Query 014910
Match_columns 416
No_of_seqs 182 out of 944
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 01:16:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014910.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014910hhsearch_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 2.3E-84 4.9E-89 631.9 29.6 396 12-416 260-661 (661)
2 KOG2166 Cullins [Cell cycle co 100.0 3.2E-82 6.9E-87 655.8 35.1 396 11-414 330-725 (725)
3 COG5647 Cullin, a subunit of E 100.0 5E-79 1.1E-83 607.5 33.4 401 9-416 364-773 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 6.2E-70 1.3E-74 510.5 19.7 377 5-416 344-728 (728)
5 KOG2285 E3 ubiquitin ligase, C 100.0 6.5E-65 1.4E-69 480.8 29.7 410 6-416 326-777 (777)
6 PF00888 Cullin: Cullin family 100.0 2.7E-56 5.9E-61 468.7 35.4 308 10-320 279-588 (588)
7 smart00182 CULLIN Cullin. 100.0 4.1E-35 8.9E-40 251.4 17.9 141 100-241 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 2.5E-30 5.4E-35 257.7 26.2 302 93-406 441-758 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 3E-21 6.5E-26 143.0 1.6 68 343-410 1-68 (68)
10 TIGR01610 phage_O_Nterm phage 95.6 0.042 9.1E-07 43.3 6.4 65 248-320 21-93 (95)
11 PF09339 HTH_IclR: IclR helix- 94.4 0.072 1.6E-06 36.8 4.0 45 255-301 6-51 (52)
12 PF13412 HTH_24: Winged helix- 94.1 0.11 2.4E-06 35.1 4.5 41 251-291 2-42 (48)
13 PF12802 MarR_2: MarR family; 94.0 0.08 1.7E-06 37.7 3.8 51 250-302 3-55 (62)
14 PF02082 Rrf2: Transcriptional 93.9 0.19 4.1E-06 38.4 6.0 60 253-319 11-71 (83)
15 PF01047 MarR: MarR family; I 93.0 0.078 1.7E-06 37.5 2.4 51 250-302 1-51 (59)
16 PF08220 HTH_DeoR: DeoR-like h 92.8 0.19 4.2E-06 35.5 4.1 46 254-301 2-47 (57)
17 PF13463 HTH_27: Winged helix 92.2 0.25 5.5E-06 35.8 4.2 50 250-301 1-51 (68)
18 TIGR02337 HpaR homoprotocatech 91.8 0.36 7.8E-06 39.4 5.3 52 249-302 25-76 (118)
19 PF01022 HTH_5: Bacterial regu 91.2 0.53 1.1E-05 31.7 4.6 44 253-299 3-46 (47)
20 PRK11512 DNA-binding transcrip 91.1 0.47 1E-05 40.3 5.4 53 248-302 36-88 (144)
21 PF12840 HTH_20: Helix-turn-he 91.0 0.35 7.7E-06 34.5 3.8 49 251-301 9-57 (61)
22 smart00550 Zalpha Z-DNA-bindin 90.5 0.87 1.9E-05 33.4 5.6 47 253-301 7-55 (68)
23 COG3682 Predicted transcriptio 89.5 0.35 7.5E-06 39.7 3.0 62 350-416 6-67 (123)
24 TIGR02698 CopY_TcrY copper tra 89.2 0.46 1E-05 39.8 3.7 60 352-416 6-65 (130)
25 PF08279 HTH_11: HTH domain; 88.8 0.99 2.1E-05 31.2 4.6 36 256-291 4-40 (55)
26 TIGR01889 Staph_reg_Sar staphy 88.7 1.2 2.6E-05 35.8 5.7 52 249-302 22-77 (109)
