379 VLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFN 438 (540)
Q Consensus 379 iLl~Fn~-~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N 438 (540)
||..+++ +.++|..||++.+|++...++..|..|. +.|.+.+.|.++.- ...|.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~rG~--~~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRRGK--STYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SSSS--S-EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCCCc--ceeeeec
Confidence 4556666 7889999999999999999999999996 46777765543211 2356665
No 39
>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=84.79 E-value=0.98 Score=32.85 Aligned_cols=47 Identities=15% Similarity=0.351 Sum_probs=41.9
Q ss_pred HHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 479 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 479 a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
..|+..++.++.++..+|.+ .|.++..-+.+-|..|.++|.|.|.-+
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 46788899999999999987 678999999999999999999998654
No 40
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=84.56 E-value=2.2 Score=41.70 Aligned_cols=57 Identities=7% Similarity=0.208 Sum_probs=46.0
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
-..||.+|.+...+|+.||++.+|+|...+-+.|..|.. .+.|.+.+ .++.|.+...
T Consensus 16 ~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~------~~~~Y~lG~~ 72 (257)
T PRK15090 16 VFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG------ESEKYSLTLK 72 (257)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC------CCCcEEecHH
Confidence 356888898888899999999999999999999999974 78898754 2345666444
No 41
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=84.35 E-value=1.8 Score=39.92 Aligned_cols=53 Identities=9% Similarity=0.008 Sum_probs=46.5
Q ss_pred EEEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 370 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 370 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
..+|..|+.||..+...+.+|..+|++.++++...+.+.+..|. +.|++.+.+
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE--~kGlI~R~~ 93 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE--ERGYLTFSK 93 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH--HCCCEEecC
Confidence 34778899999999999999999999999999999999999995 578988754
No 42
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=84.09 E-value=1.7 Score=35.12 Aligned_cols=52 Identities=23% Similarity=0.408 Sum_probs=45.6
Q ss_pred EEEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 370 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 370 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
..++..+..||..+...+.+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEec
Confidence 45788899999999888889999999999999999999999996 46888754
No 43
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=83.94 E-value=2.4 Score=37.72 Aligned_cols=59 Identities=14% Similarity=0.283 Sum_probs=45.1
Q ss_pred HHHHHHHHhcCCC-CccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 375 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
+++.+.+.-+..+ ..|+++|++..|+|+..+.+.+..|. |.+++.... ..++-|.++.+
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~r-----G~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVR-----GKGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeec-----CCCCCccCCCC
Confidence 4455555555554 68899999999999999999999994 689997654 23566777765
No 44
>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=82.40 E-value=0.72 Score=38.98 Aligned_cols=60 Identities=15% Similarity=0.253 Sum_probs=45.6
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
+..|++++=..+.++..+++..+.+ ...+...-+...|..|.+||||.+...+ ..|.|-|
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 ELEIMEILWESGEATVREIHEALPE--ERSWAYSTVQTLLNRLVEKGFLTREKIG-RAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHHCT--TSS--HHHHHHHHHHHHHTTSEEEEEET-TCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHh--ccccchhHHHHHHHHHHhCCceeEeecC-CceEEEe
Confidence 5567788877888888887765544 3567889999999999999999998643 5788854
No 45
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=82.20 E-value=2.3 Score=28.77 Aligned_cols=36 Identities=19% Similarity=0.529 Sum_probs=28.1
Q ss_pred HHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 377 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 377 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
-.||..+.+....|+.+|++.+|++...+.+.+..|
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 467777888899999999999999999998877654
No 46
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=81.71 E-value=2.4 Score=37.20 Aligned_cols=53 Identities=25% Similarity=0.293 Sum_probs=45.2
Q ss_pred EEEcHHHHHHHHHhcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 370 LAVSLFQTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 370 l~~s~~Q~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+.+|..|..+|....+. +..|..+|++.+|++...+.+.+..|. +.|++.+.+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le--~~GlV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE--EKGLISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH--HCCCEeeec
Confidence 34788899999888764 568999999999999999999999996 578998765
No 47
>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=80.65 E-value=3.5 Score=35.57 Aligned_cols=46 Identities=17% Similarity=0.395 Sum_probs=35.6
Q ss_pred HHHHHHHhcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 376 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 376 Q~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
++.+.+.-++. ..+|.++|++.+|+|...+.+.|..|. +.+++...
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~~ 58 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVESV 58 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 44444443433 489999999999999999999999996 47888653
No 48
>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=79.51 E-value=4 Score=38.26 Aligned_cols=52 Identities=19% Similarity=0.222 Sum_probs=46.2
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
.++..|..||..+.+++.++..+|++.+|++...+.+.|..|. +.+++.+.+
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 4688899999999988889999999999999999999999996 478888754
No 49
>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=79.25 E-value=4 Score=30.40 Aligned_cols=53 Identities=11% Similarity=0.281 Sum_probs=37.0
Q ss_pred HHHHHhhhc-CCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc--CCCCCce
Q 009222 478 DAAIVRIMK-TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD--KNNPQIY 536 (540)
Q Consensus 478 ~a~IVRimK-~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~--~~~~~~y 536 (540)
+..|.+.+. ..+.++..+|.. .+..+...+-+.|+.|+++|||++. +.|....
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~ 60 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAE------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSK 60 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHH------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSE
T ss_pred HHHHHHHHHccCCCcCHHHHHH------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCee
Confidence 556777777 778888888776 4457788899999999999999774 4444433
No 50
>PHA00738 putative HTH transcription regulator
Probab=79.14 E-value=4.1 Score=33.62 Aligned_cols=68 Identities=18% Similarity=0.171 Sum_probs=53.2
Q ss_pred EEEEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCC
Q 009222 369 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 442 (540)
Q Consensus 369 ~l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 442 (540)
++...+.=-.||..+.+.+.+++.+|++.++++...+-++|.-|- ..||+.....|+ .-.|++|.+..
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr----~vyY~Ln~~~~ 74 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGR----TLYAKIRENSK 74 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECC----EEEEEECCCcc
Confidence 455666666788878777789999999999999999999999995 478998665432 34688888743
No 51
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=78.95 E-value=1.7 Score=34.07 Aligned_cols=45 Identities=20% Similarity=0.428 Sum_probs=35.3
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
...||..++..+.+++.+|.+.+|+++..+-++|..|.. .|.+..
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~--~GyV~~ 46 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEE--AGYVEV 46 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHH--TTSEEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEEE
Confidence 345676677778899999999999999999999999964 567653
No 52
>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=78.87 E-value=2.7 Score=30.71 Aligned_cols=38 Identities=13% Similarity=0.348 Sum_probs=31.0
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
|.-+|.++-+.+.+|+++|++.+|++...++.-+.-|.
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56667666558899999999999999999999888774
No 53
>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=78.63 E-value=4.4 Score=30.85 Aligned_cols=47 Identities=21% Similarity=0.415 Sum_probs=37.0
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
+..| .||+..... +.|+++|.+.||++.+.+...|.-|. +.|++.+.
T Consensus 5 t~~~-~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~Rk 51 (72)
T PF05584_consen 5 TVTQ-KILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIERK 51 (72)
T ss_pred hHHH-HHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 3444 455555554 89999999999999999999999996 57888753
No 54
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=78.49 E-value=2.5 Score=38.25 Aligned_cols=47 Identities=17% Similarity=0.441 Sum_probs=39.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCCCC
Q 009222 389 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAP 444 (540)
Q Consensus 389 ~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~ 444 (540)
+|..+|++.+|++...+.+++..|. +.++|.+. ..+.|.+|+++...
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~-------~~G~Y~iNP~~~~k 122 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKI-------RNGAYMINPNFFFK 122 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEc-------cCCeEEECcHHhee
Confidence 6788999999999999999999996 46899874 35689999997644
No 55
>PRK10870 transcriptional repressor MprA; Provisional
Probab=78.25 E-value=4.4 Score=37.04 Aligned_cols=51 Identities=12% Similarity=0.158 Sum_probs=43.7
Q ss_pred EcHHHHHHHHHhcC--CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~--~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+|..|..||..... ..++|..+|++.++++...+.+.+..|. +.|++.+.+
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~ 105 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRE 105 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 66779999988764 4579999999999999999999999996 578998765
No 56
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=78.05 E-value=3.7 Score=33.75 Aligned_cols=48 Identities=21% Similarity=0.373 Sum_probs=39.6
Q ss_pred EEcHHHHHHHHHhcC----CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceee
Q 009222 371 AVSLFQTVVLMLFND----AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 420 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~----~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL 420 (540)
.++..|-.||..+.+ .+.+++++|++.++++.+.++.+|..|+. .+.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~--eG~I 95 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSN--EGHI 95 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHH--TTSE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHh--CCeE
Confidence 588999999999988 36799999999999999999999999976 3444
No 57
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=77.42 E-value=3 Score=31.94 Aligned_cols=36 Identities=17% Similarity=0.248 Sum_probs=29.2
Q ss_pred cCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 384 NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 384 n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
.....+|+.||++.+|+|...++..+..+. +.++|.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~ 63 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLV 63 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHH
Confidence 333668999999999999999999998874 456654
No 58
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=77.30 E-value=20 Score=38.66 Aligned_cols=50 Identities=10% Similarity=0.214 Sum_probs=44.6
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
.+|+.|..||..+...+.+|..+|++.+|++...+.+++.+|.. .+++..
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~--kGlV~~ 52 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEE--KGLVKV 52 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHh--CCCEEE
Confidence 46889999999999888999999999999999999999999963 577764
No 59
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=77.27 E-value=5.4 Score=39.26 Aligned_cols=57 Identities=14% Similarity=0.097 Sum_probs=45.3
Q ss_pred HHHHHHHhcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 376 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 376 Q~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
-..||.+|.+. ..+|+.||++.+|+|...+-+.|.+|.. .+.|.+.+ .++.|.+...
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~~------~~~~Y~lG~~ 84 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQDS------QLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC------CCCeEEecHH
Confidence 35788899865 5799999999999999999999999975 78887754 2455665444
No 60
>PRK11569 transcriptional repressor IclR; Provisional
Probab=77.19 E-value=5 Score=39.55 Aligned_cols=47 Identities=9% Similarity=0.258 Sum_probs=40.3
Q ss_pred HHHHHHHhcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 376 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 376 Q~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
-..||.+|.+. ..+|+.||++.+|++...+-+.|.+|.. .+.|.+.+
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG 77 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 35678889875 5799999999999999999999999974 78997754
No 61
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=77.00 E-value=5.5 Score=38.61 Aligned_cols=56 Identities=20% Similarity=0.425 Sum_probs=44.8
Q ss_pred HHHHHHhcCCCC-ccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 377 TVVLMLFNDAQK-LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 377 ~~iLl~Fn~~~~-~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
..||.+|..... +++.||++.+|+|...+.+.|..|. ..|++.+.+. +..|.+-..
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~~------~g~Y~Lg~~ 63 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDPE------DGRYRLGPR 63 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcCC------CCcEeehHH
Confidence 468888987644 6899999999999999999999996 4899988652 345666444
No 62
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=76.74 E-value=4.6 Score=30.27 Aligned_cols=48 Identities=15% Similarity=0.298 Sum_probs=39.7
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
+..+..|+..+.+.+ ++..+|++.+|++...+.+.|..|.. .+++...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~--~g~i~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEE--AGLVESR 53 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHH--CCCeEEE
Confidence 456778888877766 99999999999999999999999964 5777643
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=76.02 E-value=5.8 Score=34.15 Aligned_cols=55 Identities=16% Similarity=0.324 Sum_probs=39.9
Q ss_pred HHHHHhcC--CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEcc
Q 009222 378 VVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 439 (540)
Q Consensus 378 ~iLl~Fn~--~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 439 (540)
.+|..+.. .+.+|+.+|++.+|+|...+.+.|..|. +.|++..... .++.|.++.
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~~g-----~~ggy~l~~ 69 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSKRG-----VEGGYTLAR 69 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEecCC-----CCCChhhcC
Confidence 34444443 3579999999999999999999999996 5788865321 234566644
No 64
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=75.66 E-value=5.6 Score=27.08 Aligned_cols=33 Identities=27% Similarity=0.475 Sum_probs=29.3
Q ss_pred CccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 388 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 388 ~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
++|..+|++.+|++...+.+.|..|. +.+++..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 47899999999999999999999996 4788865
No 65
>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=75.45 E-value=6.3 Score=27.17 Aligned_cols=45 Identities=13% Similarity=0.313 Sum_probs=36.4
Q ss_pred HHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccc
Q 009222 477 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLE 527 (540)
Q Consensus 477 i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~ 527 (540)
.+-.|+..+..+..++..+|-..+ ..+...+.+.|..|.++|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKL------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHH------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHh------CCCHHHHHHHHHHHHHCcCcC
Confidence 455678888889999999988744 578999999999999999985
No 66
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=74.38 E-value=4.6 Score=28.95 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=32.8
Q ss_pred hcCCCCc-cHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 383 FNDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 383 Fn~~~~~-t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+...+.+ |..+|++.+|++...+.++|..|. +.+++...+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEec
Confidence 4444567 899999999999999999999996 468886543
No 67
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=74.19 E-value=4.7 Score=33.33 Aligned_cols=45 Identities=11% Similarity=0.298 Sum_probs=39.2
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
..-.||..+.+.+..|..+|++.+|++...+.+.+..|.. .|++.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~--~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEE--EGVIK 48 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 4557888888888999999999999999999999999964 67776
No 68
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=73.55 E-value=5.9 Score=33.53 Aligned_cols=62 Identities=15% Similarity=0.205 Sum_probs=45.8
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
++.-..||.++-+.++.++.||++.+|++...+-++|.-|. ..|++.....|+ .-.|++|.+
T Consensus 15 dptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~~ 76 (117)
T PRK10141 15 DETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSPH 76 (117)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECch
Confidence 34445666666555679999999999999999999999995 478997654332 235777653
No 69
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=73.46 E-value=6.8 Score=38.34 Aligned_cols=55 Identities=24% Similarity=0.358 Sum_probs=43.6
Q ss_pred HHHHHHhcCCC-CccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEcc
Q 009222 377 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 439 (540)
Q Consensus 377 ~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 439 (540)
+.||.+|.+.+ .+|+.||++.+|++...+-+.|..|. ..+++.+.+. ++.|++..
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~~------~~~Y~Lg~ 69 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSAS------DDSFRLTL 69 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecC------CCcEEEcH
Confidence 46788887654 59999999999999999999999996 4789987642 34566643
No 70
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=73.18 E-value=9.1 Score=33.52 Aligned_cols=50 Identities=6% Similarity=0.292 Sum_probs=38.6
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEcc
Q 009222 383 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 439 (540)
Q Consensus 383 Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 439 (540)
+.....+|..+|++.+|+|...++++|..|. +.|++...+. .++.|.+..
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~G-----~~GG~~l~~ 69 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVRG-----KNGGIRLGK 69 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEecC-----CCCCeeecC
Confidence 3344578999999999999999999999995 5899976552 344566654
No 71
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=72.69 E-value=6.5 Score=32.87 Aligned_cols=51 Identities=18% Similarity=0.373 Sum_probs=44.9
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+++.|+.+|......+..+..+|++.++++...+.+.+..|. +.|++.+.+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le--~~glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLE--DKGLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 788999999988888777669999999999999999999995 578888764
No 72
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=72.56 E-value=2.5 Score=38.88 Aligned_cols=58 Identities=19% Similarity=0.329 Sum_probs=41.2
Q ss_pred hHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 476 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 476 ~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
.++. .|...|.+|.+..++|-. .|..+++++-.+|..|...|-|.=.-+|.+.|+||.
T Consensus 100 lL~~-Fi~yIK~~Kvv~ledla~------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQE-FINYIKEHKVVNLEDLAA------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHH-HHHHHHH-SEE-HHHHHH------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHH-HHHHHHHcceeeHHHHHH------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 4444 458889999999999876 778999999999999999998887767889999984
No 73
>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=72.49 E-value=8.5 Score=37.25 Aligned_cols=44 Identities=25% Similarity=0.414 Sum_probs=38.4
Q ss_pred HHHHHHhcC-CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 377 TVVLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 377 ~~iLl~Fn~-~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
..||.+|.. ...+|+.||++.+|+|...+-+.|..|.. .|.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 468888986 46799999999999999999999999975 688875
No 74
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=72.48 E-value=6.1 Score=28.51 Aligned_cols=46 Identities=11% Similarity=0.240 Sum_probs=33.7
Q ss_pred HHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCC
Q 009222 481 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNP 533 (540)
Q Consensus 481 IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~ 533 (540)
|++.+. .+.++..++... +..+...+.+.|+.|.++|++....++.
T Consensus 2 il~~l~-~~~~~~~~i~~~------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 2 ILKLLA-EGELCVCELAEI------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHHhh-cCCccHHHHHHH------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 344555 667777776552 3467788999999999999999876443
No 75
>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=71.43 E-value=6.2 Score=29.01 Aligned_cols=45 Identities=18% Similarity=0.320 Sum_probs=35.7
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+|..+-.+...++..+|++.+|+++..+...+..|. +.|++...+
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 344444577899999999999999999999999996 468887654
No 76
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=71.43 E-value=8.9 Score=28.70 Aligned_cols=37 Identities=35% Similarity=0.456 Sum_probs=32.4
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
.|-.++++...+|+.+|++.+|++.+++..+|.-|..
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 4667788999999999999999999999999999975
No 77
>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=71.38 E-value=4.5 Score=30.60 Aligned_cols=42 Identities=14% Similarity=0.282 Sum_probs=31.4
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
|.....+++.+|++||+..++++++.+...|..|+. .|-+.+
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~--kG~I~~ 46 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIR--KGYIRK 46 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC--CTSCEE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCcEEE
Confidence 445566778999999999999999999999999974 445543
No 78
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=71.08 E-value=7.2 Score=28.13 Aligned_cols=36 Identities=11% Similarity=0.265 Sum_probs=30.9
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 386 AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 386 ~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
.++.|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeeee
Confidence 56789999999999999999999999964 6777643
No 79
>PF13730 HTH_36: Helix-turn-helix domain
Probab=71.06 E-value=7.7 Score=27.58 Aligned_cols=25 Identities=16% Similarity=0.387 Sum_probs=23.4
Q ss_pred cHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 390 SFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 390 t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
|.+.|++.+|++...+.+++..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999963
No 80
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=70.96 E-value=5.7 Score=37.49 Aligned_cols=43 Identities=21% Similarity=0.376 Sum_probs=37.4
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
.||.+.+..+++|.+||++.+|++...++++|..|. ..+++..