27 smart00346 HTH_ICLR helix_turn 88.1 1.5 3.2E-05 33.7 5.7 45 255-301 8-53 (91)
28 PF09012 FeoC: FeoC like trans 88.0 0.28 6E-06 36.1 1.4 44 356-407 6-49 (69)
29 smart00347 HTH_MARR helix_turn 87.1 1.3 2.8E-05 34.4 4.9 52 248-301 6-57 (101)
30 PF03965 Penicillinase_R: Peni 86.6 0.74 1.6E-05 37.5 3.3 59 353-416 6-64 (115)
31 PF01978 TrmB: Sugar-specific 86.6 0.59 1.3E-05 34.1 2.5 49 251-301 7-55 (68)
32 PRK15090 DNA-binding transcrip 86.3 1.7 3.6E-05 40.8 6.0 45 255-301 17-61 (257)
33 PRK11920 rirA iron-responsive 86.0 2.4 5.2E-05 36.5 6.4 57 255-318 13-69 (153)
34 smart00420 HTH_DEOR helix_turn 85.6 1.9 4E-05 29.1 4.5 44 255-300 3-46 (53)
35 PRK10857 DNA-binding transcrip 85.5 2.7 5.9E-05 36.6 6.5 45 254-300 12-57 (164)
36 COG3355 Predicted transcriptio 85.4 2.3 4.9E-05 35.2 5.5 39 262-302 38-76 (126)
37 PRK03573 transcriptional regul 85.1 1.9 4.2E-05 36.4 5.3 53 248-302 27-80 (144)
38 PRK13777 transcriptional regul 85.1 2 4.4E-05 38.2 5.6 53 248-302 41-93 (185)
39 PF04703 FaeA: FaeA-like prote 84.5 2.3 4.9E-05 30.6 4.6 56 257-316 5-61 (62)
40 TIGR02010 IscR iron-sulfur clu 83.1 3.6 7.8E-05 34.5 6.0 44 255-300 13-57 (135)
41 PF04492 Phage_rep_O: Bacterio 82.9 3.6 7.7E-05 32.7 5.5 62 249-320 29-98 (100)
42 PF05732 RepL: Firmicute plasm 82.6 2.5 5.5E-05 36.9 5.1 49 266-323 75-123 (165)
43 PRK10870 transcriptional repre 81.9 3.6 7.8E-05 36.3 5.9 52 249-302 52-105 (176)
44 PHA00738 putative HTH transcri 81.6 4 8.7E-05 32.7 5.3 68 247-320 7-74 (108)
45 PF13404 HTH_AsnC-type: AsnC-t 81.2 2.6 5.6E-05 27.7 3.5 36 255-290 6-41 (42)
46 COG1959 Predicted transcriptio 80.2 4.7 0.0001 34.6 5.8 59 253-318 11-70 (150)
47 PF05584 Sulfolobus_pRN: Sulfo 80.0 4.9 0.00011 29.7 4.9 42 256-300 9-50 (72)
48 cd00090 HTH_ARSR Arsenical Res 79.7 4.8 0.0001 29.0 5.1 47 251-300 6-52 (78)
49 PRK11569 transcriptional repre 79.6 4.1 8.8E-05 38.7 5.8 46 255-302 31-77 (274)
50 PF13601 HTH_34: Winged helix 79.6 1.9 4.1E-05 32.7 2.8 44 254-299 2-45 (80)
51 PRK10163 DNA-binding transcrip 79.3 4.6 9.9E-05 38.3 6.0 45 255-301 28-73 (271)
52 smart00419 HTH_CRP helix_turn_ 79.3 4.7 0.0001 26.5 4.5 33 266-300 8-40 (48)
53 PF08280 HTH_Mga: M protein tr 78.9 3.1 6.7E-05 29.4 3.6 38 254-291 7-44 (59)
54 COG1414 IclR Transcriptional r 78.8 4.8 0.0001 37.6 5.9 46 255-302 7-53 (246)
55 PF08784 RPA_C: Replication pr 78.1 4 8.8E-05 32.3 4.5 44 249-292 44-91 (102)
56 PF01978 TrmB: Sugar-specific 78.0 2.7 5.8E-05 30.5 3.1 47 361-415 19-65 (68)