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le--~~Glv~~ 57 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLE--AEGLVEV 57 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHH--hCcceee
Confidence 677778888999999999999999999999999996 4577653
No 81
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=70.93 E-value=4.7 Score=39.32 Aligned_cols=48 Identities=15% Similarity=0.190 Sum_probs=42.5
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
-|..||...++++.+++.||++.+|++...+++-|..|- +.+++.+..
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~~ 53 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEEE
Confidence 367899999999999999999999999999999999995 568887654
No 82
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=69.98 E-value=9.3 Score=28.17 Aligned_cols=35 Identities=26% Similarity=0.406 Sum_probs=31.1
Q ss_pred CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 387 QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 387 ~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
..+|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE--EEGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 579999999999999999999999996 46888764
No 83
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=68.66 E-value=5.8 Score=38.62 Aligned_cols=49 Identities=22% Similarity=0.478 Sum_probs=43.0
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCC
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 426 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 426 (540)
|-.||.+.++++.++++||++.+|+++..+++=|..|. +.++|.+...|
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~hGG 55 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRVHGG 55 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEEeCC
Confidence 56789999999999999999999999999999999996 47888876544
No 84
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=68.48 E-value=12 Score=27.96 Aligned_cols=57 Identities=16% Similarity=0.286 Sum_probs=38.2
Q ss_pred hhHHhHHHHHHhhhcCCC-CCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCC
Q 009222 472 DRQYQVDAAIVRIMKTRK-VLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNP 533 (540)
Q Consensus 472 ~r~~~i~a~IVRimK~~k-~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~ 533 (540)
+|...|=.+|...++.++ .-+..||. +.+.+. +..-+...|+.|.++|||+|+++-+
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa----~~~g~~-S~~tv~~~L~~Le~kG~I~r~~~~~ 63 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREIA----EALGLK-STSTVQRHLKALERKGYIRRDPGKA 63 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHHH----HHHTSS-SHHHHHHHHHHHHHTTSEEEGCCSC
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHH----HHhCCC-ChHHHHHHHHHHHHCcCccCCCCCC
Confidence 455556666676666654 44444443 444554 6788999999999999999998643
No 85
>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=67.76 E-value=13 Score=31.11 Aligned_cols=58 Identities=16% Similarity=0.147 Sum_probs=42.9
Q ss_pred HHHhhhcC-CCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q 009222 480 AIVRIMKT-RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 538 (540)
Q Consensus 480 ~IVRimK~-~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Y 538 (540)
+|..+|.. .+.++.++|...+.++ ...++...+=+.|+.|.+.|+|.+-..+.+...|
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~-~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKK-GPSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhc-CCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 34555555 5679999999888765 3357888999999999999999986543333444
No 86
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=66.91 E-value=7.6 Score=26.90 Aligned_cols=45 Identities=13% Similarity=0.261 Sum_probs=35.4
Q ss_pred HHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 481 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 481 IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
|.+.+.+++.++..+|... |..+..-+.+.|..|.++|+|.+..+
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 4555556677888887763 46788999999999999999998754
No 87
>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=66.62 E-value=8.8 Score=28.40 Aligned_cols=41 Identities=22% Similarity=0.355 Sum_probs=29.9
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
|.-..-.++..|+.+|.+.+++|.+.++.+|-.|+. .+++.
T Consensus 18 V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQ--h~~v~ 58 (62)
T PF08221_consen 18 VGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQ--HNLVQ 58 (62)
T ss_dssp HHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--cCCee
Confidence 333334457899999999999999999999999964 66664
No 88
>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=64.22 E-value=2.7 Score=30.44 Aligned_cols=47 Identities=19% Similarity=0.353 Sum_probs=36.2
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
+..+..++-..+.++..+|-.. +..+...+.+.+..|..+|||+|..
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~------~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEK------LGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHH------HTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH------HCCChhHHHHHHHHHHHCCCEEecc
Confidence 4555666667777888887763 3578899999999999999999954
No 89
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=62.73 E-value=13 Score=33.05 Aligned_cols=48 Identities=4% Similarity=0.235 Sum_probs=42.4
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
++..--.||..+..+...|+.+|++.+|+++..+.+.++.|.. .|++.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~--~GvI~ 54 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ--AGIIT 54 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 5566778899999989999999999999999999999999975 67775
No 90
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=62.61 E-value=11 Score=36.77 Aligned_cols=50 Identities=20% Similarity=0.355 Sum_probs=42.9
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCC
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 426 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 426 (540)
-|..|+..+++++.+++.||++.+|++...+++-|..|. +.+++.+...|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~gg 55 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVRNG 55 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecCC
Confidence 466789999999999999999999999999999999995 46788775543
No 91
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=62.35 E-value=10 Score=34.23 Aligned_cols=48 Identities=10% Similarity=0.211 Sum_probs=42.3
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
+.-.-..||..+.++...|..+|++.+|++...+.+.++.|. +.|++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~--~~GvI~ 59 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLE--RQGFIQ 59 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeE
Confidence 455677899999999999999999999999999999999996 467775
No 92
>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=61.84 E-value=22 Score=29.70 Aligned_cols=62 Identities=21% Similarity=0.203 Sum_probs=46.4
Q ss_pred hHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q 009222 476 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 538 (540)
Q Consensus 476 ~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Y 538 (540)
.+|+.|.+- ....-.....++.+|+......++...+--||+.||++|.++-.++-.++-.|
T Consensus 48 ~yD~~Il~~-~~~~~~~~arvIg~vl~~~~~~i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQ-APDEFQKAARVIGEVLGHSDQGIGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhc-CCccccHHHHHHHHHHHhcCcCCChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 567777772 22334557788999998883347789999999999999999998876555554
No 93
>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=61.73 E-value=12 Score=28.06 Aligned_cols=55 Identities=24% Similarity=0.243 Sum_probs=34.0
Q ss_pred HHHHHHhhhcCC-CCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 477 VDAAIVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 477 i~a~IVRimK~~-k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
.=+.||..||++ ..++.+||..++. +..+ ...++.|-+-+-|+.+++ .+.|.|.|
T Consensus 6 ql~~~VeymK~r~~Plt~~eI~d~l~----~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 6 QLAKAVEYMKKRDHPLTLEEILDYLS----LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHHHT----SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHc----CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 347889999997 6888888886653 3333 234566668889999974 37999975
No 94
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=60.99 E-value=17 Score=34.00 Aligned_cols=45 Identities=16% Similarity=0.233 Sum_probs=37.7
Q ss_pred HHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 377 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 377 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
..||......+.+|..+|++.+|++...+.++|..|. +.+++.+.
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le--~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLE--TEGLIEYE 48 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEe
Confidence 3566666666779999999999999999999999996 46888765
No 95
>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=60.84 E-value=15 Score=28.73 Aligned_cols=35 Identities=6% Similarity=0.130 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
=|..|+-...+ +.+|+.+|++..|++...+.+.|+
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 46788888889 999999999999999999977654
No 96
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=60.43 E-value=11 Score=31.12 Aligned_cols=46 Identities=15% Similarity=0.340 Sum_probs=39.9
Q ss_pred HHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccc
Q 009222 477 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 528 (540)
Q Consensus 477 i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r 528 (540)
+|-.|++.+.....++..+|-..+ ..+...+.+++..|.++|+|.+
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l------~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKV------GLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeec
Confidence 567788999999999999988733 6888999999999999999985
No 97
>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=60.28 E-value=11 Score=28.22 Aligned_cols=51 Identities=20% Similarity=0.357 Sum_probs=36.6
Q ss_pred EcHHHHHHHHHhcCC-----CCccHHHHHHHhCCC-HHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVLMLFNDA-----QKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~-----~~~t~~ei~~~~~i~-~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+|.-|.-||..+-+. -+-|+.||++.+|+. ...+..+|..|. +.|.|.+.+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le--~kG~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE--RKGYIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH--HTTSEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCcCccCCC
Confidence 456677777655432 356999999999996 999999999996 468888765
No 98
>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=59.78 E-value=8 Score=31.91 Aligned_cols=45 Identities=20% Similarity=0.226 Sum_probs=32.3
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
-.+.|+..+..++.++-++|++.+|++...+++.|..|.. .+++.
T Consensus 14 ~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv~ 58 (105)
T PF02002_consen 14 EAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLVS 58 (105)
T ss_dssp TTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-E
T ss_pred hHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeE
Confidence 3456777777678899999999999999999999999974 56763
No 99
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.56 E-value=14 Score=33.92 Aligned_cols=45 Identities=22% Similarity=0.235 Sum_probs=38.1
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
....||.++-.++.+|-++|++.+|++...++++|..|.. .+++.
T Consensus 23 ~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e--~gLv~ 67 (178)
T PRK06266 23 EGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYD--ARLAD 67 (178)
T ss_pred cHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeE
Confidence 3456777777778999999999999999999999999974 57775
No 100
>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=58.84 E-value=11 Score=30.80 Aligned_cols=45 Identities=9% Similarity=0.252 Sum_probs=33.1
Q ss_pred hHHHHHHhhhcC----CCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccc
Q 009222 476 QVDAAIVRIMKT----RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYL 526 (540)
Q Consensus 476 ~i~a~IVRimK~----~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi 526 (540)
-++..|..++|. ...++.++|...+ ..+..+|+++|+.|++.|+|
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l------~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQL------GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHS------TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHh------CcCHHHHHHHHHHHHhCCeE
Confidence 345555666666 5678888877533 46789999999999999976
No 101
>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=58.76 E-value=24 Score=27.26 Aligned_cols=39 Identities=21% Similarity=0.353 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
+.-.+|-++-...++|.++|+..+|.+.+.+...|..+.
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 345677778889999999999999999999999998883
No 102
>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=58.58 E-value=20 Score=27.33 Aligned_cols=49 Identities=18% Similarity=0.262 Sum_probs=40.9
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
.+=|+.++-++...+.-|+++|++.+|-....++-+|..+...|.++-.
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i 57 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTI 57 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEE
Confidence 4568999999999899999999999999999999999988543445543
No 103
>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=58.51 E-value=24 Score=24.42 Aligned_cols=30 Identities=23% Similarity=0.532 Sum_probs=22.5
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
|-+.| ...+|++||++.+|++...+.....
T Consensus 13 i~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 13 IRLRY--FEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHH--TST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHh--cCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 33555 4568999999999999988876654
No 104
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=58.03 E-value=13 Score=36.28 Aligned_cols=50 Identities=16% Similarity=0.298 Sum_probs=42.9
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCC
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 426 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 426 (540)
-|..|+..+++.+.+++.||++.++++...+++-|..|. +.|+|.+..+|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le--~~g~l~r~~GG 55 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLA--EQNKILRHHGG 55 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCC
Confidence 466788888999999999999999999999999999996 46788776543
No 105
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=57.79 E-value=15 Score=34.72 Aligned_cols=50 Identities=18% Similarity=0.361 Sum_probs=43.7
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
.|.+-..||.++..++++.+.||++.+|+|...+..++..|. +.+|+..+
T Consensus 21 aS~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le--~aGlirT~ 70 (308)
T COG4189 21 ASKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLE--KAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHH--hcCceeee
Confidence 455666899999999999999999999999999999999995 68898755
No 106
>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=57.74 E-value=19 Score=32.29 Aligned_cols=44 Identities=20% Similarity=0.239 Sum_probs=36.5
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
...|+..+-.++.+|-+||++.+|++.+.+++.|..|.. .+|+.
T Consensus 16 ~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e--~~Lv~ 59 (158)
T TIGR00373 16 VGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYD--AGLAD 59 (158)
T ss_pred HHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCce
Confidence 345666665667899999999999999999999999975 57774
No 107
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=57.57 E-value=7.2 Score=28.35 Aligned_cols=48 Identities=15% Similarity=0.299 Sum_probs=35.3
Q ss_pred HHHHHhhhcCCCC--CChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 478 DAAIVRIMKTRKV--LSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 478 ~a~IVRimK~~k~--l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
+..|...+..+.. ++..+|...+ ..+..-+...|..|.++|||+|..+
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l------~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERL------GISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHH------TS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4555666666665 7888877633 4678899999999999999999754
No 108
>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=57.28 E-value=16 Score=24.89 Aligned_cols=32 Identities=19% Similarity=0.381 Sum_probs=21.9
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhh
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 411 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 411 (540)
.|+-++.+. +|+.+|++.+|++...+.+.|..
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHhc
Confidence 344445543 89999999999999999887753
No 109
>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=57.10 E-value=29 Score=24.83 Aligned_cols=30 Identities=13% Similarity=0.472 Sum_probs=24.6
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 383 FNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 383 Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
|+.-...|++||++.+|++...+-.+|..=
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 555568999999999999999888777643
No 110
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=57.00 E-value=13 Score=36.62 Aligned_cols=49 Identities=12% Similarity=0.179 Sum_probs=42.8
Q ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 374 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 374 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
--|..|+.++++.+.+++.||++.+|++...+++-|..|- ..|++.+..
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le--~~G~l~r~~ 65 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLE--KQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHH--hCCCeEEEe
Confidence 4578899999999999999999999999999999999995 367777654
No 111
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=56.90 E-value=19 Score=32.93 Aligned_cols=63 Identities=19% Similarity=0.321 Sum_probs=48.4
Q ss_pred eeeEeccCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCC--CCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 346 RRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 346 R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~--~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
|.-.|.+.+|..+++- .+.|. ||+.||.-|+.-... ..||.+-|++..+++.+++...|..+.
T Consensus 97 r~~~~~~~fg~~ep~~-vPkGk----ltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 97 RDTIPDFEFGFYEPEK-VPKGK----LTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCcccccccccCccc-CCCCc----eeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 3345777888877653 34444 788899888764443 579999999999999999999998884
No 112
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=56.46 E-value=22 Score=30.46 Aligned_cols=40 Identities=15% Similarity=0.291 Sum_probs=33.8
Q ss_pred hhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 484 IMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 484 imK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
+|..++.++.++|-+.+ ..+.+-+.+++..|++.|++.|.
T Consensus 36 LL~~~~~~tvdelae~l------nr~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 36 LLEENGPLTVDELAEIL------NRSRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred HHhhcCCcCHHHHHHHH------CccHHHHHHHHHHHHHcCCeeee
Confidence 34478999999988744 57889999999999999999995
No 113
>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=56.13 E-value=9.2 Score=24.19 Aligned_cols=26 Identities=31% Similarity=0.489 Sum_probs=20.9
Q ss_pred CccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 388 KLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 388 ~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
++|-+||++.+|++.+.+-+.|..|-
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36789999999999999999999885
No 114
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=55.18 E-value=18 Score=31.85 Aligned_cols=49 Identities=14% Similarity=0.341 Sum_probs=42.5
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
+.-.-.-||..+.+....|+.+|++.+|++...+.+.+..|. +.|++..
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~--~~GiI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLE--EEGVIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCceee
Confidence 445667789889998899999999999999999999999996 5788864
No 115
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=54.69 E-value=12 Score=34.41 Aligned_cols=47 Identities=11% Similarity=0.193 Sum_probs=40.9
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
-+..|+...++++.+++++|++.+|++...+++=|..|. ..+++.+.
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~--~~g~~~r~ 54 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELG--IPELRERI 54 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHh--cchHHHHH
Confidence 467889999999999999999999999999999999996 45676543
No 116
>PRK00215 LexA repressor; Validated
Probab=54.30 E-value=21 Score=33.33 Aligned_cols=52 Identities=21% Similarity=0.329 Sum_probs=42.3
Q ss_pred EcHHHHHHHHHhcC-----CCCccHHHHHHHhCC-CHHHHHHHhhhhhcCCceeeecCCC
Q 009222 372 VSLFQTVVLMLFND-----AQKLSFQDIKDATGI-EDKELRRTLQSLACGKVRVLQKLPK 425 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~-----~~~~t~~ei~~~~~i-~~~~l~~~L~~L~~~k~~iL~~~~~ 425 (540)
++.-|..+|..+.+ ....|+.||++.+|+ +...+.+.|..|. +.+++.+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~~ 59 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDPG 59 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCCC
Confidence 46778888876653 356899999999999 9999999999996 4688877653
No 117
>PHA02943 hypothetical protein; Provisional
Probab=54.23 E-value=20 Score=31.51 Aligned_cols=55 Identities=20% Similarity=0.271 Sum_probs=40.0
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
||-.+ ..+..|..||++.+|++-..++-+|.-|- +.|.+.+.. ++....|++|++
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLE--rEG~VkrV~----~G~~tyw~l~~d 70 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLA--KEGMVLKVE----IGRAAIWCLDED 70 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCceEEEe----ecceEEEEEChH
Confidence 55555 56778999999999999999999998884 567776543 223455666663
No 118
>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=53.56 E-value=19 Score=26.57 Aligned_cols=46 Identities=13% Similarity=0.256 Sum_probs=33.4
Q ss_pred hhcCCCCC-ChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCce
Q 009222 484 IMKTRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIY 536 (540)
Q Consensus 484 imK~~k~l-~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y 536 (540)
-.+....+ +..+|.. +|.++..-+.+++..|.+.|+|.+.++ .+.+
T Consensus 17 ~~~~g~~lps~~~la~------~~~vsr~tvr~al~~L~~~g~i~~~~~-~G~~ 63 (64)
T PF00392_consen 17 RLPPGDRLPSERELAE------RYGVSRTTVREALRRLEAEGLIERRPG-RGTF 63 (64)
T ss_dssp SS-TTSBE--HHHHHH------HHTS-HHHHHHHHHHHHHTTSEEEETT-TEEE
T ss_pred CCCCCCEeCCHHHHHH------HhccCCcHHHHHHHHHHHCCcEEEECC-ceEE
Confidence 44555566 6666665 678999999999999999999999874 4444
No 119
>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=53.48 E-value=14 Score=37.46 Aligned_cols=145 Identities=13% Similarity=0.178 Sum_probs=40.8
Q ss_pred EEEcHHHHHHHHHhcC--CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCCCCcee
Q 009222 370 LAVSLFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYR 447 (540)
Q Consensus 370 l~~s~~Q~~iLl~Fn~--~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~ 447 (540)
-.++..+..|..+..+ +..+-..+|..++|++...+.++|..|.. .+++.... +.+.+++|
T Consensus 80 ~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~--k~lIK~vk---------------sv~~~~rK 142 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLES--KKLIKSVK---------------SVKNPNRK 142 (327)
T ss_dssp -SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHH--TTSEEEE-----------------SS-SS--
T ss_pred cCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHh--CCCEEEec---------------CcCCCCeE
Confidence 3467778888877765 46788999999999999999999999975 46665421 11223333
Q ss_pred EEecc-c-cccc-chhhhhhhhHHHHHhhHHhHHHHHHhhhcCCCC-----------------------------CChHH
Q 009222 448 IKVNA-I-QMKE-TVEENTSTTERVFQDRQYQVDAAIVRIMKTRKV-----------------------------LSHTL 495 (540)
Q Consensus 448 i~i~~-~-~~~~-~~~e~~~~~~~~~~~r~~~i~a~IVRimK~~k~-----------------------------l~~~~ 495 (540)
+-+-. + |..+ |... =-+..+...+-...+...|.+.+.++.. .+.++
T Consensus 143 ~Yml~~l~Ps~eiTGG~-wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~e 221 (327)
T PF05158_consen 143 VYMLYDLEPSEEITGGP-WYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEE 221 (327)
T ss_dssp EEEESSS-------------------------------------------------------------------------
T ss_pred EEEEccCCcCcccCCCC-cccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHH
Confidence 33311 0 0000 0000 0000112222223344444444444433 44455
Q ss_pred HHHHHHHHc--CCCCChHHHHHHHHHhhhhccccccCCC
Q 009222 496 LITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNN 532 (540)
Q Consensus 496 L~~~v~~~l--~F~~~~~~ik~~Ie~Li~~eyi~r~~~~ 532 (540)
+...+.+.- .-..+.++|...|+.|+=.|-|++-...
T Consensus 222 I~~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~ 260 (327)
T PF05158_consen 222 IAEFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSG 260 (327)
T ss_dssp ---------------------------------------
T ss_pred HHHHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEecc
Confidence 444433221 3457889999999999999998886543
No 120
>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=53.13 E-value=23 Score=24.91 Aligned_cols=44 Identities=18% Similarity=0.411 Sum_probs=32.3
Q ss_pred HHhhhcCCC-CCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 481 IVRIMKTRK-VLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 481 IVRimK~~k-~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
|.+.+...+ .++..+|...+ ..+..-+-+.+..|.+.||++||+
T Consensus 8 iL~~l~~~~~~~t~~eia~~~------gl~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARAL------GLPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHH------TS-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHcCCCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCcCeecCc
Confidence 445555554 47888877644 356778999999999999999985
No 121
>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=52.58 E-value=27 Score=24.51 Aligned_cols=24 Identities=29% Similarity=0.645 Sum_probs=17.4
Q ss_pred CCccHHHHHHHhCCCHHHHHHHhh
Q 009222 387 QKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 387 ~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
+.+|.+||++.+|++...++..+.
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 458999999999999999887764
No 122
>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=52.37 E-value=18 Score=26.10 Aligned_cols=41 Identities=20% Similarity=0.316 Sum_probs=32.0
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
.|.-+..||.++... .|..+|++.+|+++..+..++..+..
T Consensus 4 LT~~E~~vl~~l~~G--~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 4 LTERELEVLRLLAQG--MSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp S-HHHHHHHHHHHTT--S-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHhc--CCcchhHHhcCcchhhHHHHHHHHHH
Confidence 355677778777664 78999999999999999999988863
No 123
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=52.24 E-value=2e+02 Score=26.64 Aligned_cols=34 Identities=24% Similarity=0.473 Sum_probs=28.9
Q ss_pred HHhcCCCC-ccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 381 MLFNDAQK-LSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 381 l~Fn~~~~-~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
++|-..++ +|+++|++.+|++...+..+|..|..
T Consensus 12 ~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~ 46 (188)
T PRK00135 12 LLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQE 46 (188)
T ss_pred HHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45667776 99999999999999999999998853
No 124
>PRK14999 histidine utilization repressor; Provisional
Probab=51.48 E-value=24 Score=33.87 Aligned_cols=54 Identities=13% Similarity=0.282 Sum_probs=40.9
Q ss_pred HHHHHH-hhhcCCCCC-ChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q 009222 477 VDAAIV-RIMKTRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 537 (540)
Q Consensus 477 i~a~IV-RimK~~k~l-~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~ 537 (540)
|.+.|. ..++....+ +..+|.. .|.++...++++|+.|.++|+|.|..+ +++|+
T Consensus 21 i~~~I~~g~~~~G~~LPsE~eLa~------~~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 21 ICKKIAGGVWQPHDRIPSEAELVA------QYGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred HHHHHHcCCCCCCCcCCCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 444443 355666666 5667665 788999999999999999999999874 57775
No 125
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=51.25 E-value=32 Score=23.92 Aligned_cols=39 Identities=23% Similarity=0.398 Sum_probs=29.9
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
+.-+..++.++. ..+|..+|++.+|++...+...+..+.
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 455556665553 447999999999999999988887663
No 126
>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=50.89 E-value=35 Score=24.72 Aligned_cols=32 Identities=16% Similarity=0.382 Sum_probs=28.0
Q ss_pred cHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 390 SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 390 t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
|..+|++.+|++...+.++|..|.. .|+|...
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~~ 58 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA--EGLVERR 58 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 5999999999999999999999964 6788654
No 127
>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=50.25 E-value=34 Score=23.84 Aligned_cols=39 Identities=23% Similarity=0.372 Sum_probs=28.5
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
+..|..++.++- +.+|..+|++.+|++...+...+..+.
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 344455554442 458999999999999999888877653
No 128
>smart00526 H15 Domain in histone families 1 and 5.
Probab=50.19 E-value=68 Score=23.77 Aligned_cols=53 Identities=21% Similarity=0.130 Sum_probs=39.2
Q ss_pred hHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCC--hHHHHHHHHHhhhhcccccc
Q 009222 476 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIK--PADLKKRIESLIDREYLERD 529 (540)
Q Consensus 476 ~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~--~~~ik~~Ie~Li~~eyi~r~ 529 (540)
+|..||.. |+.+++.+...+...+...-...+. ...++.+|..++++|-+.+-
T Consensus 10 mI~eAI~~-l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 10 MITEAISA-LKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred HHHHHHHH-cCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeec
Confidence 56666665 6999999999999888775322222 25688899999999988764
No 129
>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=50.11 E-value=16 Score=34.07 Aligned_cols=51 Identities=22% Similarity=0.300 Sum_probs=42.3
Q ss_pred EcHHHHHHHHHhcCC-----CCccHHHHHHHhCCC-HHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVLMLFNDA-----QKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~-----~~~t~~ei~~~~~i~-~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
++..|..||....+. -+.|+.||++.+|++ ...+.++|..|. +.++|.+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecCC
Confidence 478899999877643 358899999999998 999999999996 578888754
No 130
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.81 E-value=18 Score=34.18 Aligned_cols=57 Identities=21% Similarity=0.339 Sum_probs=47.5
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
-+--|-..|+.|.+..+||-. .|....++.-.+|..|+..|.|.=.-+|.+.|+||.
T Consensus 202 l~eFv~YIk~nKvV~ledLas------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 202 LSEFVEYIKKNKVVPLEDLAS------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHHHHhcCeeeHHHHHH------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 344567789999999999876 566777888889999999999998888999999983
No 131
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=49.54 E-value=23 Score=34.22 Aligned_cols=47 Identities=15% Similarity=0.262 Sum_probs=39.6
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
-|..|+..+++++.++.+||++.+|++...+++-|..|.. .+.+.+.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~--~~~l~r~ 51 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT--QGKILRN 51 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEe
Confidence 3567888888999999999999999999999999999963 4556553
No 132
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=49.47 E-value=25 Score=25.84 Aligned_cols=50 Identities=18% Similarity=0.295 Sum_probs=34.3
Q ss_pred HHhhhcCCCCCChHHHHHHHHHHc-----CCCCChHHHHHHHHHhhhhccccccCC
Q 009222 481 IVRIMKTRKVLSHTLLITELFQQL-----KFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 481 IVRimK~~k~l~~~~L~~~v~~~l-----~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
|+..+..-+.++.+.+..-. +.+ .++++.++++..++.+++.|-|+-+++
T Consensus 2 I~gMLtN~gsl~l~RIh~mL-kmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~~G 56 (60)
T PF08672_consen 2 IVGMLTNLGSLPLDRIHSML-KMFPKDPGGYDISLEELQEFLDRLVEEGKLECSGG 56 (60)
T ss_dssp HHHHHHHH-SEEHHHHHHHH-HHH-GGG--TT--HHHHHHHHHHHHHTTSEE--TT
T ss_pred HhHHhhcCCCCCHHHHHHHH-HhccCCCCCCCCCHHHHHHHHHHHHHCCcEEecCC
Confidence 56667777778888866533 332 688999999999999999999998853
No 133
>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=49.20 E-value=30 Score=28.68 Aligned_cols=37 Identities=30% Similarity=0.419 Sum_probs=30.3
Q ss_pred CCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 487 TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 487 ~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
..+.++..+|... ...+..-+-+.|+.|.++|||.|.
T Consensus 40 ~~~~~t~~eL~~~------l~~~~stvs~~i~~Le~kg~I~r~ 76 (109)
T TIGR01889 40 NEGKLTLKEIIKE------ILIKQSALVKIIKKLSKKGYLSKE 76 (109)
T ss_pred cCCcCcHHHHHHH------HCCCHHHHHHHHHHHHHCCCEecc
Confidence 4577888887763 347788899999999999999974
No 134
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=49.19 E-value=18 Score=33.30 Aligned_cols=26 Identities=38% Similarity=0.630 Sum_probs=22.2
Q ss_pred CCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 387 QKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 387 ~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
..+|+++|++.||+..+++..+|+.|
T Consensus 149 ~~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 149 KSISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp --EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred CeEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 36999999999999999999999988
No 135
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=49.14 E-value=38 Score=30.75 Aligned_cols=55 Identities=20% Similarity=0.154 Sum_probs=41.2
Q ss_pred EEEEEcHHHHHHHHHhcCCCCc-cHHHHHHHh--CCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 368 KELAVSLFQTVVLMLFNDAQKL-SFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 368 ~~l~~s~~Q~~iLl~Fn~~~~~-t~~ei~~~~--~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+++.-+.+..+|.-+..-.+.- +.++|++.+ +++.+.++.+|..|. +.|+|.+..
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 3344455565666555444333 899999999 999999999999996 689998854
No 136
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=48.98 E-value=33 Score=29.19 Aligned_cols=52 Identities=17% Similarity=0.286 Sum_probs=44.9
Q ss_pred HHhHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 474 QYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 474 ~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
...|.+.||-..+.++.++..++...+ -.+...++..+..|+++|.|-+.+.
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~T------GasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAKT------GASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHHH------CCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 346899999999999999999988733 4788899999999999999988764
No 137
>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=48.50 E-value=31 Score=27.43 Aligned_cols=45 Identities=18% Similarity=0.339 Sum_probs=37.1
Q ss_pred HHHHHHHhcCCCCccHHHHHHHh-CCCHHHHHHHhhhhhcCCceeeecC
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~-~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
-+.||..... +...+.||.+.+ |++...|.+.|..|.. .+++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~--~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEE--AGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHH--cchhhcc
Confidence 3567777766 789999999999 9999999999999974 7888764
No 138
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=47.89 E-value=26 Score=34.05 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=36.2
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
-|..|+.+.++++.+++.+|++.+|+++..+++=|..|-
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 477899999999999999999999999999999999884
No 139
>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=47.86 E-value=24 Score=30.10 Aligned_cols=49 Identities=10% Similarity=0.150 Sum_probs=38.6
Q ss_pred EcHHHHHHHHH--hc--------CCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 372 VSLFQTVVLML--FN--------DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 372 ~s~~Q~~iLl~--Fn--------~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
+..+.-.+++. .| +.-+.|.++||..++-+.+.++.+|..|. +.+++..
T Consensus 27 ~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~ 85 (121)
T PF09681_consen 27 TVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEI 85 (121)
T ss_pred HHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 44555555555 43 44589999999999999999999999995 6889875
No 140
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=47.69 E-value=16 Score=35.57 Aligned_cols=45 Identities=18% Similarity=0.307 Sum_probs=41.4
Q ss_pred HHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 479 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 479 a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
-.|+..+++++.++.++|.+ .|.+|...|++=|..|-++|++.|.
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~------~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKEKGKVSVEELAE------LFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHH------HhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 35789999999999999998 8899999999999999999999994
No 141
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=47.58 E-value=38 Score=23.89 Aligned_cols=41 Identities=12% Similarity=0.260 Sum_probs=31.6
Q ss_pred hcCCCCC-ChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 485 MKTRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 485 mK~~k~l-~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
++....+ +..+|.. .|..+..-+.+.+..|.++|+|.+.++
T Consensus 14 ~~~~~~l~s~~~la~------~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 14 LRPGDKLPSERELAA------QLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred CCCCCcCcCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3444455 5666555 667899999999999999999988764
No 142
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=47.46 E-value=58 Score=25.43 Aligned_cols=42 Identities=19% Similarity=0.268 Sum_probs=32.6
Q ss_pred HHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 380 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 380 Ll~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
++..++.+.+|=++|++.+|++...+-++++.|-.....|..
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEe
Confidence 344556678999999999999999999999999653344443
No 143
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=47.30 E-value=30 Score=30.43 Aligned_cols=50 Identities=18% Similarity=0.359 Sum_probs=43.5
Q ss_pred HhHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 475 YQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 475 ~~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
..+|..|.+++......+..+|-..+ ..+...+..+|+.|.+.|.|++-.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l------glS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV------GLSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH------CCCHHHHHHHHHHHHHCCceeeEE
Confidence 45788899999999999999988755 478899999999999999998853
No 144
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=47.06 E-value=30 Score=33.58 Aligned_cols=43 Identities=12% Similarity=0.289 Sum_probs=35.9
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
.||+++-+ ++.|++||.+.++++...+..+|.-|. +.+++.++
T Consensus 17 ~lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~--~~~LV~~~ 59 (260)
T COG4742 17 DLLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLK--DKGLVVQE 59 (260)
T ss_pred HHHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHh--hCCCEEec
Confidence 35555555 788999999999999999999999995 47888775
No 145
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=47.03 E-value=63 Score=24.87 Aligned_cols=54 Identities=20% Similarity=0.233 Sum_probs=42.0
Q ss_pred hHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCC----hHHHHHHHHHhhhhccccccC
Q 009222 476 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIK----PADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 476 ~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~----~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
+|..|| +-|+.++..+...+...+........+ ...++.+|..++++|-|.+..
T Consensus 8 mI~eAI-~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 8 MILEAI-KALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHH-HHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHH-HHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 455555 688999999999999988885532222 367999999999999998865
No 146
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=46.90 E-value=17 Score=35.35 Aligned_cols=46 Identities=20% Similarity=0.190 Sum_probs=40.9
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
+..|+..+++++.++..||.+ .|.++...|.+-|+.|-++|.|.|.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~------~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQ------YFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 345788899999999999987 7789999999999999999999884
No 147
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=46.77 E-value=32 Score=27.32 Aligned_cols=47 Identities=17% Similarity=0.306 Sum_probs=36.9
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
+..|...+...+.++..+|... +.++...+.+.|..|.++|+|.+..
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKR------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 5566777777778888887753 2466788999999999999998764
No 148
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=46.35 E-value=33 Score=27.22 Aligned_cols=49 Identities=27% Similarity=0.275 Sum_probs=39.6
Q ss_pred cCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q 009222 486 KTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 540 (540)
Q Consensus 486 K~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yia 540 (540)
+..|-++...|.+ ++.++.+.-+++|..|.++|.|..-..+...-+|.|
T Consensus 37 ~~~K~ITps~lse------rlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 37 KKEKIVTPYTLAS------KYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred ccCcEEcHHHHHH------HhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 3456666666555 677899999999999999999998877888888875
No 149
>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=46.32 E-value=31 Score=24.30 Aligned_cols=41 Identities=15% Similarity=0.306 Sum_probs=33.8
Q ss_pred HHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 381 MLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 381 l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
-+|.+++.+|+.++.+.+|++-+.....|+-| .+.++..+.
T Consensus 3 ~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~l--D~~g~T~R~ 43 (50)
T PF09107_consen 3 ELLQKNGEITVAEFRDLLGLSRKYAIPLLEYL--DREGITRRV 43 (50)
T ss_dssp HHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHH--HHTTSEEEE
T ss_pred HHHhcCCcCcHHHHHHHHCccHHHHHHHHHHH--hccCCEEEe
Confidence 46778899999999999999999999899888 456777664
No 150
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=45.45 E-value=31 Score=30.16 Aligned_cols=47 Identities=11% Similarity=0.237 Sum_probs=34.6
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
+..|...+-.++.++..+|.. .+..+...+-..|+.|.++|||.|..