57 TIGR01884 cas_HTH CRISPR locus 77.9 4 8.6E-05 36.9 4.9 51 249-301 140-190 (203)
58 TIGR00738 rrf2_super rrf2 fami 77.8 6.1 0.00013 32.7 5.7 45 254-300 12-57 (132)
59 PRK09834 DNA-binding transcrip 76.6 5.4 0.00012 37.5 5.7 46 255-302 14-60 (263)
60 TIGR02431 pcaR_pcaU beta-ketoa 76.6 6.1 0.00013 36.8 6.0 44 255-300 12-56 (248)
61 smart00345 HTH_GNTR helix_turn 75.8 6.3 0.00014 27.2 4.5 39 261-301 14-53 (60)
62 COG1846 MarR Transcriptional r 75.7 6 0.00013 31.7 5.1 51 250-302 20-70 (126)
63 smart00550 Zalpha Z-DNA-bindin 75.5 4.1 8.8E-05 29.8 3.5 53 352-412 8-62 (68)
64 TIGR02944 suf_reg_Xantho FeS a 74.5 7.9 0.00017 32.1 5.5 43 256-300 13-57 (130)
65 smart00344 HTH_ASNC helix_turn 73.7 6.4 0.00014 31.3 4.6 45 253-299 4-48 (108)
66 PF13463 HTH_27: Winged helix 73.6 3 6.6E-05 29.9 2.4 53 353-413 6-61 (68)
67 TIGR03879 near_KaiC_dom probab 73.5 4.2 9.2E-05 30.2 3.1 28 264-291 30-57 (73)
68 PRK10141 DNA-binding transcrip 73.0 8.3 0.00018 31.6 5.1 62 251-318 15-76 (117)
69 PF08220 HTH_DeoR: DeoR-like h 71.9 2.3 4.9E-05 29.9 1.3 45 354-406 4-48 (57)
70 COG2345 Predicted transcriptio 71.8 5.6 0.00012 36.3 4.2 43 255-299 14-56 (218)
71 smart00418 HTH_ARSR helix_turn 71.5 8.6 0.00019 26.6 4.5 35 264-300 8-42 (66)
72 PF10771 DUF2582: Protein of u 70.2 7.5 0.00016 28.2 3.7 38 255-292 11-48 (65)
73 PF09756 DDRGK: DDRGK domain; 69.7 2.6 5.6E-05 37.6 1.5 58 350-416 100-157 (188)
74 PF13730 HTH_36: Helix-turn-he 69.6 11 0.00024 25.8 4.5 24 268-291 27-50 (55)
75 cd00092 HTH_CRP helix_turn_hel 68.3 14 0.0003 26.2 5.0 35 265-301 24-58 (67)
76 PF01325 Fe_dep_repress: Iron 68.3 12 0.00026 26.6 4.4 43 257-301 13-55 (60)
77 PRK11014 transcriptional repre 66.5 19 0.00041 30.3 6.2 40 261-302 20-59 (141)
78 PRK10434 srlR DNA-bindng trans 65.9 8.5 0.00019 36.1 4.3 47 253-301 6-52 (256)
79 COG1349 GlpR Transcriptional r 65.4 9.3 0.0002 35.8 4.4 47 253-301 6-52 (253)
80 PF02796 HTH_7: Helix-turn-hel 65.2 9.2 0.0002 25.3 3.2 31 256-288 13-43 (45)
81 smart00418 HTH_ARSR helix_turn 64.6 10 0.00022 26.2 3.6 44 356-408 3-46 (66)
82 PF08221 HTH_9: RNA polymerase 64.2 10 0.00022 27.1 3.5 35 263-299 24-58 (62)
83 PF14394 DUF4423: Domain of un 64.1 19 0.00042 31.5 5.9 54 247-302 19-75 (171)
84 PF04545 Sigma70_r4: Sigma-70, 63.7 18 0.00039 24.2 4.5 32 256-289 12-43 (50)
85 PF09012 FeoC: FeoC like trans 63.3 9 0.0002 27.9 3.1 35 258-292 6-40 (69)
86 PF02002 TFIIE_alpha: TFIIE al 62.7 7.3 0.00016 31.0 2.8 45 253-299 14-58 (105)