T Consensus 42 q~~vL~~l~~~~~~t~~eLa~------~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 42 QFKVLCSIRCAACITPVELKK------VLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HHHHHHHHHHcCCCCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 334444444466788888776 33577888999999999999999954
No 151
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=45.36 E-value=42 Score=30.16 Aligned_cols=48 Identities=15% Similarity=0.297 Sum_probs=42.6
Q ss_pred HhHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccc
Q 009222 475 YQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 528 (540)
Q Consensus 475 ~~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r 528 (540)
..+|..|.+.|.....++..+|-..| ..+...+.++|+.|.+.|.|++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l------glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV------GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeEE
Confidence 34788999999999999999988755 4788999999999999999985
No 152
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=44.65 E-value=21 Score=34.75 Aligned_cols=46 Identities=20% Similarity=0.484 Sum_probs=41.0
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
...|..++++++.++..+|.+ .|.++...|.+-|..|-++|.|.|.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVE------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHH------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 446788889999999999987 6789999999999999999999984
No 153
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=44.52 E-value=3.5e+02 Score=27.33 Aligned_cols=83 Identities=12% Similarity=0.249 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHccCChhhHHHHHHHhhhc----cchHHHHHHHHHHHHHHhhhhhcCchh-------hHHHHHHHHHHH-
Q 009222 82 AILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMDEEK-------DKDMVSSLLEFK- 149 (540)
Q Consensus 82 ~ll~~~~~~ll~~~~~~~l~~ly~l~~~~----~~~~~l~~~~~~~i~~~g~~~~~~~~~-------~~~~i~~l~~l~- 149 (540)
.++.+.|..-++++|...+.+++.||--. .|++.+..-+.+.|........+.... .-.|...+..++
T Consensus 10 ~~~~~~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~~~~~~~~~~~~a~~lt~Lfe 89 (324)
T smart00762 10 ELFKERFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAGASDDTRAAVFYADTLTHLFE 89 (324)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhccccccccccccchHHHHHHHHHH
Confidence 34456788888899999999999998776 567777666666666655444433211 112333333333
Q ss_pred ------HHHHHHHHHhcCCCH
Q 009222 150 ------ASLDTIWEQSFSKNE 164 (540)
Q Consensus 150 ------~~~~~l~~~~F~~~~ 164 (540)
+....++..+||.+.
T Consensus 90 ~ia~ii~~h~~~I~~~yG~~~ 110 (324)
T smart00762 90 NVATIIEQHQPVIEKYYGPDG 110 (324)
T ss_pred HHHHHHHhccHHHHHHcCchh
Confidence 344556777887543
No 154
>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=43.83 E-value=3.6e+02 Score=27.29 Aligned_cols=156 Identities=13% Similarity=0.222 Sum_probs=85.2
Q ss_pred HHHHHHHHHHccCChhhHHHHHHHhhhc----cchHHHHHHHHHHHHHHhhhhhcCch-------hhHHHHHHHHHHH--
Q 009222 83 ILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMDEE-------KDKDMVSSLLEFK-- 149 (540)
Q Consensus 83 ll~~~~~~ll~~~~~~~l~~ly~l~~~~----~~~~~l~~~~~~~i~~~g~~~~~~~~-------~~~~~i~~l~~l~-- 149 (540)
++.+.|..-...+|.+.+.+.+.||--. .|++.+..-+.+.|.....+.+.... .+--|...+..++
T Consensus 11 ~f~~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~LFe~ 90 (331)
T PF08318_consen 11 IFLKKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTKLFEH 90 (331)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHHHHHH
Confidence 4445777788889999999999998876 56777766666666666655554331 1113334444443
Q ss_pred -----HHHHHHHHHhcCCCHHHH--HHHHHH--------HHHHhhcCC-CCcHHHHHHHHHHHHhc--------------
Q 009222 150 -----ASLDTIWEQSFSKNEAFC--NTIKDA--------FEYLINLRQ-NRPAELIAKFLDEKLRA-------------- 199 (540)
Q Consensus 150 -----~~~~~l~~~~F~~~~~f~--~~l~~~--------f~~~ln~~~-~~~~e~La~y~d~~l~~-------------- 199 (540)
+....++..+||...... ..+..- +..|..... .+....+-.|-...+.+
T Consensus 91 ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 170 (331)
T PF08318_consen 91 IATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSSRAAS 170 (331)
T ss_pred HHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhcccccccccccccccc
Confidence 344456777898664211 111111 111111110 01112233333332222
Q ss_pred ----CCCCCChHHHHHHHHhhhhhhhcccChhHHHHHHHHHHHHHhcCCC
Q 009222 200 ----GNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGK 245 (540)
Q Consensus 200 ----~~~~~~~~~~~~~l~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLL~~~ 245 (540)
...+.+.-+++..|+.+..++.. -..|.++++.|.-...
T Consensus 171 ~~~~~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~~ 213 (331)
T PF08318_consen 171 SSQSEDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEFS 213 (331)
T ss_pred ccccccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhccc
Confidence 00112234677888888777753 4579999999988743
No 155
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=43.52 E-value=46 Score=32.69 Aligned_cols=39 Identities=36% Similarity=0.523 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcC-CCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 374 LFQTVVLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 374 ~~Q~~iLl~Fn~-~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
-+...|+..+.+ ...+|+++|++.|||..+++..+|+.|
T Consensus 208 YW~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 208 YWTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 344556655544 478999999999999999999999988
No 156
>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=42.88 E-value=33 Score=26.35 Aligned_cols=50 Identities=18% Similarity=0.254 Sum_probs=41.3
Q ss_pred cHHHHHHHHHhcCC--CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 373 SLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~--~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+..|.++|...-.. .+++-.+|+..+|++...+-..+..|. +.+++.+.+
T Consensus 1 t~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~~ 52 (75)
T PF04182_consen 1 TDIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQS 52 (75)
T ss_pred CchHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEEE
Confidence 35688888887654 678999999999999999999999996 478887654
No 157
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=42.67 E-value=49 Score=26.66 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=45.2
Q ss_pred EEEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 370 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 370 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+..+.....||..+...++=...-|+..+++|.+.+...|..|. ..|+|.+..
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEec
Confidence 44567788899999888877888899999999999999999996 479998764
No 158
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=42.66 E-value=45 Score=26.22 Aligned_cols=45 Identities=18% Similarity=0.325 Sum_probs=35.3
Q ss_pred HHhhhcCC-CCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 481 IVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 481 IVRimK~~-k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
|...+.+. +.++..+|...+ ..+...+.+.+..|.+.|||.+++.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 34445544 689999988754 4678889999999999999999753
No 159
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=42.65 E-value=31 Score=23.73 Aligned_cols=33 Identities=15% Similarity=0.358 Sum_probs=21.7
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
++.++.+ .+|..+|++.+|++...+.+-+..+.
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 4444444 78999999999999999988877663
No 160
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=42.48 E-value=42 Score=32.17 Aligned_cols=54 Identities=11% Similarity=0.369 Sum_probs=39.4
Q ss_pred HHHHHHhhhcCCCCCCh-HHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q 009222 477 VDAAIVRIMKTRKVLSH-TLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 537 (540)
Q Consensus 477 i~a~IVRimK~~k~l~~-~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~ 537 (540)
|...|...++....++- .+|.. .|.++...++++|+.|++.|+|.|..+ +++|+
T Consensus 21 L~~~I~~~~~~G~~LPsE~eLa~------~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 21 LEQELRQHYRCGDYLPAEQQLAA------RYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred HHHHHhcccCCCCcCCCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 44455445666655553 33333 788999999999999999999999874 56765
No 161
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.25 E-value=30 Score=30.57 Aligned_cols=36 Identities=28% Similarity=0.318 Sum_probs=29.7
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
|+..+-..+.+|-++|++.+|++.+.+++.|..|-.
T Consensus 6 v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 6 VLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred ehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 344333456899999999999999999999999964
No 162
>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=41.96 E-value=30 Score=29.39 Aligned_cols=49 Identities=18% Similarity=0.316 Sum_probs=38.6
Q ss_pred EcHHHHHHHHHhcCC--------CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 372 VSLFQTVVLMLFNDA--------QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~--------~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
+..+.-..|+..|.. -+.+.++||..++-+.+.++.+|..|. +.+++..
T Consensus 27 ~~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~ 83 (119)
T TIGR01714 27 TIIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEK 83 (119)
T ss_pred HHHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 344555555555544 578999999999999999999999995 6889875
No 163
>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=41.23 E-value=53 Score=26.24 Aligned_cols=33 Identities=18% Similarity=0.466 Sum_probs=23.0
Q ss_pred HHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 381 MLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 381 l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
.+..+... ++..|.+.||+|...++.+|.+|-.
T Consensus 15 ~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~ 47 (90)
T PF09904_consen 15 YLIDSGER-NVPALMEATGMPRRTIQDTIKALPE 47 (90)
T ss_dssp HHHHHS-B--HHHHHHHH---HHHHHHHHHGGGG
T ss_pred HHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhc
Confidence 34445555 9999999999999999999999964
No 164
>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=40.99 E-value=42 Score=28.09 Aligned_cols=47 Identities=21% Similarity=0.195 Sum_probs=34.7
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
+..|...+...+.++..+|-.. ...+...+-..|+.|.++|+|+|..
T Consensus 30 q~~iL~~l~~~~~~t~~ela~~------~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 30 QWRILRILAEQGSMEFTQLANQ------ACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH------hCCCchhHHHHHHHHHHCCCEEecc
Confidence 4445566667788888776653 2355667899999999999999954
No 165
>PRK13239 alkylmercury lyase; Provisional
Probab=40.88 E-value=49 Score=30.97 Aligned_cols=39 Identities=18% Similarity=0.303 Sum_probs=34.8
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
+...||.++-+..++|+++|++.+|.+.+.+++.|..|.
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 556777778888999999999999999999999999884
No 166
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=40.84 E-value=99 Score=26.63 Aligned_cols=52 Identities=23% Similarity=0.283 Sum_probs=42.8
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCC
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 426 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 426 (540)
|+--..+|-+..+.+..|+.|+++.+|=+.+.+-+.|..|.+ +||+..+.+|
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~--~GlI~fe~~g 114 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLAD--LGLIFFEEDG 114 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHh--cCeEEEecCC
Confidence 444456677788889999999999999999999999999964 8898765543
No 167
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=40.84 E-value=53 Score=24.59 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=40.9
Q ss_pred HHHhhhcCC-CCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 480 AIVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 480 ~IVRimK~~-k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
.|.++++.. +.++..+|....... .+..+.+.+..++..|=++||+++.+
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~-g~~~se~avRrrLr~me~~Glt~~~g 52 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLR-GEELSEEAVRRRLRAMERDGLTRKVG 52 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhc-ChhhhHHHHHHHHHHHHHCCCccccC
Confidence 366777776 579999988766544 78899999999999999999998765
No 168
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=40.82 E-value=46 Score=29.50 Aligned_cols=47 Identities=13% Similarity=0.268 Sum_probs=41.4
Q ss_pred hHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccc
Q 009222 476 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 528 (540)
Q Consensus 476 ~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r 528 (540)
.+|-.|.+.|......++.+|-.++ ..+.+.+..+|+.|.+.|+|++
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l------glS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF------GVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeee
Confidence 3677889999999999999988755 5789999999999999999985
No 169
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=40.57 E-value=38 Score=22.43 Aligned_cols=27 Identities=26% Similarity=0.455 Sum_probs=19.9
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 386 AQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 386 ~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
...+|+++|++..|++...+.+.....
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999998888877655
No 170
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=40.40 E-value=64 Score=27.53 Aligned_cols=48 Identities=15% Similarity=0.293 Sum_probs=40.8
Q ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 374 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 374 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
.+.+-|+-+.-+++.+|+.++...||++-..+...+.-|+. .|-|..+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~ 59 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeC
Confidence 45678888888999999999999999999999999999975 4555544
No 171
>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=40.25 E-value=54 Score=25.28 Aligned_cols=58 Identities=24% Similarity=0.290 Sum_probs=35.1
Q ss_pred HhHHHHHHhhhcCCC--CCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccc---cccCCCCCceeecC
Q 009222 475 YQVDAAIVRIMKTRK--VLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYL---ERDKNNPQIYNYLA 540 (540)
Q Consensus 475 ~~i~a~IVRimK~~k--~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi---~r~~~~~~~y~Yia 540 (540)
...=|.||..||++. .++.+|+..++.. +... ..++ +.|-+-.-+ +.+.. .++|.|.|
T Consensus 8 ~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~---~d~~-~~~~---~~L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 8 FTQLAKIVDYMKKRHQHPLTLDEILDYLSL---LDIG-PKLK---EWLKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhhHHHHHHHHHhcCCCCccHHHHHHHHhc---cCcc-HHHH---HHHHhhhhccCceeccC-CCEEEecc
Confidence 445688999999975 8888888776642 3333 2222 333333333 44443 46999875
No 172
>PRK11050 manganese transport regulator MntR; Provisional
Probab=40.05 E-value=41 Score=29.85 Aligned_cols=43 Identities=16% Similarity=0.249 Sum_probs=35.9
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
.|+.++...+.++..+|++.++++...+.+.+..|.. .+++.+
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~--~GlI~r 83 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLAR--DGLVEM 83 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 4555677778899999999999999999999999964 577764
No 173
>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=39.98 E-value=28 Score=33.23 Aligned_cols=47 Identities=15% Similarity=0.236 Sum_probs=35.9
Q ss_pred hhcCCCCC-ChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q 009222 484 IMKTRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 537 (540)
Q Consensus 484 imK~~k~l-~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~ 537 (540)
.++....+ +-.+|.. .|.++...++++|+.|++.|+|.|..+ +++|+
T Consensus 17 ~~~~G~~LPsE~eLa~------~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 17 QYKEGDYLPSEHELMD------QYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred CCCCCCCCcCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 44544445 3555554 788999999999999999999999874 57765
No 174
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=39.97 E-value=41 Score=29.34 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=35.3
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
.|..+.+..+..++.+|++.++++...+...|..|. +.|++..
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~--~~Gli~~ 54 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD--KDEYLIY 54 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH--HCCCEEE
Confidence 344556677888999999999999999999999996 4577764
No 175
>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=39.22 E-value=70 Score=24.87 Aligned_cols=48 Identities=13% Similarity=0.349 Sum_probs=37.6
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+++.|=+.-....++.-.+|++.++++...++..+..|- ..|+|...|
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le--~lGlve~~p 57 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE--ELGLVESQP 57 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH--HCCCccCCC
Confidence 344444455566899999999999999999999999995 478887543
No 176
>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=39.10 E-value=42 Score=27.13 Aligned_cols=38 Identities=16% Similarity=0.230 Sum_probs=31.7
Q ss_pred CCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 487 TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 487 ~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
....+++.+|...+ -.+.+.+.+.|..|.++|+|+|..
T Consensus 44 ~~~~is~~eLa~~~------g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAELT------GLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeeeec
Confidence 56788888887633 467889999999999999999876
No 177
>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=38.91 E-value=40 Score=26.81 Aligned_cols=54 Identities=24% Similarity=0.316 Sum_probs=40.0
Q ss_pred HHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC--CCCCceee
Q 009222 479 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK--NNPQIYNY 538 (540)
Q Consensus 479 a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~--~~~~~y~Y 538 (540)
..|++.+.. +.+.+++|...+. ..+...+.+++..|.+.|.|.|.. ..|....|
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~-----~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y 63 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLP-----GISPKVLSQRLKELEEAGLVERRVYPEVPPRVEY 63 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHST-----TS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcc-----hhHHHHHHHHHHHHHHcchhhcccccCCCCCCcc
Confidence 456777777 7888999877542 367899999999999999999963 33444455
No 178
>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=38.88 E-value=69 Score=21.58 Aligned_cols=40 Identities=23% Similarity=0.381 Sum_probs=28.8
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
++..+..++.++- .+.+|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3555555554443 245899999999999999988777654
No 179
>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=38.45 E-value=39 Score=24.85 Aligned_cols=37 Identities=19% Similarity=0.466 Sum_probs=30.4
Q ss_pred CCCc-cHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 386 AQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 386 ~~~~-t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
.+.+ |..+|++..|++...++++|..|.. .+++...+
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~--~g~i~~~~ 58 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEA--EGLIERRP 58 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEET
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHH--CCcEEEEC
Confidence 3678 9999999999999999999999975 68887654
No 180
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=38.38 E-value=22 Score=27.43 Aligned_cols=40 Identities=13% Similarity=0.376 Sum_probs=31.8
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCC
Q 009222 386 AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 426 (540)
Q Consensus 386 ~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 426 (540)
.+++.++.|+..+|.+.+.+.....+.. .+.+++.+.|.|
T Consensus 23 ggPvGl~tlA~~l~ed~~Tie~v~EPyL-iq~G~I~RT~rG 62 (76)
T PF05491_consen 23 GGPVGLDTLAAALGEDKETIEDVIEPYL-IQIGFIQRTPRG 62 (76)
T ss_dssp TS-B-HHHHHHHTTS-HHHHHHTTHHHH-HHTTSEEEETTE
T ss_pred CCCeeHHHHHHHHCCCHhHHHHHhhHHH-HHhhhHhhCccH
Confidence 3789999999999999999999999886 578899887754
No 181
>PRK09462 fur ferric uptake regulator; Provisional
Probab=38.37 E-value=77 Score=27.86 Aligned_cols=51 Identities=16% Similarity=0.169 Sum_probs=39.8
Q ss_pred HHHHhhhcC--CCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 479 AAIVRIMKT--RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 479 a~IVRimK~--~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
-+|.++|.. .+-++.++|...+.+.. ..++..-|=+.|+.|.+.|.|.+-.
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~-~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMG-EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 345566654 36999999998887653 4577888999999999999998853
No 182
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=38.31 E-value=43 Score=35.55 Aligned_cols=57 Identities=18% Similarity=0.274 Sum_probs=49.7
Q ss_pred HHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceeec
Q 009222 477 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYL 539 (540)
Q Consensus 477 i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Yi 539 (540)
-+.+|++.++..+.++-.+|-+ .|..+...+.+.|..|+.+|++++-+.+..-+.||
T Consensus 403 ~~~~il~~~~en~~~T~~~L~~------~l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v 459 (467)
T COG2865 403 RQEKILELIKENGKVTARELRE------ILGISSETIRRRIANLVKRGLLKQLGSSGRGTWYV 459 (467)
T ss_pred HHHHHHHHHhhccccCHHHHHH------HhCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEe
Confidence 3489999999999999999886 44588999999999999999999988777777776
No 183
>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=38.13 E-value=55 Score=31.17 Aligned_cols=47 Identities=15% Similarity=0.379 Sum_probs=35.9
Q ss_pred hhcCCCCC-ChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q 009222 484 IMKTRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 537 (540)
Q Consensus 484 imK~~k~l-~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~ 537 (540)
..+....+ +-.+|.. +|.++...++++|+.|.++|+|.|..+ .++|+
T Consensus 25 ~~~~G~~LPsE~eLa~------~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 25 HLRAGDYLPAEMQLAE------RFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred CCCCCCcCcCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 44444455 4455555 788999999999999999999999864 56765
No 184
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=38.00 E-value=56 Score=31.30 Aligned_cols=47 Identities=19% Similarity=0.383 Sum_probs=36.9
Q ss_pred hhcCCCCC-ChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q 009222 484 IMKTRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 537 (540)
Q Consensus 484 imK~~k~l-~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~ 537 (540)
.++....+ +-.+|.+ .|.++...++++|+.|+..|+|.|..+ .++|+
T Consensus 22 ~~~~G~~LPsE~eL~~------~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 69 (240)
T PRK09764 22 ELKPGDALPTESALQT------EFGVSRVTVRQALRQLVEQQILESIQG-SGTYV 69 (240)
T ss_pred CCCCCCcCCCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 55556666 4566665 778999999999999999999999874 56665
No 185
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=37.80 E-value=55 Score=31.08 Aligned_cols=47 Identities=15% Similarity=0.243 Sum_probs=36.7
Q ss_pred hhcCCCCC-ChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q 009222 484 IMKTRKVL-SHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 537 (540)
Q Consensus 484 imK~~k~l-~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~ 537 (540)
.++....+ +..+|.+ .|.++...++++|+.|++.|+|.|..+ +++|+
T Consensus 18 ~~~~g~~LPsE~eLa~------~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 65 (230)
T TIGR02018 18 EWPPGHRIPSEHELVA------QYGCSRMTVNRALRELTDAGLLERRQG-VGTFV 65 (230)
T ss_pred CCCCCCcCcCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 44555556 5556665 788999999999999999999999874 56664
No 186
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=37.68 E-value=43 Score=31.88 Aligned_cols=58 Identities=16% Similarity=0.298 Sum_probs=43.9
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCC
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 442 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 442 (540)
+-..++.+|.++..||+.+|.+.|+-|...|+.+|..++ ++.+.++ ...+|.+-+.|.
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 444667889999999999999999999999999999885 4544321 235677666653
No 187
>PRK06474 hypothetical protein; Provisional
Probab=37.44 E-value=77 Score=28.96 Aligned_cols=53 Identities=11% Similarity=0.214 Sum_probs=42.1
Q ss_pred EEEcHHHHHHHHHhcCCCC-ccHHHHHHHh-CCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 370 LAVSLFQTVVLMLFNDAQK-LSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 370 l~~s~~Q~~iLl~Fn~~~~-~t~~ei~~~~-~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+-.++.-..||..+-..++ +|..+|++.+ +++...+-++|..|. +.||+....
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~~ 61 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVVK 61 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEee
Confidence 3456677788877766554 9999999999 799999999999996 478887643
No 188
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=37.26 E-value=55 Score=29.18 Aligned_cols=45 Identities=13% Similarity=0.270 Sum_probs=36.9
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+|..++.+.......+|++.+++++..+...++-|. +.|++...+
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~~ 58 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYEP 58 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEec
Confidence 444555577889999999999999999999999995 578887644
No 189
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=37.01 E-value=42 Score=34.51 Aligned_cols=64 Identities=28% Similarity=0.389 Sum_probs=41.6
Q ss_pred eeEeccCCceEEEEEEecCceEEEE-------EcHHHHHHHHHhcCC--CCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 347 RLMWQNSLGHCVLKAEFPKGKKELA-------VSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 347 ~L~w~~~l~~~~l~~~~~~~~~~l~-------~s~~Q~~iLl~Fn~~--~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
=+.+.+.||+.|=++--+.+. |. -+-+-..||-++-+. ..+|+++|++.|||..+++...|.+|
T Consensus 281 LIdFSYeLSr~E~~~GsPEKP--LSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L 353 (396)
T KOG2747|consen 281 LIDFSYELSRREGKIGSPEKP--LSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSL 353 (396)
T ss_pred hhhhhhhhhcccCcCCCCCCC--cchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhh
Confidence 356777888876554333221 21 122333444443332 23999999999999999999999988
No 190
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=36.90 E-value=77 Score=21.90 Aligned_cols=35 Identities=23% Similarity=0.484 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhh
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 411 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 411 (540)
+...|+.+.-+. .|+.++++.+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 344555444332 69999999999999999888764
No 191
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=36.71 E-value=22 Score=27.82 Aligned_cols=46 Identities=22% Similarity=0.363 Sum_probs=36.5
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
.-.|+-.+...+.+++.+|.+.+ ..+...+.+.+..|.+.|||++.
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~l------~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEEL------GLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHHT------T--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHHh------CcCHHHHHHHHHHHHHCCCEEEE
Confidence 34577777788889999988633 47889999999999999999985
No 192
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=36.39 E-value=34 Score=32.85 Aligned_cols=47 Identities=15% Similarity=0.276 Sum_probs=35.5
Q ss_pred hhcCCCCCC-hHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q 009222 484 IMKTRKVLS-HTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 537 (540)
Q Consensus 484 imK~~k~l~-~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~ 537 (540)
.++....++ -.+|.. .|.++...++++|+.|++.|+|.|..+ +++|+
T Consensus 26 ~~~~g~kLPsE~eLa~------~~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 26 VYQAGQQIPTENELCT------QYNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred CCCCCCcCcCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 455444443 445544 788999999999999999999999864 57765
No 193
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=36.36 E-value=34 Score=30.83 Aligned_cols=58 Identities=17% Similarity=0.379 Sum_probs=39.0
Q ss_pred HHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCC
Q 009222 380 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 442 (540)
Q Consensus 380 Ll~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 442 (540)
++.++. +++|++||++.||++...+-..+.-|.. .+|+.+.-..+ .-.+.|..-.+|.
T Consensus 34 ilyls~-~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~--~~lV~~~~~~G--~Rk~~F~a~~df~ 91 (177)
T COG1510 34 ILYLSR-KPLTLDEIAEALGMSKSNVSMGLKKLQD--WNLVKKVFEKG--DRKDYFEAEKDFS 91 (177)
T ss_pred hheecC-CCccHHHHHHHHCCCcchHHHHHHHHHh--cchHHhhhccC--cchhhhcccchHH
Confidence 444544 7899999999999999988888888853 56665432100 1134566666665
No 194
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=36.32 E-value=70 Score=24.64 Aligned_cols=44 Identities=14% Similarity=0.171 Sum_probs=31.7
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
-+.||.... .++.+..+|+..+|++...+.+.|..|.. .+++..
T Consensus 8 i~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~--~gLI~~ 51 (77)
T PF14947_consen 8 IFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEE--KGLIKK 51 (77)
T ss_dssp HHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHH--TTSEEE
T ss_pred HHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CcCeeC
Confidence 355677665 57789999999999999999999999974 678743
No 195
>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=36.25 E-value=53 Score=24.13 Aligned_cols=45 Identities=13% Similarity=0.337 Sum_probs=32.2
Q ss_pred HHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCC
Q 009222 481 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNN 532 (540)
Q Consensus 481 IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~ 532 (540)
|...+...+ ++..++.. .+..+...+.+.++.|..+|+|.+..+.
T Consensus 12 il~~l~~~~-~~~~ei~~------~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 12 ILRLLLEGP-LTVSELAE------RLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHCC-cCHHHHHH------HHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 344444444 77777654 3346788899999999999999986543
No 196
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=34.99 E-value=2.4e+02 Score=26.06 Aligned_cols=111 Identities=16% Similarity=0.149 Sum_probs=62.5
Q ss_pred ChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEE--e-------cCceEEEEEcHHHHHHHHHhcCCCCccHHHHH
Q 009222 325 PHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAE--F-------PKGKKELAVSLFQTVVLMLFNDAQKLSFQDIK 395 (540)
Q Consensus 325 P~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~--~-------~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei~ 395 (540)
|..+..+++....-|.... |-+.....=|...+... + ......-..|...+-+|-..--+.++|-.+|.
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 3578999999999998653 33333222222222221 0 00111223455555556555555789999999
Q ss_pred HHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCC
Q 009222 396 DATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 442 (540)
Q Consensus 396 ~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 442 (540)
+..|++. ..++..|.. .+++...+..........|.++..|-
T Consensus 112 ~irGv~~---~~ii~~L~~--~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNS---DGALQTLLA--KGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCH---HHHHHHHHH--CCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999996 445666643 57876543221112334566777764
No 197
>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=34.47 E-value=1e+02 Score=22.05 Aligned_cols=49 Identities=16% Similarity=0.219 Sum_probs=33.5
Q ss_pred HHHHHHhhh-cCCCCCC-hHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 477 VDAAIVRIM-KTRKVLS-HTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 477 i~a~IVRim-K~~k~l~-~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
|...|.+.. +....++ ..+|.. .|..+...+.+.|..|.++|+|.+.++
T Consensus 10 i~~~i~~~~~~~~~~~~~~~~la~------~~~is~~~v~~~l~~L~~~G~i~~~~~ 60 (66)
T cd07377 10 LREAILSGELKPGDRLPSERELAE------ELGVSRTTVREALRELEAEGLVERRPG 60 (66)
T ss_pred HHHHHHcCCCCCCCCCCCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 334444443 3344444 666554 556889999999999999999988753
No 198
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=34.15 E-value=81 Score=28.95 Aligned_cols=44 Identities=14% Similarity=0.149 Sum_probs=36.1
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
-++.-++.++..|..+|++.+|++...+.++|-.|. +.+.+...
T Consensus 17 ~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~--~~~~v~~~ 60 (183)
T PHA03103 17 KEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQ--REGMVYMS 60 (183)
T ss_pred HHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHH--hcCceecC
Confidence 456667778899999999999999999999999995 45566544
No 199
>PHA02591 hypothetical protein; Provisional
Probab=34.06 E-value=50 Score=25.49 Aligned_cols=25 Identities=24% Similarity=0.480 Sum_probs=22.1
Q ss_pred CCccHHHHHHHhCCCHHHHHHHhhh
Q 009222 387 QKLSFQDIKDATGIEDKELRRTLQS 411 (540)
Q Consensus 387 ~~~t~~ei~~~~~i~~~~l~~~L~~ 411 (540)
..+|.++|++.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 4689999999999999999888765
No 200
>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=33.20 E-value=1.9e+02 Score=21.35 Aligned_cols=39 Identities=23% Similarity=0.336 Sum_probs=30.0
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceee
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 420 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL 420 (540)
||-.+.+ ...|..+|++.+|++...+.+.+..|.. .++.
T Consensus 5 il~~L~~-~~~~~~eLa~~l~vS~~tv~~~l~~L~~--~g~~ 43 (69)
T TIGR00122 5 LLALLAD-NPFSGEKLGEALGMSRTAVNKHIQTLRE--WGVD 43 (69)
T ss_pred HHHHHHc-CCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCe
Confidence 3444444 3578999999999999999999999954 4553
No 201
>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=33.15 E-value=61 Score=31.94 Aligned_cols=58 Identities=21% Similarity=0.362 Sum_probs=33.5
Q ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCC
Q 009222 374 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 441 (540)
Q Consensus 374 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 441 (540)
-+--.|.-+|.++.-||+.+|.+.|+-|+..|+..|..++ ++.+.++ ....|.+=+.|
T Consensus 216 eL~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 216 ELLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 3555778899999999999999999999999999999884 5655432 23567665555
No 202
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=32.68 E-value=3e+02 Score=29.53 Aligned_cols=45 Identities=13% Similarity=0.258 Sum_probs=37.8
Q ss_pred HHHHHHHHhcCCCC-ccHHHHHHHhCCCHHHHHHHhhhhhcCCceeee
Q 009222 375 FQTVVLMLFNDAQK-LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 421 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~-~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 421 (540)
.+..||..+.+.+. ++.+++++.+|++.+.+...+.+|.. .+++.
T Consensus 4 ~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~--kg~v~ 49 (492)
T PLN02853 4 AEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHG--FRYVD 49 (492)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHh--CCCEE
Confidence 57788988888774 89999999999999999999999964 35554
No 203
>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=32.66 E-value=6.3e+02 Score=28.59 Aligned_cols=129 Identities=16% Similarity=0.246 Sum_probs=75.1
Q ss_pred HHHHHHHHHHHHHHHHhhc-CChHHHHHHHHHHHHHHHHHHchhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Q 009222 16 FLECTSEFYAAEGMKYMQQ-SDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDG 94 (540)
Q Consensus 16 ~l~~t~~yY~~~~~~~~~~-~~~~~Yl~~v~~~l~~E~~~~~~~l~~~s~~~l~~~~~~~Li~~~~~~ll~~~~~~ll~~ 94 (540)
+++...-||...... +. ..+.++.+.+...++++.+.+-..+-.....++.+.+. |...++..
T Consensus 552 ~leN~~~~~e~l~~~--~~~~~l~~~~~~A~~~~~~~~~~Y~~~~l~r~~~kL~~F~~--------------gve~l~~~ 615 (701)
T PF09763_consen 552 LLENYHHFYEELSQL--KINSVLEEFRKEAKQIYDEHLEAYVTFLLRRPFGKLLDFFE--------------GVEALLQT 615 (701)
T ss_pred HHHHHHHHHHHHhhc--cchhhHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHH--------------HHHHHHhc
Confidence 455566666666653 33 56778899999988888876544433344444444332 33333332
Q ss_pred -----------CChhhHHHHHHHhhh--c-cchHHHHHHHHHHHHHHhh------hhhcCchhhHHHHHHHHHHHHHHHH
Q 009222 95 -----------HRTEDLQRMYSLFSR--V-NALESLRQALAMYIRRTGH------GIVMDEEKDKDMVSSLLEFKASLDT 154 (540)
Q Consensus 95 -----------~~~~~l~~ly~l~~~--~-~~~~~l~~~~~~~i~~~g~------~~~~~~~~~~~~i~~l~~l~~~~~~ 154 (540)
..+..|+.+-.-+.. + .+++.+.+.+.+|+...+. .++...+ ..+-+..+..|.++..
T Consensus 616 ~~~~ei~~~~~ySk~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~vW--~~~q~~~i~~~~~l~~ 693 (701)
T PF09763_consen 616 VSPEEISYQAAYSKQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQVVW--SAMQEEFIRQYERLET 693 (701)
T ss_pred cCchhcccchhccHHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHHHH--HHHHHHHHHHHHHHHH
Confidence 124556666555332 2 6777777777777722111 1111111 2455668888999999
Q ss_pred HHHHhcCC
Q 009222 155 IWEQSFSK 162 (540)
Q Consensus 155 l~~~~F~~ 162 (540)
++..|+.+
T Consensus 694 li~~~Y~g 701 (701)
T PF09763_consen 694 LIQKCYPG 701 (701)
T ss_pred HHHHhCCC
Confidence 99999864
No 204
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=32.56 E-value=69 Score=27.84 Aligned_cols=36 Identities=17% Similarity=0.282 Sum_probs=27.2
Q ss_pred CCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 489 KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 489 k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
..++..+|.. .+..+...+.+.|+.|.++|||+|..
T Consensus 45 ~~~t~~eLa~------~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 45 PEQSQIQLAK------AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred CCCCHHHHHH------HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 4566666554 33466778999999999999999964
No 205
>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=32.37 E-value=65 Score=27.03 Aligned_cols=60 Identities=15% Similarity=0.180 Sum_probs=41.6
Q ss_pred HHHHHhhhcC-CCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q 009222 478 DAAIVRIMKT-RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 538 (540)
Q Consensus 478 ~a~IVRimK~-~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Y 538 (540)
.-+|..+|++ .+.++.++|...+.+. ...++..-|=+.|+.|.+.|.|.+-..+.+...|
T Consensus 10 R~~Il~~l~~~~~~~ta~ei~~~l~~~-~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 10 RLAILELLKESPEHLTAEEIYDKLRKK-GPRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp HHHHHHHHHHHSSSEEHHHHHHHHHHT-TTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHhhhc-cCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 3345555555 4588999988877643 4567888999999999999999996544344443
No 206
>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=32.29 E-value=67 Score=23.63 Aligned_cols=23 Identities=22% Similarity=0.567 Sum_probs=19.3
Q ss_pred cCCCCccHHHHHHHhCCCHHHHH
Q 009222 384 NDAQKLSFQDIKDATGIEDKELR 406 (540)
Q Consensus 384 n~~~~~t~~ei~~~~~i~~~~l~ 406 (540)
..++.+++.+|++.+|+++..+.