87 TIGR02844 spore_III_D sporulat 62.7 13 0.00029 28.1 4.0 35 253-288 7-41 (80)
88 PF11994 DUF3489: Protein of u 61.9 18 0.00039 26.7 4.4 47 251-297 9-55 (72)
89 PF06784 UPF0240: Uncharacteri 60.7 16 0.00035 32.3 4.8 64 223-291 96-161 (179)
90 cd07153 Fur_like Ferric uptake 60.4 13 0.00027 30.0 3.9 57 355-414 6-63 (116)
91 TIGR02702 SufR_cyano iron-sulf 60.3 23 0.0005 31.8 5.9 45 255-301 4-48 (203)
92 COG4189 Predicted transcriptio 60.2 15 0.00032 33.7 4.5 50 250-301 21-70 (308)
93 PRK13509 transcriptional repre 60.1 15 0.00033 34.3 4.9 48 253-302 6-53 (251)
94 PF12324 HTH_15: Helix-turn-he 59.3 25 0.00053 26.4 4.8 38 254-291 26-63 (77)
95 PF01726 LexA_DNA_bind: LexA D 58.8 19 0.0004 26.1 4.0 24 385-408 39-62 (65)
96 PRK11169 leucine-responsive tr 58.4 16 0.00034 31.7 4.4 48 250-299 12-59 (164)
97 PRK00215 LexA repressor; Valid 58.0 24 0.00053 31.6 5.7 51 250-302 2-58 (205)
98 smart00421 HTH_LUXR helix_turn 57.4 23 0.0005 23.7 4.3 39 251-291 5-43 (58)
99 PF05158 RNA_pol_Rpc34: RNA po 57.0 13 0.00028 36.3 3.8 50 248-299 80-131 (327)
100 PF13412 HTH_24: Winged helix- 57.0 8.3 0.00018 25.7 1.9 43 353-403 6-48 (48)
101 PF00325 Crp: Bacterial regula 56.9 14 0.00031 22.7 2.7 26 266-291 2-27 (32)
102 PRK11179 DNA-binding transcrip 56.4 21 0.00045 30.6 4.7 49 249-299 6-54 (153)
103 TIGR00373 conserved hypothetic 56.0 22 0.00048 30.7 4.8 44 254-299 16-59 (158)
104 PRK06266 transcription initiat 55.9 19 0.0004 31.9 4.4 45 253-299 23-67 (178)
105 cd06170 LuxR_C_like C-terminal 55.7 26 0.00056 23.5 4.3 39 251-291 2-40 (57)
106 PRK10906 DNA-binding transcrip 55.4 18 0.0004 33.8 4.5 47 253-301 6-52 (252)
107 PRK10681 DNA-binding transcrip 55.4 18 0.00039 33.8 4.5 39 253-291 8-46 (252)
108 PF08281 Sigma70_r4_2: Sigma-7 55.4 27 0.00059 23.7 4.3 24 265-288 25-48 (54)
109 PF02186 TFIIE_beta: TFIIE bet 55.0 7 0.00015 28.4 1.3 53 353-416 8-61 (65)
110 cd07377 WHTH_GntR Winged helix 54.5 41 0.00089 23.4 5.4 33 267-301 26-58 (66)
111 PF00196 GerE: Bacterial regul 53.6 20 0.00044 24.9 3.5 40 250-291 4-43 (58)
112 PRK09802 DNA-binding transcrip 53.4 20 0.00043 34.0 4.4 48 252-301 17-64 (269)
113 PF01853 MOZ_SAS: MOZ/SAS fami 53.2 14 0.0003 32.9 3.0 25 266-290 150-174 (188)
114 COG1654 BirA Biotin operon rep 52.1 45 0.00098 25.2 5.3 41 259-299 12-52 (79)
115 PF01726 LexA_DNA_bind: LexA D 51.1 22 0.00047 25.8 3.3 51 250-302 4-60 (65)
116 TIGR02404 trehalos_R_Bsub treh 50.9 11 0.00024 34.6 2.3 34 379-413 31-64 (233)