T Consensus 18 ~~~g~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 18 ESNGKIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred HhCCCccHHHHHHHHCCCHHHHH
Confidence 34578999999999999987764
No 207
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=31.99 E-value=69 Score=30.23 Aligned_cols=46 Identities=15% Similarity=0.213 Sum_probs=38.5
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCcee
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRV 419 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~i 419 (540)
.+|+-+..||.+.-++ .|.+|||+.+++++..++.++..+.. |.++
T Consensus 143 ~LS~RE~eVL~Lia~G--~SnkEIA~~L~IS~~TVk~hvs~I~~-KLgv 188 (217)
T PRK13719 143 KVTKYQNDVFILYSFG--FSHEYIAQLLNITVGSSKNKISEILK-FFGI 188 (217)
T ss_pred CCCHHHHHHHHHHHCC--CCHHHHHHHhCCCHHHHHHHHHHHHH-HhCC
Confidence 4788999999888774 89999999999999999999988863 4443
No 208
>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=31.98 E-value=49 Score=26.30 Aligned_cols=46 Identities=11% Similarity=0.247 Sum_probs=34.9
Q ss_pred HHHHHHhcCCCCccHHHHHHHh--CCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 377 TVVLMLFNDAQKLSFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 377 ~~iLl~Fn~~~~~t~~ei~~~~--~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
+.||-..-+++-+|..++++.+ .++...+...+..|+ |.+++.+++
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLI--KkglIEKSG 66 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLI--KKGLIEKSG 66 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHH--HcCcccccC
Confidence 4566666677889999999977 788899999999995 678998754
No 209
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=31.82 E-value=58 Score=22.43 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHHHhh
Q 009222 390 SFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 390 t~~ei~~~~~i~~~~l~~~L~ 410 (540)
|+.||++..|++...+-+.|+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 689999999999999877765
No 210
>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=31.79 E-value=96 Score=27.95 Aligned_cols=59 Identities=19% Similarity=0.311 Sum_probs=44.4
Q ss_pred HHHHHHHhcCC-CCccHHHHHHHh--CCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 009222 376 QTVVLMLFNDA-QKLSFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 440 (540)
Q Consensus 376 Q~~iLl~Fn~~-~~~t~~ei~~~~--~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 440 (540)
...|+..|..+ .++|..+|...+ +++...+.++|..|+. +..|..+. ++...+|..|.+
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~-~g~i~~K~-----~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVE-EGKIVEKE-----YGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHh-CCCeeeee-----ecceEEEeeCcc
Confidence 35677777765 689999999999 5899999999999985 44555543 334567887766
No 211
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.61 E-value=80 Score=21.35 Aligned_cols=31 Identities=19% Similarity=0.320 Sum_probs=18.7
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
.+..+-+ ..+|..+|++.+|.+...+.+.|.
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 3434433 458999999999999998876653
No 212
>PLN03239 histone acetyltransferase; Provisional
Probab=31.06 E-value=78 Score=32.09 Aligned_cols=45 Identities=20% Similarity=0.324 Sum_probs=33.7
Q ss_pred cHHHHHHHHHhcCC----CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 373 SLFQTVVLMLFNDA----QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~----~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
+-+...|+-.+-+. ..+|+++|++.|||..+++..+|+.| ++|..
T Consensus 265 ~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l-----~~l~~ 313 (351)
T PLN03239 265 PYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL-----GILKF 313 (351)
T ss_pred HHHHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC-----CcEEE
Confidence 33455666554332 46999999999999999999999988 56653
No 213
>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=31.04 E-value=1.1e+02 Score=26.43 Aligned_cols=50 Identities=16% Similarity=0.092 Sum_probs=39.7
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHh----CCCHHHHHHHhhhhhcCCceeeecC
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDAT----GIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~----~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
+|..+..|+..+=+.++.|..+|.+.+ |.+...+...|..|. +.|++.+.
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~--~KG~v~~~ 55 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLV--DKGCLTTE 55 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHH--HCCceeee
Confidence 467788888887677789999977765 788899999999996 45788653
No 214
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=30.94 E-value=1e+02 Score=23.64 Aligned_cols=44 Identities=18% Similarity=0.335 Sum_probs=27.8
Q ss_pred HHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 480 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 480 ~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
-|-+.++ .+..+..+|.. .-..+...+.+.|+.|.++|+|+.++
T Consensus 10 ~IL~~l~-~~~~~~t~i~~------~~~L~~~~~~~yL~~L~~~gLI~~~~ 53 (77)
T PF14947_consen 10 DILKILS-KGGAKKTEIMY------KANLNYSTLKKYLKELEEKGLIKKKD 53 (77)
T ss_dssp HHHHHH--TT-B-HHHHHT------TST--HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHH-cCCCCHHHHHH------HhCcCHHHHHHHHHHHHHCcCeeCCC
Confidence 3344444 56666666664 33577889999999999999996643
No 215
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=30.76 E-value=75 Score=30.10 Aligned_cols=46 Identities=22% Similarity=0.305 Sum_probs=37.5
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
+.+.+-..++...+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 9 ~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LE--e~GlI~R~ 54 (217)
T PRK14165 9 KLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLE--DEGYITRT 54 (217)
T ss_pred HHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 44445555666789999999999999999999999995 57888764
No 216
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=29.84 E-value=48 Score=31.81 Aligned_cols=47 Identities=13% Similarity=0.292 Sum_probs=35.1
Q ss_pred hhcCCCCCC-hHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q 009222 484 IMKTRKVLS-HTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYN 537 (540)
Q Consensus 484 imK~~k~l~-~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~ 537 (540)
..+..-.++ -.+|.. +|.++.-.++++|..|.+.|+|.|..+ +++|+
T Consensus 24 ~~~~G~~LPsE~eLa~------~f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 24 ELPPGDKLPSERELAE------QFGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred CCCCCCCCCCHHHHHH------HHCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 445544444 334443 789999999999999999999999863 57775
No 217
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=29.81 E-value=78 Score=29.42 Aligned_cols=44 Identities=20% Similarity=0.195 Sum_probs=37.8
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCce
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVR 418 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~ 418 (540)
.|.-+.-||.+.-+ +.|..||++.++++...++.++..+.. |.+
T Consensus 151 Lt~rE~evl~~~~~--G~s~~eIA~~l~iS~~TV~~h~~~i~~-Kl~ 194 (216)
T PRK10840 151 LSPKESEVLRLFAE--GFLVTEIAKKLNRSIKTISSQKKSAMM-KLG 194 (216)
T ss_pred CCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHH-HcC
Confidence 78889999988865 489999999999999999999998864 444
No 218
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=29.78 E-value=47 Score=32.59 Aligned_cols=47 Identities=9% Similarity=0.156 Sum_probs=41.4
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
...|+..+++++.++.++|.+ .|.++..-|.+=|..|-++|++.|.-
T Consensus 19 ~~~Il~~L~~~~~vtv~eLa~------~l~VS~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 19 REQIIQRLRQQGSVQVNDLSA------LYGVSTVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHcCCEeHHHHHH------HHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 456788999999999999987 67899999999999999999999854
No 219
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=29.64 E-value=1.2e+02 Score=31.77 Aligned_cols=38 Identities=21% Similarity=0.347 Sum_probs=33.8
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 383 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 383 Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
+.....+|.++|++.++++...+++.|..|. +.+++.+
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~--~agLI~~ 342 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELA--RIGLLRR 342 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--hCCCeEe
Confidence 5666899999999999999999999999996 5789875
No 220
>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=29.27 E-value=65 Score=24.27 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=28.8
Q ss_pred CccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 388 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 388 ~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
.+|-++|++.+|++...+.+.|..|. +.+++..
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~--~~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLK--DEGIIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHH--HTTSEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 47889999999999999999999996 4678864
No 221
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=29.14 E-value=90 Score=28.51 Aligned_cols=41 Identities=10% Similarity=0.173 Sum_probs=36.3
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
+|+-+..||.+..+ +.|..||++.+++++..++..+..+..
T Consensus 134 LSpRErEVLrLLAq--GkTnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 134 FSVTERHLLKLIAS--GYHLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred CCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 78999999988876 478999999999999999999888864
No 222
>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=28.87 E-value=89 Score=27.32 Aligned_cols=38 Identities=16% Similarity=0.268 Sum_probs=29.0
Q ss_pred EcHHHHHHHHH-hcCCCCccHHHHHHHhCCCHHHHHHHhhh
Q 009222 372 VSLFQTVVLML-FNDAQKLSFQDIKDATGIEDKELRRTLQS 411 (540)
Q Consensus 372 ~s~~Q~~iLl~-Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 411 (540)
+|+-|..|+.+ +- ..+|.+||++.+|+|...+...+.-
T Consensus 112 L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 112 LPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 56667666665 43 4689999999999999988776643
No 223
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=28.82 E-value=1.3e+02 Score=26.33 Aligned_cols=60 Identities=18% Similarity=0.153 Sum_probs=44.6
Q ss_pred HHHHHhhhcCC-CCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q 009222 478 DAAIVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 538 (540)
Q Consensus 478 ~a~IVRimK~~-k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Y 538 (540)
..+|.++|.+. +.++.++|..++.+. ....+...|=+.++.|.+.|+|.+-+...+...|
T Consensus 23 R~~vl~~L~~~~~~~sAeei~~~l~~~-~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y 83 (145)
T COG0735 23 RLAVLELLLEADGHLSAEELYEELREE-GPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRY 83 (145)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHh-CCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEE
Confidence 34566677654 569999999888774 3456788899999999999999997654444443
No 224
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=28.78 E-value=4.7e+02 Score=24.12 Aligned_cols=32 Identities=19% Similarity=0.417 Sum_probs=24.4
Q ss_pred HHhcCCCC-ccHHHHHHHhCCC-HHHHHHHhhhh
Q 009222 381 MLFNDAQK-LSFQDIKDATGIE-DKELRRTLQSL 412 (540)
Q Consensus 381 l~Fn~~~~-~t~~ei~~~~~i~-~~~l~~~L~~L 412 (540)
++|-..++ +|+++|++.++++ .+.+...+.-|
T Consensus 9 lLF~sg~pgls~~~La~il~~~~~~~~~~~l~~l 42 (186)
T TIGR00281 9 LLFVSGEPGVTLAELVRILGKEKAEKLNAIMELL 42 (186)
T ss_pred HHHHcCCCCCCHHHHHHHhCCCchHHHHHHHHHH
Confidence 45666776 9999999999998 44666666655
No 225
>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=28.75 E-value=82 Score=29.36 Aligned_cols=46 Identities=11% Similarity=0.216 Sum_probs=36.1
Q ss_pred HHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 480 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 480 ~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
.|...+..++.++..+|...+ ..+...+.+.|..|.++|+|+|.+.
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l------~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKL------GKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 455666666778888877633 4677789999999999999999874
No 226
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=28.56 E-value=81 Score=29.63 Aligned_cols=42 Identities=17% Similarity=0.299 Sum_probs=37.1
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
..|.-|..||.++-+. +|..||++.+++++.+++.+...+..
T Consensus 148 ~LT~RE~eVL~lla~G--~snkeIA~~L~iS~~TVk~h~~~i~~ 189 (211)
T COG2197 148 LLTPRELEVLRLLAEG--LSNKEIAEELNLSEKTVKTHVSNILR 189 (211)
T ss_pred CCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHhHHHHHHHHHHH
Confidence 4789999999888764 89999999999999999999988864
No 227
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=28.46 E-value=1e+02 Score=20.83 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHhhcCCCCcHHHHHHHHHH
Q 009222 166 FCNTIKDAFEYLINLRQNRPAELIAKFLDE 195 (540)
Q Consensus 166 f~~~l~~~f~~~ln~~~~~~~e~La~y~d~ 195 (540)
+...+.+|+.++....+....++||.|+-.
T Consensus 10 v~p~L~~gL~~l~~~rP~DPi~~La~~Ll~ 39 (42)
T PF05186_consen 10 VGPVLTEGLAELAKERPEDPIEFLAEYLLK 39 (42)
T ss_dssp THHHHHHHHHHHHHH--SSHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHCCCChHHHHHHHHHH
Confidence 456778889999888888899999999754
No 228
>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=28.42 E-value=34 Score=24.28 Aligned_cols=23 Identities=22% Similarity=0.458 Sum_probs=18.9
Q ss_pred CccHHHHHHHhCCCHHHHHHHhh
Q 009222 388 KLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 388 ~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
.+++.||++.+|++.+.+...|.
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~ 25 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLF 25 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-
T ss_pred ceEHHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999888773
No 229
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=28.25 E-value=1.4e+02 Score=21.29 Aligned_cols=41 Identities=17% Similarity=0.292 Sum_probs=35.3
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
.+|.-+..++.++.+. .+..||+..++++...+..++....
T Consensus 4 ~Lt~rE~~v~~l~~~G--~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 4 DLTPREREILRLVAQG--KSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred cCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4677888888888775 7999999999999999999988775
No 230
>PF11784 DUF3320: Protein of unknown function (DUF3320); InterPro: IPR021754 This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.
Probab=28.01 E-value=1.1e+02 Score=21.67 Aligned_cols=37 Identities=11% Similarity=0.144 Sum_probs=32.0
Q ss_pred HhhHHhHHHHHHhhhcCCCCCChHHHHHHHHHHcCCC
Q 009222 471 QDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFP 507 (540)
Q Consensus 471 ~~r~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~ 507 (540)
......|.+.|..|+..++.++.+.|+..+...+.|.
T Consensus 7 ~~~~~~L~~~i~~Iv~~EgPI~~~~L~~Ri~~a~G~~ 43 (52)
T PF11784_consen 7 PEYRPQLARMIRQIVEVEGPIHEDELARRIARAWGLS 43 (52)
T ss_pred hhHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHcCcc
Confidence 3456678999999999999999999999999988654
No 231
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=27.93 E-value=82 Score=29.45 Aligned_cols=42 Identities=14% Similarity=0.179 Sum_probs=37.2
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
..|.-+.-||.+.-+. +|..||++.+++++..++.++..+..
T Consensus 137 ~LT~RE~eVL~lla~G--~snkeIA~~L~iS~~TVk~h~~~I~~ 178 (207)
T PRK15411 137 SLSRTESSMLRMWMAG--QGTIQISDQMNIKAKTVSSHKGNIKR 178 (207)
T ss_pred cCCHHHHHHHHHHHcC--CCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 4899999999888764 78999999999999999999988864
No 232
>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=27.49 E-value=90 Score=31.13 Aligned_cols=41 Identities=17% Similarity=0.209 Sum_probs=33.8
Q ss_pred HHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 380 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 380 Ll~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
..++.+ .+.|.+||++.+|+++..+.+.|..|+. .+++.+.
T Consensus 16 fd~L~~-gp~t~~eLA~~~~~~~~~~~~lL~~L~~--lgll~~~ 56 (306)
T TIGR02716 16 FSHMAE-GPKDLATLAADTGSVPPRLEMLLETLRQ--MRVINLE 56 (306)
T ss_pred HHHHhc-CCCCHHHHHHHcCCChHHHHHHHHHHHh--CCCeEec
Confidence 334434 6889999999999999999999999975 7899764
No 233
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=27.46 E-value=66 Score=26.69 Aligned_cols=53 Identities=13% Similarity=0.288 Sum_probs=32.8
Q ss_pred HhHHHHHHhhhcCCCCCChHHHHHHHHHHc---CCCCChHHHHHHHHHhhhhccccc
Q 009222 475 YQVDAAIVRIMKTRKVLSHTLLITELFQQL---KFPIKPADLKKRIESLIDREYLER 528 (540)
Q Consensus 475 ~~i~a~IVRimK~~k~l~~~~L~~~v~~~l---~F~~~~~~ik~~Ie~Li~~eyi~r 528 (540)
..+.-.|+.+.-+++.-... +.++..+.. .|.|..+++=+++..|++.|+++|
T Consensus 17 aFlKlYiitm~e~~r~Yg~q-~Ld~lr~EFk~~Gy~P~hsEvYraLHeL~~dGilk~ 72 (122)
T PF02334_consen 17 AFLKLYIITMVEQERGYGLQ-LLDELRSEFKPLGYRPNHSEVYRALHELVDDGILKQ 72 (122)
T ss_dssp HHHHHHHHHHHHTT-EBCTC-HHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHhhhhcccchHHH-HHHHHHHHhhhcCCCCCHHHHHHHHHHHHhhhHHHH
Confidence 34677778877777732222 222233333 789999999999999999999965
No 234
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=26.96 E-value=92 Score=29.19 Aligned_cols=45 Identities=16% Similarity=0.171 Sum_probs=38.5
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCce
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVR 418 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~ 418 (540)
..|+-+.-||.++-+. .|..||++.+++++..++.++..+.. |.+
T Consensus 134 ~LT~RE~eVL~ll~~G--~snkeIA~~L~iS~~TV~~h~~~I~~-KLg 178 (207)
T PRK11475 134 MLSPTEREILRFMSRG--YSMPQIAEQLERNIKTIRAHKFNVMS-KLG 178 (207)
T ss_pred CCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH-HcC
Confidence 3789999999988764 89999999999999999999988864 443
No 235
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=26.93 E-value=91 Score=29.54 Aligned_cols=53 Identities=11% Similarity=0.107 Sum_probs=39.7
Q ss_pred HHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q 009222 480 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 538 (540)
Q Consensus 480 ~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~~~~~y~Y 538 (540)
+....++....++..+|-..+ ..+.+.+-+.|..|.++|||+|..+..+.+.+
T Consensus 11 allg~l~~~~~IS~~eLA~~L------~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~ 63 (217)
T PRK14165 11 ALLGAVNNTVKISSSEFANHT------GTSSKTAARILKQLEDEGYITRTIVPRGQLIT 63 (217)
T ss_pred HHHhccCCCCCcCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEEEcCCceEEE
Confidence 344566666778888877633 57889999999999999999998654444444
No 236
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=26.65 E-value=1.5e+02 Score=27.20 Aligned_cols=45 Identities=24% Similarity=0.347 Sum_probs=34.6
Q ss_pred HHHHHHhcCCC-CccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 377 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 377 ~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
..||..+...+ .+|.-+|++.+|++...+.++|-.|. +.+.+...
T Consensus 7 ~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~--~~~~v~~~ 52 (183)
T PHA02701 7 SLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLL--ESDAVSCE 52 (183)
T ss_pred HHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHh--hcCcEecC
Confidence 34565555554 69999999999999999999999995 45555444
No 237
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=26.60 E-value=1.2e+02 Score=26.54 Aligned_cols=39 Identities=18% Similarity=0.096 Sum_probs=31.6
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
+|.-|..|+.++ ...+|.+||++.+|++...+...+...