117 PRK04172 pheS phenylalanyl-tRN 50.4 27 0.00059 36.1 5.2 50 249-300 3-52 (489)
118 PF04967 HTH_10: HTH DNA bindi 50.2 25 0.00054 24.4 3.3 30 261-290 18-47 (53)
119 PRK04424 fatty acid biosynthes 50.1 23 0.00049 31.5 4.0 46 253-300 8-53 (185)
120 KOG3054 Uncharacterized conser 50.0 17 0.00037 33.4 3.1 53 356-416 206-258 (299)
121 PF07106 TBPIP: Tat binding pr 49.7 1.5E+02 0.0032 25.7 9.1 59 254-318 3-64 (169)
122 PRK10411 DNA-binding transcrip 49.2 29 0.00062 32.2 4.7 39 253-291 5-43 (240)
123 COG1522 Lrp Transcriptional re 49.1 34 0.00073 28.9 4.9 49 250-300 6-54 (154)
124 TIGR00498 lexA SOS regulatory 48.8 21 0.00045 31.9 3.7 50 250-301 4-59 (199)
125 COG1318 Predicted transcriptio 48.6 28 0.0006 30.4 4.1 50 220-290 36-85 (182)
126 PRK11402 DNA-binding transcrip 48.4 13 0.00028 34.4 2.3 32 381-413 42-73 (241)
127 PF00165 HTH_AraC: Bacterial r 48.0 26 0.00057 22.5 3.1 28 264-291 6-33 (42)
128 smart00344 HTH_ASNC helix_turn 47.8 13 0.00027 29.6 1.9 47 351-405 4-50 (108)
129 COG4190 Predicted transcriptio 47.6 67 0.0015 26.8 5.9 68 251-320 63-133 (144)
130 PLN03238 probable histone acet 47.4 33 0.00071 32.6 4.7 38 253-290 209-247 (290)
131 PF12802 MarR_2: MarR family; 47.3 11 0.00023 26.4 1.2 26 382-407 31-56 (62)
132 PF00392 GntR: Bacterial regul 46.7 13 0.00028 26.5 1.6 32 380-412 32-63 (64)
133 PF13384 HTH_23: Homeodomain-l 46.7 24 0.00052 23.5 2.9 33 256-290 9-41 (50)
134 smart00345 HTH_GNTR helix_turn 46.0 16 0.00035 25.0 2.0 27 381-407 29-55 (60)
135 TIGR02325 C_P_lyase_phnF phosp 45.6 15 0.00032 33.7 2.2 32 381-413 41-72 (238)
136 PRK10079 phosphonate metabolis 45.3 15 0.00033 33.9 2.3 35 378-413 41-75 (241)
137 PF09681 Phage_rep_org_N: N-te 45.1 36 0.00078 28.0 4.1 36 263-300 50-85 (121)
138 PF08672 APC2: Anaphase promot 44.5 23 0.0005 25.2 2.5 52 355-406 2-55 (60)
139 cd06171 Sigma70_r4 Sigma70, re 44.4 58 0.0013 21.1 4.6 40 250-290 11-50 (55)
140 PRK06474 hypothetical protein; 44.2 69 0.0015 28.2 6.1 52 248-301 7-60 (178)
141 PHA02591 hypothetical protein; 44.1 29 0.00062 26.0 3.0 25 265-289 58-82 (83)
142 PF01047 MarR: MarR family; I 43.6 13 0.00029 25.7 1.3 43 356-406 9-51 (59)
143 PRK13239 alkylmercury lyase; P 43.5 46 0.00099 30.1 4.9 40 252-291 22-61 (206)
144 smart00531 TFIIE Transcription 43.4 30 0.00065 29.4 3.6 30 263-292 12-41 (147)
145 TIGR03433 padR_acidobact trans 43.1 37 0.00081 26.7 3.9 53 351-404 5-57 (100)
146 PF13542 HTH_Tnp_ISL3: Helix-t 43.0 63 0.0014 21.6 4.6 35 253-289 16-50 (52)