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 577788888886 467999999999999998887665544
No 238
>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=26.48 E-value=1.1e+02 Score=24.42 Aligned_cols=44 Identities=16% Similarity=0.200 Sum_probs=33.7
Q ss_pred HHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceee
Q 009222 375 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 420 (540)
Q Consensus 375 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL 420 (540)
....+...+....+++++++++.++++.+.+...+..++. .|.|
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~--~~~i 90 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLIS--NGLI 90 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHH--TTSS
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHH--CCCE
Confidence 3444555556778999999999999999999999988875 3444
No 239
>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=26.44 E-value=83 Score=23.16 Aligned_cols=51 Identities=16% Similarity=0.280 Sum_probs=38.4
Q ss_pred hhHHhHHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccc
Q 009222 472 DRQYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 528 (540)
Q Consensus 472 ~r~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r 528 (540)
+.--.+=|.|...+-+++.++..+|...+ + .+...+|.++-.||..+++.-
T Consensus 9 ~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t----~--l~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 9 EHFGEIVAKVGEVLLSRGRLTLREIVRRT----G--LSPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp HHHHHHHHHHHHHHHHC-SEEHHHHHHHH----T----HHHHHHHHHHHHHTTSEEE
T ss_pred HHcChHHHHHHHHHHHcCCcCHHHHHHHh----C--CCHHHHHHHHHHHHHcCCeee
Confidence 33344667888999999999999988755 2 668899999999999987753
No 240
>PRK04217 hypothetical protein; Provisional
Probab=26.39 E-value=1.2e+02 Score=25.46 Aligned_cols=41 Identities=17% Similarity=0.207 Sum_probs=28.6
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
.++.-|..++.+.. .+.+|++||++.+|++...+...|...
T Consensus 42 ~Lt~eereai~l~~-~eGlS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 42 FMTYEEFEALRLVD-YEGLTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34555555554332 255799999999999998887776544
No 241
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=26.28 E-value=67 Score=24.46 Aligned_cols=26 Identities=27% Similarity=0.396 Sum_probs=20.6
Q ss_pred CCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 387 QKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 387 ~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
..-|.+||++.+|++.+.+...+...
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 35699999999999999999888765
No 242
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=26.27 E-value=1e+02 Score=29.00 Aligned_cols=42 Identities=26% Similarity=0.390 Sum_probs=34.0
Q ss_pred EEcHHHHHHHHH------hcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 371 AVSLFQTVVLML------FNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 371 ~~s~~Q~~iLl~------Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
..|.-|..+|.. |+.-..+++.||++.+|+++..+..+|+.=
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 688999999954 444468999999999999998877777643
No 243
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=26.16 E-value=1.1e+02 Score=29.12 Aligned_cols=49 Identities=16% Similarity=0.187 Sum_probs=36.7
Q ss_pred EcHHHHHHHHHh---cCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 372 VSLFQTVVLMLF---NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 372 ~s~~Q~~iLl~F---n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
.+.-+.-+++.+ +....+|.++|++.+++++..++.++..|++ .+++..
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~--~~~~~~ 210 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN--CHILFT 210 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh--CCEEEE
Confidence 455554444332 3347799999999999999999999999964 778843
No 244
>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=25.96 E-value=2.3e+02 Score=22.94 Aligned_cols=51 Identities=14% Similarity=0.178 Sum_probs=41.4
Q ss_pred HHHHHHhhhcCCCCCChHHHHHHHHHHc--CCCCChHHHHHHHHHhhhhccccc
Q 009222 477 VDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLER 528 (540)
Q Consensus 477 i~a~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ik~~Ie~Li~~eyi~r 528 (540)
++-+|..++. .+.+.=-+|.+.+.+.. .+.++...+=..|..|-++|+|++
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 5566777776 46778888888877665 457888999999999999999998
No 245
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=25.85 E-value=5.6e+02 Score=24.08 Aligned_cols=41 Identities=17% Similarity=0.363 Sum_probs=32.1
Q ss_pred HHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 379 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 379 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
||.++-... .=+.+|+..+|++.+.+..+|..|- +.||+..
T Consensus 20 Il~lLt~~p-~yvsEiS~~lgvsqkAVl~HL~~LE--~AGlveS 60 (217)
T COG1777 20 ILQLLTRRP-CYVSEISRELGVSQKAVLKHLRILE--RAGLVES 60 (217)
T ss_pred HHHHHhcCc-hHHHHHHhhcCcCHHHHHHHHHHHH--HcCCchh
Confidence 444444434 5678999999999999999999995 5889865
No 246
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=25.77 E-value=2.2e+02 Score=22.55 Aligned_cols=54 Identities=22% Similarity=0.089 Sum_probs=40.6
Q ss_pred hHHHHHHhhhcCCCCCChHHHHHHHHHHcCCC--CChHHHHHHHHHhhhhccccccC
Q 009222 476 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFP--IKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 476 ~i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~--~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
+|..+|. -|+.+++.+...|...+....... --...++.+|..++++|.|.+-.
T Consensus 10 MI~eAI~-~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~k 65 (88)
T cd00073 10 MVTEAIK-ALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVK 65 (88)
T ss_pred HHHHHHH-HcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeec
Confidence 4555555 679999999999998887754211 12357889999999999998865
No 247
>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=25.72 E-value=77 Score=24.75 Aligned_cols=34 Identities=12% Similarity=0.177 Sum_probs=28.3
Q ss_pred CCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceee
Q 009222 385 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 420 (540)
Q Consensus 385 ~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL 420 (540)
....+++++|++.++++.+.+...+..++. .+.|
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~--~~~l 54 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIR--DGEI 54 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHH--CCCe
Confidence 457899999999999999999988888863 4555
No 248
>smart00753 PAM PCI/PINT associated module.
Probab=25.72 E-value=77 Score=24.75 Aligned_cols=34 Identities=12% Similarity=0.177 Sum_probs=28.3
Q ss_pred CCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceee
Q 009222 385 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 420 (540)
Q Consensus 385 ~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL 420 (540)
....+++++|++.++++.+.+...+..++. .+.|
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~--~~~l 54 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIR--DGEI 54 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHH--CCCe
Confidence 457899999999999999999988888863 4555
No 249
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.69 E-value=1.3e+02 Score=28.37 Aligned_cols=60 Identities=10% Similarity=0.119 Sum_probs=47.0
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCC
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 441 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 441 (540)
|=.|+....+.++.|.-.|+...|++-..+.-++..|.. .+++.+...|+ .-.|++|+++
T Consensus 176 ~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~--~Gii~~~~~Gr----~iiy~in~s~ 235 (240)
T COG3398 176 SKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEE--LGIIPEDREGR----SIIYSINPSI 235 (240)
T ss_pred HHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHH--cCCCcccccCc----eEEEEeCHHH
Confidence 446777788888899999999999999999999999953 68887654332 3468888875
No 250
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=25.21 E-value=99 Score=24.07 Aligned_cols=32 Identities=13% Similarity=0.158 Sum_probs=28.2
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 383 FNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 383 Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
...++..+..+|+..+++|++.+...|.-|+.
T Consensus 11 l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~ 42 (78)
T PRK15431 11 LALRGRMEAAQISQTLNTPQPMINAMLQQLES 42 (78)
T ss_pred HHHcCcccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34457789999999999999999999999984
No 251
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=25.08 E-value=92 Score=29.43 Aligned_cols=55 Identities=15% Similarity=0.297 Sum_probs=42.1
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCCC
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 442 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 442 (540)
.++.+|.+.+.||+..|++.+|-|+..|+.+|...+ +|.+.++ -...|.+-+.|.
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 456789999999999999999999999999998874 5554331 124566666664
No 252
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=24.60 E-value=99 Score=26.88 Aligned_cols=48 Identities=17% Similarity=0.272 Sum_probs=36.5
Q ss_pred HHHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 477 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 477 i~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
+-.+|.++.+..+..+..+|.. .+.++..-+...|..|.++|||.+..
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~------~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAE------ALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHH------HhCCChhHHHHHHHHHHHCCCEEEec
Confidence 3345667778888777777665 34577888999999999999998753
No 253
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=24.08 E-value=69 Score=24.62 Aligned_cols=32 Identities=13% Similarity=0.237 Sum_probs=22.5
Q ss_pred HHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 381 MLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 381 l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
....+-...|+.+|++.+|+++..+.+....|
T Consensus 27 ~~~~~~~~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 27 ENPDEIAFMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp H-HHHHCT--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred hCHHHHHHccHHHHHHHcCCCHHHHHHHHHHh
Confidence 33334468999999999999999998887766
No 254
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=23.93 E-value=81 Score=30.58 Aligned_cols=45 Identities=16% Similarity=0.310 Sum_probs=39.4
Q ss_pred HHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 479 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 479 a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
..|.+.++.++.++..+|.+ .|.++..-+.+-|..|-++|.|.|.
T Consensus 8 ~~Il~~l~~~~~~~~~ela~------~l~vS~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 8 QILLELLAQLGFVTVEKVIE------RLGISPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHcCCcCHHHHHH------HHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 34788999999999999887 4679999999999999999999884
No 255
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=23.76 E-value=1e+02 Score=27.08 Aligned_cols=40 Identities=23% Similarity=0.249 Sum_probs=28.6
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
++.-|-.|+.+.- ...+|.+||++.+|+|...++..+.--
T Consensus 111 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra 150 (162)
T TIGR02983 111 LPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRA 150 (162)
T ss_pred CCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4555656664422 346899999999999999887776543
No 256
>PRK09954 putative kinase; Provisional
Probab=23.74 E-value=86 Score=32.09 Aligned_cols=44 Identities=11% Similarity=0.274 Sum_probs=38.1
Q ss_pred HHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccc
Q 009222 479 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 528 (540)
Q Consensus 479 a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r 528 (540)
..|.+.++....++..+|-.. +.++...+.++|..|.++|+|+.
T Consensus 6 ~~il~~l~~~~~~s~~~la~~------l~~s~~~v~~~i~~L~~~g~i~~ 49 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADI------LQISRSRVAAHIMDLMRKGRIKG 49 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHH------HCCCHHHHHHHHHHHHHCCCcCC
Confidence 348899999999999998863 35899999999999999999975
No 257
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=23.53 E-value=1.3e+02 Score=31.79 Aligned_cols=43 Identities=28% Similarity=0.516 Sum_probs=32.7
Q ss_pred HHHHHHHHhc-CCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 375 FQTVVLMLFN-DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 375 ~Q~~iLl~Fn-~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
+-..||..+. ....+|+++|++.|||..+++..+|+.| ++|..
T Consensus 360 W~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l-----~~l~~ 403 (450)
T PLN00104 360 WTRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL-----NLIQY 403 (450)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC-----CCEEe
Confidence 3445554433 3468999999999999999999999988 56653
No 258
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=23.48 E-value=1.7e+02 Score=24.65 Aligned_cols=56 Identities=18% Similarity=0.215 Sum_probs=41.3
Q ss_pred EEEEEEecCceEEEEEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 357 CVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 357 ~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
.+|+..|.- ..-..++.-|..-+..|=.... ++.++++.+|++...++..|..++.
T Consensus 20 t~i~G~F~l-~~~~~L~~E~~~Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rLd~ii~ 75 (113)
T PF09862_consen 20 TEIEGEFEL-PWFARLSPEQLEFIKLFIKNRG-NLKEMEKELGISYPTVRNRLDKIIE 75 (113)
T ss_pred CEEEeeecc-chhhcCCHHHHHHHHHHHHhcC-CHHHHHHHHCCCcHHHHHHHHHHHH
Confidence 345555532 2334567778888888766433 8899999999999999999999874
No 259
>PRK09954 putative kinase; Provisional
Probab=23.47 E-value=1.4e+02 Score=30.49 Aligned_cols=42 Identities=12% Similarity=0.177 Sum_probs=35.9
Q ss_pred HHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceee
Q 009222 377 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 420 (540)
Q Consensus 377 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL 420 (540)
.-||..+.++..+|..+|++.+|++...+.+.|..|.. .+++
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~--~g~i 47 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMR--KGRI 47 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCc
Confidence 35788888888999999999999999999999999964 3444
No 260
>PF13551 HTH_29: Winged helix-turn helix
Probab=23.46 E-value=1.4e+02 Score=24.20 Aligned_cols=36 Identities=19% Similarity=0.356 Sum_probs=28.3
Q ss_pred HHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 378 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 378 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
.+|+++.+..+ |..++++.+|++...+.+.+..+..
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 35555655433 7999999999999999999988853
No 261
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=23.32 E-value=99 Score=20.60 Aligned_cols=21 Identities=14% Similarity=0.398 Sum_probs=17.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHh
Q 009222 389 LSFQDIKDATGIEDKELRRTL 409 (540)
Q Consensus 389 ~t~~ei~~~~~i~~~~l~~~L 409 (540)
+|++|+++.+|++...+.+.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 689999999999987776544
No 262
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=22.99 E-value=1.5e+02 Score=26.04 Aligned_cols=39 Identities=23% Similarity=0.193 Sum_probs=30.2
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhh
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 411 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 411 (540)
.+|.-|..||.++ ...+|.+||++.+|++...+......
T Consensus 6 ~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 6 FLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678888888875 36699999999999998766555443
No 263
>PRK12423 LexA repressor; Provisional
Probab=22.86 E-value=1.2e+02 Score=28.15 Aligned_cols=54 Identities=17% Similarity=0.332 Sum_probs=0.0
Q ss_pred EcHHHHHHHHHhcCC---CCc--cHHHHHHHhC-CCHHHHHHHhhhhhcCCceeeecCCCCC
Q 009222 372 VSLFQTVVLMLFNDA---QKL--SFQDIKDATG-IEDKELRRTLQSLACGKVRVLQKLPKGR 427 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~---~~~--t~~ei~~~~~-i~~~~l~~~L~~L~~~k~~iL~~~~~~~ 427 (540)
+|.-|-.||..+.+. ..+ |+.||++.+| .+...+..+|..| .+.|+|...+.+.
T Consensus 4 lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L--~~~G~l~~~~~~~ 63 (202)
T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQAL--AEAGLIEVVPNQA 63 (202)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH--HHCCCEEecCCCc
No 264
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=22.77 E-value=1e+02 Score=30.12 Aligned_cols=51 Identities=16% Similarity=0.325 Sum_probs=39.4
Q ss_pred EcHHHHHHH-HHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 372 VSLFQTVVL-MLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 372 ~s~~Q~~iL-l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
.+--.-.|| ..-+..+.++-+||.+.+|+|+..+=++|..|- |.|++.+..
T Consensus 193 L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE--k~GlIe~~K 244 (258)
T COG2512 193 LNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE--KRGLIEKEK 244 (258)
T ss_pred CCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH--hCCceEEEE
Confidence 333334444 445556779999999999999999999999994 789997654
No 265
>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=22.60 E-value=1.4e+02 Score=28.66 Aligned_cols=45 Identities=18% Similarity=0.251 Sum_probs=38.2
Q ss_pred HHHHHhcC-CCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecCC
Q 009222 378 VVLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 378 ~iLl~Fn~-~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 424 (540)
.||-.++. ...++..+|++.+|++...+.+++..|. ..|++...|
T Consensus 187 ~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE--~aGvIe~r~ 232 (251)
T TIGR02787 187 HIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLE--SAGVIESRS 232 (251)
T ss_pred HHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 46777777 4789999999999999999999999996 478887654
No 266
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=22.54 E-value=1e+02 Score=24.02 Aligned_cols=29 Identities=17% Similarity=0.337 Sum_probs=23.0
Q ss_pred CCCCccHHHHHHHhCCCHHHHHHHhhhhh
Q 009222 385 DAQKLSFQDIKDATGIEDKELRRTLQSLA 413 (540)
Q Consensus 385 ~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 413 (540)
..+.+|++++++.++++...+.+.+..+.
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~ 55 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLN 55 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44678999999999999999999988883
No 267
>PRK00118 putative DNA-binding protein; Validated
Probab=22.43 E-value=1.6e+02 Score=24.41 Aligned_cols=39 Identities=10% Similarity=0.171 Sum_probs=26.7
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
+.-|-.++.+. -....|+.+|++.+|++...+...+..-
T Consensus 19 ~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RA 57 (104)
T PRK00118 19 TEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRT 57 (104)
T ss_pred CHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 44444444332 1246899999999999999887776543
No 268
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=22.28 E-value=1.2e+02 Score=22.29 Aligned_cols=35 Identities=17% Similarity=0.232 Sum_probs=26.7
Q ss_pred CCCChHHHHHHHHHHcCCCCCh--HHHHHHHHHhhhhccccc
Q 009222 489 KVLSHTLLITELFQQLKFPIKP--ADLKKRIESLIDREYLER 528 (540)
Q Consensus 489 k~l~~~~L~~~v~~~l~F~~~~--~~ik~~Ie~Li~~eyi~r 528 (540)
++++++||++ +.|+++. ..|+++=+.|+++||=--
T Consensus 2 ~tv~k~dLi~-----lGf~~~tA~~IIrqAK~~lV~~G~~~Y 38 (59)
T PF11372_consen 2 KTVTKKDLIE-----LGFSESTARDIIRQAKALLVQKGFSFY 38 (59)
T ss_pred CccCHHHHHH-----cCCCHHHHHHHHHHHHHHHHHcCCCcc
Confidence 5678888885 2677644 689999999999997443
No 269
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=22.20 E-value=1.7e+02 Score=31.81 Aligned_cols=36 Identities=11% Similarity=0.082 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHH
Q 009222 14 KPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEE 51 (540)
Q Consensus 14 ~~~l~~t~~yY~~~~~~~~~~~~~~~Yl~~v~~~l~~E 51 (540)
.+|+..+++.|..+++. ....+.+||......+-.+
T Consensus 289 e~f~~~~~~afe~fink--~~~rpAelIak~~dt~Lr~ 324 (661)
T KOG2167|consen 289 EKFLNSMSKAFETFINK--RRNRPAELIAKYVDTKLRA 324 (661)
T ss_pred HHHHHHHHHHHHHHHhc--ccCCHHHHHHHHHHHHHHh
Confidence 78999999999999993 6668999999988776655
No 270
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.10 E-value=1.2e+02 Score=27.06 Aligned_cols=24 Identities=13% Similarity=0.335 Sum_probs=20.2
Q ss_pred CCccHHHHHHHhCCCHHHHHHHhh
Q 009222 387 QKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 387 ~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
+.+|.+||++.+|++...++..|.