147 PRK09334 30S ribosomal protein 43.0 20 0.00044 27.5 2.2 36 381-416 50-85 (86)
148 PF14947 HTH_45: Winged helix- 43.0 64 0.0014 24.0 5.0 43 254-299 8-50 (77)
149 PF06163 DUF977: Bacterial pro 42.2 51 0.0011 27.2 4.5 41 252-292 12-52 (127)
150 KOG2747 Histone acetyltransfer 41.3 35 0.00075 34.0 4.0 63 226-290 282-353 (396)
151 PRK14999 histidine utilization 41.2 18 0.00039 33.4 2.1 47 358-413 29-76 (241)
152 PF13730 HTH_36: Helix-turn-he 40.7 19 0.00042 24.5 1.7 21 382-402 35-55 (55)
153 COG2188 PhnF Transcriptional r 40.4 19 0.00042 33.2 2.1 35 378-413 37-71 (236)
154 PF01638 HxlR: HxlR-like helix 40.3 51 0.0011 25.3 4.2 46 253-301 6-52 (90)
155 PF09860 DUF2087: Uncharacteri 39.9 43 0.00094 24.7 3.5 18 394-412 51-68 (71)
156 PF04182 B-block_TFIIIC: B-blo 39.7 50 0.0011 24.5 3.9 48 252-301 2-51 (75)
157 PRK03902 manganese transport t 39.1 56 0.0012 27.4 4.6 43 256-300 12-54 (142)
158 TIGR00122 birA_repr_reg BirA b 39.0 1.3E+02 0.0028 21.5 6.0 34 258-292 6-39 (69)
159 PLN03239 histone acetyltransfe 38.9 48 0.001 32.5 4.5 38 253-290 267-308 (351)
160 PF09107 SelB-wing_3: Elongati 38.8 66 0.0014 21.9 4.0 41 259-301 3-43 (50)
161 PF09904 HTH_43: Winged helix- 38.4 66 0.0014 24.9 4.3 33 259-292 15-47 (90)
162 TIGR01714 phage_rep_org_N phag 38.2 49 0.0011 27.1 3.9 48 251-300 28-83 (119)
163 cd07977 TFIIE_beta_winged_heli 37.8 23 0.0005 26.5 1.8 58 349-416 8-70 (75)
164 PRK00135 scpB segregation and 37.7 1.5E+02 0.0033 26.4 7.3 111 203-320 34-153 (188)
165 PRK11050 manganese transport r 36.9 75 0.0016 27.1 5.1 43 256-300 41-83 (152)
166 PRK09764 DNA-binding transcrip 36.9 25 0.00055 32.4 2.3 32 381-413 38-69 (240)
167 TIGR02018 his_ut_repres histid 36.9 24 0.00051 32.3 2.1 32 381-413 34-65 (230)
168 COG4742 Predicted transcriptio 36.7 60 0.0013 30.5 4.7 43 256-301 17-59 (260)
169 PF04760 IF2_N: Translation in 36.0 24 0.00053 24.2 1.6 22 266-287 3-24 (54)
170 cd07377 WHTH_GntR Winged helix 35.9 29 0.00064 24.2 2.1 27 380-406 33-59 (66)
171 COG3355 Predicted transcriptio 35.7 49 0.0011 27.4 3.5 40 359-406 37-76 (126)
172 PF00356 LacI: Bacterial regul 35.6 44 0.00094 22.3 2.7 22 268-289 1-22 (46)
173 PF01399 PCI: PCI domain; Int 35.6 69 0.0015 24.6 4.4 40 253-292 47-86 (105)
174 PHA02943 hypothetical protein; 35.2 74 0.0016 27.3 4.5 54 257-317 16-69 (165)
175 PF10007 DUF2250: Uncharacteri 35.1 80 0.0017 24.6 4.4 53 248-302 3-55 (92)
176 PF02270 TFIIF_beta: Transcrip 35.1 61 0.0013 30.8 4.6 57 253-319 217-273 (275)
177 PF08820 DUF1803: Domain of un 35.0 30 0.00066 27.0 2.1 27 378-405 34-60 (93)
178 TIGR01889 Staph_reg_Sar staphy 34.8 32 0.0007 27.4 2.4 41 361-409 40-82 (109)
179 TIGR02698 CopY_TcrY copper tra 34.6 1.1E+02 0.0024 25.4 5.6 49 250-300 2-54 (130)
180 TIGR00721 tfx DNA-binding prot 34.3 74 0.0016 26.8 4.5 40 249-290 6-45 (137)
181 PF09114 MotA_activ: Transcrip 34.3 65 0.0014 24.9 3.7 46 255-302 19-66 (96)
182 TIGR02989 Sig-70_gvs1 RNA poly 34.0 72 0.0016 26.8 4.6 39 249-289 111-150 (159)
183 PF00392 GntR: Bacterial regul 33.9 56 0.0012 23.1 3.3 37 263-301 20-57 (64)
184 smart00346 HTH_ICLR helix_turn 33.9 63 0.0014 24.3 3.8 44 356-407 11-55 (91)
185 PRK13719 conjugal transfer tra 33.8 73 0.0016 29.1 4.6 41 249-291 143-183 (217)
186 COG1349 GlpR Transcriptional r 33.7 22 0.00047 33.3 1.3 44 354-405 9-52 (253)
187 COG2197 CitB Response regulato 33.7 67 0.0015 29.0 4.5 41 249-291 148-188 (211)
188 PRK04214 rbn ribonuclease BN/u 33.4 1.2E+02 0.0025 30.7 6.6 38 261-300 305-342 (412)
189 COG1522 Lrp Transcriptional re 33.4 25 0.00055 29.7 1.6 50 349-406 7-56 (154)
190 PRK15411 rcsA colanic acid cap 33.4 71 0.0015 28.7 4.6 41 249-291 137-177 (207)
191 PF02847 MA3: MA3 domain; Int 33.3 59 0.0013 25.8 3.7 48 29-76 58-109 (113)
192 KOG2905 Transcription initiati 33.2 59 0.0013 30.0 3.9 57 254-320 188-244 (254)
193 smart00088 PINT motif in prote 33.2 63 0.0014 24.3 3.7 30 262-291 20-49 (88)
194 smart00753 PAM PCI/PINT associ 33.2 63 0.0014 24.3 3.7 30 262-291 20-49 (88)
195 smart00347 HTH_MARR helix_turn 33.0 49 0.0011 25.1 3.1 47 352-406 12-58 (101)
196 PF03444 HrcA_DNA-bdg: Winged 32.7 1.7E+02 0.0036 22.1 5.6 48 253-302 10-57 (78)
197 PF13545 HTH_Crp_2: Crp-like h 32.4 86 0.0019 22.7 4.2 33 266-300 28-60 (76)
198 PF04539 Sigma70_r3: Sigma-70 32.3 48 0.001 24.4 2.8 26 265-290 19-44 (78)
199 PF06163 DUF977: Bacterial pro 32.2 41 0.00089 27.8 2.5 52 348-407 10-61 (127)
200 COG2771 CsgD DNA-binding HTH d 32.2 1.2E+02 0.0027 20.8 4.9 41 249-291 4-44 (65)
201 PRK03573 transcriptional regul 31.7 36 0.00078 28.5 2.3 26 381-406 55-80 (144)
202 PF14394 DUF4423: Domain of un 31.5 42 0.00091 29.4 2.7 56 343-407 21-76 (171)
203 PRK10840 transcriptional regul 31.4 80 0.0017 28.1 4.7 41 249-291 150-190 (216)
204 PRK10434 srlR DNA-bindng trans 31.2 22 0.00047 33.4 0.9 45 353-405 8-52 (256)
205 PF12395 DUF3658: Protein of u 30.7 61 0.0013 26.1 3.3 48 365-414 62-109 (111)
206 COG1321 TroR Mn-dependent tran 30.7 98 0.0021 26.6 4.8 44 256-301 14-57 (154)