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 347999999999999998877654
No 271
>PRK10870 transcriptional repressor MprA; Provisional
Probab=21.87 E-value=1.5e+02 Score=26.96 Aligned_cols=38 Identities=13% Similarity=0.233 Sum_probs=29.2
Q ss_pred CCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccCC
Q 009222 488 RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 531 (540)
Q Consensus 488 ~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~~ 531 (540)
.+.++..+|-. .+..+...+-..|+.|.++|||+|..+
T Consensus 69 ~~~it~~eLa~------~l~l~~~tvsr~v~rLe~kGlV~R~~~ 106 (176)
T PRK10870 69 NHSIQPSELSC------ALGSSRTNATRIADELEKRGWIERRES 106 (176)
T ss_pred CCCcCHHHHHH------HHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 35677777665 334677889999999999999999543
No 272
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=21.82 E-value=1.4e+02 Score=26.49 Aligned_cols=40 Identities=15% Similarity=0.239 Sum_probs=28.3
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
++.-|-.|+.+.-- +.+|++||++.+|++...++..|.--
T Consensus 113 L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra 152 (164)
T PRK12547 113 LSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRA 152 (164)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 45555555554322 45899999999999998887776543
No 273
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=21.77 E-value=3.7e+02 Score=21.03 Aligned_cols=37 Identities=19% Similarity=0.237 Sum_probs=26.4
Q ss_pred hHHHHHhhHHhHHHHHHhhhcCCCCCChHHHHHHHHHHc
Q 009222 466 TERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL 504 (540)
Q Consensus 466 ~~~~~~~r~~~i~a~IVRimK~~k~l~~~~L~~~v~~~l 504 (540)
.-.+++.|...|++++.+. |+.+..+.+. +++|.+++
T Consensus 21 F~~Le~~RE~aIeeav~~c-~~g~pFs~d~-IN~vT~~m 57 (84)
T PF10752_consen 21 FLQLEQQREAAIEEAVSLC-KQGEPFSTDK-INEVTKEM 57 (84)
T ss_pred HHHHHHHHHHHHHHHHHHH-HCCCCCcHHH-HHHHHHHH
Confidence 3467899999999998765 4555666555 77776554
No 274
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=21.57 E-value=1.4e+02 Score=27.60 Aligned_cols=46 Identities=17% Similarity=0.041 Sum_probs=33.0
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
+..|.-++-.++.++-.+|-..+ ..+.+.+-..|+.|.++|||.|.
T Consensus 47 q~~iL~~L~~~~~itq~eLa~~l------~l~~sTvtr~l~rLE~kGlI~R~ 92 (185)
T PRK13777 47 EHHILWIAYHLKGASISEIAKFG------VMHVSTAFNFSKKLEERGYLTFS 92 (185)
T ss_pred HHHHHHHHHhCCCcCHHHHHHHH------CCCHhhHHHHHHHHHHCCCEEec
Confidence 34455556667788888876532 23455688899999999999985
No 275
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=21.43 E-value=1.1e+02 Score=29.57 Aligned_cols=45 Identities=16% Similarity=0.338 Sum_probs=38.9
Q ss_pred HHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhccccccC
Q 009222 480 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 530 (540)
Q Consensus 480 ~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~~ 530 (540)
.|..++++++.++.++|.+ .|.++..-+++-|..|.++|.|.|..
T Consensus 8 ~Il~~l~~~~~~~~~eLa~------~l~VS~~TiRRdL~~L~~~~~l~r~~ 52 (240)
T PRK10411 8 AIVDLLLNHTSLTTEALAE------QLNVSKETIRRDLNELQTQGKILRNH 52 (240)
T ss_pred HHHHHHHHcCCCcHHHHHH------HHCcCHHHHHHHHHHHHHCCCEEEec
Confidence 3788888999999999887 45789999999999999999998853
No 276
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.39 E-value=1.1e+02 Score=27.51 Aligned_cols=38 Identities=11% Similarity=0.175 Sum_probs=26.1
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
++.-|-.|+.+.- -+..|++||++.+|++...++..|.
T Consensus 130 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 130 LEKDRAAAVRRAY-LEGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCCChHHHHHHHH
Confidence 4545554443321 2458999999999999988876654
No 277
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=21.26 E-value=1.3e+02 Score=26.31 Aligned_cols=37 Identities=22% Similarity=0.170 Sum_probs=25.7
Q ss_pred EcHHHHHHH-HHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 372 VSLFQTVVL-MLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 372 ~s~~Q~~iL-l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
++.-|-.|+ +.+- ..+|.+||++.+|++...++..|.
T Consensus 107 Lp~~~r~v~~l~~~--~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 107 LPENYRDVVLAHYL--EEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred CCHHHHHHHHHHHH--hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 455444444 3332 458999999999999998876654
No 278
>PF12728 HTH_17: Helix-turn-helix domain
Probab=21.24 E-value=1.1e+02 Score=21.01 Aligned_cols=21 Identities=19% Similarity=0.371 Sum_probs=17.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHh
Q 009222 389 LSFQDIKDATGIEDKELRRTL 409 (540)
Q Consensus 389 ~t~~ei~~~~~i~~~~l~~~L 409 (540)
+|.+|+++.+|++...+.+.+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~ 22 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWI 22 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 689999999999987765443
No 279
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=21.23 E-value=74 Score=29.26 Aligned_cols=46 Identities=17% Similarity=0.178 Sum_probs=39.7
Q ss_pred HHHHHhhhcCCCCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhhcccccc
Q 009222 478 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 529 (540)
Q Consensus 478 ~a~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~eyi~r~ 529 (540)
+..|...+++++.++..+|.. .|.++..-|.+=|..|.++|.+.|-
T Consensus 9 ~~~Il~~l~~~~~~~~~~La~------~~~vS~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 9 QKALQELIEENPFITDEELAE------KFGVSIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHCCCEEHHHHHH------HHCcCHHHHHHHHHHHhcchHHHHH
Confidence 345677888899999999887 7889999999999999999998884
No 280
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.11 E-value=1.3e+02 Score=27.19 Aligned_cols=38 Identities=11% Similarity=0.160 Sum_probs=27.5
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
++.-|-.|+.+. ..+.+|++||++.+|+|...++..|.
T Consensus 128 Lp~~~R~v~~L~-~~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 128 LRPRVKQAFLMA-TLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 555565555542 12568999999999999998876653
No 281
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=21.09 E-value=98 Score=30.19 Aligned_cols=34 Identities=29% Similarity=0.403 Sum_probs=29.5
Q ss_pred CccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeecC
Q 009222 388 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 388 ~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
.=|-++|.+..|+|....+++|..|. |.+.+..+
T Consensus 246 KSsPEdIk~~FgiSKg~FKrAiGgL~--K~g~I~q~ 279 (287)
T COG2996 246 KSSPEDIKATFGISKGQFKRAIGGLM--KAGKIKQD 279 (287)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHH--hCCeEEEc
Confidence 45789999999999999999999996 67777664
No 282
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=21.08 E-value=1.5e+02 Score=26.38 Aligned_cols=24 Identities=13% Similarity=0.374 Sum_probs=20.1
Q ss_pred CCccHHHHHHHhCCCHHHHHHHhh
Q 009222 387 QKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 387 ~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
+.+|++||++.+|+|...++..|.
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 458999999999999988776653
No 283
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=21.03 E-value=2e+02 Score=20.33 Aligned_cols=46 Identities=24% Similarity=0.395 Sum_probs=29.1
Q ss_pred hHHHHHHhhhcCC--CCCChHHHHHHHHHHcCCCCChHHHHHHHHHhhhh
Q 009222 476 QVDAAIVRIMKTR--KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDR 523 (540)
Q Consensus 476 ~i~a~IVRimK~~--k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Li~~ 523 (540)
.|.++|..||+.. .+++..++...+.+ +|..+...-|..|+.+|..
T Consensus 4 ~i~~~i~~iL~~~dl~~vT~k~vr~~Le~--~~~~dL~~~K~~I~~~I~~ 51 (54)
T PF08766_consen 4 EIREAIREILREADLDTVTKKQVREQLEE--RFGVDLSSRKKFIKELIDE 51 (54)
T ss_dssp HHHHHHHHHHTTS-GGG--HHHHHHHHHH--H-SS--SHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHhHhhHHHHHHHHHH--HHCCCcHHHHHHHHHHHHH
Confidence 5788899999987 46677776666655 4555556777777777654
No 284
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.89 E-value=1.4e+02 Score=27.04 Aligned_cols=40 Identities=13% Similarity=0.198 Sum_probs=27.7
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
++.-|-.++.++- .+.+|.+||++.+|+|...++..|..-
T Consensus 130 L~~~~r~v~~l~~-~~g~s~~EIA~~l~is~~tV~~~l~ra 169 (181)
T PRK12536 130 LPDRQRLPIVHVK-LEGLSVAETAQLTGLSESAVKVGIHRG 169 (181)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3555555543321 245899999999999999888776543
No 285
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=20.88 E-value=1.2e+02 Score=28.03 Aligned_cols=38 Identities=26% Similarity=0.342 Sum_probs=27.5
Q ss_pred cHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhh
Q 009222 373 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 412 (540)
Q Consensus 373 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 412 (540)
+..+..|+.++- ..+|.+||++.+|++...++..+.-.
T Consensus 157 ~~~~r~vl~l~~--e~~s~~EIA~~lgis~~tV~~~l~ra 194 (208)
T PRK08295 157 SELEKEVLELYL--DGKSYQEIAEELNRHVKSIDNALQRV 194 (208)
T ss_pred CHHHHHHHHHHH--ccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 444555554433 46899999999999999887766543
No 286
>PRK09483 response regulator; Provisional
Probab=20.87 E-value=1.5e+02 Score=27.08 Aligned_cols=42 Identities=7% Similarity=0.161 Sum_probs=35.8
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhc
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC 414 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 414 (540)
..|.-+.-||.++.+ +.|..+|++.++++...++.++..+..
T Consensus 148 ~Lt~rE~~vl~~~~~--G~~~~~Ia~~l~is~~TV~~~~~~i~~ 189 (217)
T PRK09483 148 SLSERELQIMLMITK--GQKVNEISEQLNLSPKTVNSYRYRMFS 189 (217)
T ss_pred ccCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 378888888887754 478999999999999999999988863
No 287
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=20.83 E-value=2.5e+02 Score=22.08 Aligned_cols=68 Identities=16% Similarity=0.285 Sum_probs=45.3
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHh----CCCHHHHHHHhhhhhcCCceeeecCCCCCCCCCCCeEEEccCC
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDAT----GIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 441 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~----~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 441 (540)
..+++-=.+|-+|-+.+++|+++|-+.+ .++...+...+. +++.|.|||.-..+ .......|++-++|
T Consensus 8 D~~GiRr~vL~~fl~~~~~T~~di~e~L~~~f~vs~~~VasMVG-~i~SrlGIL~~~k~--~~g~~~~Y~LKe~Y 79 (83)
T PF10826_consen 8 DKDGIRRAVLKLFLKGKKFTTDDIYERLKEKFDVSYRGVASMVG-LIHSRLGILSIHKD--SYGDHNVYSLKEKY 79 (83)
T ss_pred CCccHHHHHHHHHHhCCCeeHHHHHHHHHHHcCchHHHHHHHHH-HHHHhhhheeeccc--ccCCccEEEecHHh
Confidence 3456667889999999999999887765 566666655554 44468999975221 11234567766554
No 288
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=20.81 E-value=1.7e+02 Score=28.27 Aligned_cols=50 Identities=16% Similarity=0.297 Sum_probs=40.6
Q ss_pred EEcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 371 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 371 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
-.|-++|-+-+.+-..++.|..||++.+|+|..-+-..|++|. +.|++..
T Consensus 13 Glt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe--~kG~v~~ 62 (247)
T COG1378 13 GLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLE--KKGLVEV 62 (247)
T ss_pred CCCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHH--HCCCEEe
Confidence 3566777776666666889999999999999999999999996 4577754
No 289
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=20.67 E-value=1.4e+02 Score=26.84 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=26.2
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
++.-|-.|+.+.- .+.+|.+||++.+|+|...++..|.
T Consensus 135 Lp~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 135 VDPRQAEVVELRF-FAGLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4444444444322 2458999999999999998877664
No 290
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=20.60 E-value=2.3e+02 Score=24.01 Aligned_cols=45 Identities=22% Similarity=0.402 Sum_probs=36.6
Q ss_pred HHHHHHHhcCCCCccHHHHHHHhC-CCHHHHHHHhhhhhcCCceeeecC
Q 009222 376 QTVVLMLFNDAQKLSFQDIKDATG-IEDKELRRTLQSLACGKVRVLQKL 423 (540)
Q Consensus 376 Q~~iLl~Fn~~~~~t~~ei~~~~~-i~~~~l~~~L~~L~~~k~~iL~~~ 423 (540)
-+.||....+ +..-+.||...++ ++...|.+.|+.|. ..|++.+.
T Consensus 25 ~~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le--~~Glv~R~ 70 (120)
T COG1733 25 TLLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELE--EDGLVERV 70 (120)
T ss_pred HHHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHH--HCCCEEee
Confidence 3455655555 7889999999998 99999999999996 47888765
No 291
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=20.51 E-value=1.6e+02 Score=26.05 Aligned_cols=39 Identities=15% Similarity=0.141 Sum_probs=28.1
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 411 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 411 (540)
+|+-|-.|+.+.- ...+|.+||++.+|++...++..+.-
T Consensus 123 L~~~~r~vl~l~~-~~g~s~~eIA~~l~is~~tv~~~l~r 161 (170)
T TIGR02952 123 LTPKQQHVIALRF-GQNLPIAEVARILGKTEGAVKILQFR 161 (170)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5566666665521 13589999999999999988777643
No 292
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=20.41 E-value=1.5e+02 Score=27.85 Aligned_cols=43 Identities=21% Similarity=0.259 Sum_probs=34.5
Q ss_pred HHHHHhcCC-CCccHHHHHHHhCCCHHHHHHHhhhhhcCCceeeec
Q 009222 378 VVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 422 (540)
Q Consensus 378 ~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 422 (540)
.||.++.+. ...|.+||++.+|+++..++.++..|.. .+++..
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~--~~~~~~ 209 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCAS--RHLIIA 209 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHh--CCeEEE
Confidence 566666553 2689999999999999999999999974 566654
No 293
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.31 E-value=1.4e+02 Score=26.15 Aligned_cols=38 Identities=11% Similarity=0.159 Sum_probs=25.3
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
++.-|-.|+.+.- .+.+|++||++.+|++...++..+.
T Consensus 107 Lp~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 107 LPARQREAFLLRY-WEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred CCHHHHHHHHHHH-HhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 3444444443321 2458999999999999988876653
No 294
>KOG3852 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.20 E-value=5.4e+02 Score=25.65 Aligned_cols=107 Identities=17% Similarity=0.234 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCC-------CHHHHHHHHHHHHHHhhcCCC-C-cHHHHHHHHHHHHhcCCCCCChHHHHHH
Q 009222 142 VSSLLEFKASLDTIWEQSFSK-------NEAFCNTIKDAFEYLINLRQN-R-PAELIAKFLDEKLRAGNKGTSEEELEGT 212 (540)
Q Consensus 142 i~~l~~l~~~~~~l~~~~F~~-------~~~f~~~l~~~f~~~ln~~~~-~-~~e~La~y~d~~l~~~~~~~~~~~~~~~ 212 (540)
...|+.+|.--..-+.+||.. ..+|.+|+..-....+..... . -+-.|-+||+-++++ .+..+..++.
T Consensus 220 LD~lL~fy~cs~~~lte~~~ptv~~ESmYGDfqeA~~HL~~rlI~Tr~PEEIRGGGLLKYc~Llvrg-fkpa~~~eik-- 296 (426)
T KOG3852|consen 220 LDPLLLFYSCSNNPLTECFHPTVTGESMYGDFQEAMTHLQHRLIATRKPEEIRGGGLLKYCHLLVRG-FKPAKPWEIK-- 296 (426)
T ss_pred ehhhhhhhcccCCccchhcCceeeeeeccccHHHHHHHHHHhhhccCCHHHccCchHHHHHHHHHcc-CCCCCHHHHH--
Confidence 455666666555566677743 347777777766666654320 0 012488999999884 4443434432
Q ss_pred HHhhhhhhhcccChhHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcchhHHh
Q 009222 213 LDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNK 270 (540)
Q Consensus 213 l~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~L~~~~g~~~~~k 270 (540)
...+|++.|+.-..+.-.+.++.+=.-|...+|.+...|
T Consensus 297 -------------------~LeRYMCSRFFIDFpdi~eQqrkle~YL~nHF~g~~~~k 335 (426)
T KOG3852|consen 297 -------------------ALERYMCSRFFIDFPDIIEQQRKLESYLQNHFGGEENRK 335 (426)
T ss_pred -------------------HHHHHHHhhhcccccHHHHHHHHHHHHHHHhhccccchh
Confidence 235566777666544334555566666666666544333
No 295
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=20.04 E-value=1.1e+02 Score=27.19 Aligned_cols=49 Identities=18% Similarity=0.236 Sum_probs=40.0
Q ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCC-------CHHH-------HHHHhhhhhcCCceeeecCC
Q 009222 374 LFQTVVLMLFNDAQKLSFQDIKDATGI-------EDKE-------LRRTLQSLACGKVRVLQKLP 424 (540)
Q Consensus 374 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i-------~~~~-------l~~~L~~L~~~k~~iL~~~~ 424 (540)
+-.|+||-.+-....+.+..++...|. |... ++.+|+.|- +.+++.+.+
T Consensus 53 ~R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE--~~glVek~~ 115 (150)
T PRK09333 53 VRAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLE--KAGLVEKTK 115 (150)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHH--HCCCeeeCC
Confidence 446899988877889999999999998 5444 899999995 578887654
No 296
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=20.00 E-value=1.5e+02 Score=26.06 Aligned_cols=38 Identities=26% Similarity=0.416 Sum_probs=27.5
Q ss_pred EcHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHhh
Q 009222 372 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 410 (540)
Q Consensus 372 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 410 (540)
+++-|-.|+.+. .-..+|.+||++.+|++...++..+.
T Consensus 113 L~~~~r~v~~l~-~~~~~s~~eIA~~lgis~~tv~~~l~ 150 (161)
T PRK12541 113 LPLERRNVLLLR-DYYGFSYKEIAEMTGLSLAKVKIELH 150 (161)
T ss_pred CCHHHHHHhhhH-HhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 556566666552 12458999999999999988877664
Done!