207 PRK03975 tfx putative transcri 30.5 93 0.002 26.4 4.5 39 249-289 6-44 (141)
208 PF01418 HTH_6: Helix-turn-hel 30.3 56 0.0012 24.2 2.9 33 259-291 27-59 (77)
209 PF13936 HTH_38: Helix-turn-he 30.0 98 0.0021 20.2 3.7 24 265-288 19-42 (44)
210 COG2996 Predicted RNA-bindinin 29.9 62 0.0014 30.5 3.6 33 266-300 246-278 (287)
211 TIGR02983 SigE-fam_strep RNA p 29.6 78 0.0017 26.7 4.1 40 250-290 111-150 (162)
212 PHA03103 double-strand RNA-bin 29.6 1.2E+02 0.0026 27.0 5.1 43 257-301 18-60 (183)
213 PRK15201 fimbriae regulatory p 29.6 1E+02 0.0022 27.3 4.6 41 249-291 133-173 (198)
214 smart00544 MA3 Domain in DAP-5 29.6 1.5E+02 0.0032 23.5 5.5 50 27-76 56-109 (113)
215 PF10668 Phage_terminase: Phag 29.5 77 0.0017 22.6 3.2 24 262-285 18-41 (60)
216 COG3413 Predicted DNA binding 29.5 87 0.0019 28.4 4.5 41 249-289 155-201 (215)
217 PF08784 RPA_C: Replication pr 29.2 39 0.00084 26.6 1.9 42 353-402 50-95 (102)
218 PRK09462 fur ferric uptake reg 29.2 81 0.0018 26.6 4.1 50 354-406 21-72 (148)
219 PLN00104 MYST -like histone ac 28.9 87 0.0019 31.9 4.7 38 253-290 360-398 (450)
220 PRK11169 leucine-responsive tr 28.5 51 0.0011 28.5 2.7 47 350-404 14-60 (164)
221 PRK14165 winged helix-turn-hel 28.4 1.1E+02 0.0024 27.9 4.9 44 256-301 11-54 (217)
222 PRK10430 DNA-binding transcrip 28.3 99 0.0021 28.1 4.8 47 250-298 159-208 (239)
223 PRK11475 DNA-binding transcrip 28.2 1E+02 0.0022 27.9 4.7 41 249-291 134-174 (207)
224 PRK10906 DNA-binding transcrip 28.0 34 0.00073 32.0 1.6 45 353-405 8-52 (252)
225 PF13551 HTH_29: Winged helix- 27.8 1.1E+02 0.0025 23.8 4.5 35 256-291 3-37 (112)
226 PRK04217 hypothetical protein; 27.8 1.1E+02 0.0024 24.7 4.3 41 249-290 42-82 (110)
227 TIGR02147 Fsuc_second hypothet 27.2 1.6E+02 0.0034 27.9 5.9 35 266-302 137-173 (271)
228 TIGR03076 near_not_gcvH Chlamy 26.9 5.4E+02 0.012 26.8 9.7 104 12-123 174-307 (686)
229 PF10007 DUF2250: Uncharacteri 26.8 45 0.00098 26.0 1.8 26 382-407 31-56 (92)
230 PRK12529 RNA polymerase sigma 26.8 80 0.0017 27.4 3.7 37 250-288 128-165 (178)
231 PRK12514 RNA polymerase sigma 26.8 80 0.0017 27.3 3.7 37 250-288 130-167 (179)
232 COG1510 Predicted transcriptio 26.6 67 0.0015 28.1 3.0 40 258-300 34-73 (177)
233 PRK00135 scpB segregation and 26.3 95 0.0021 27.7 4.0 33 259-291 12-45 (188)
234 PRK09954 putative kinase; Prov 26.1 1.3E+02 0.0027 29.6 5.4 38 255-292 6-43 (362)
235 PF04079 DUF387: Putative tran 25.9 85 0.0018 27.2 3.6 32 259-291 6-37 (159)
236 PRK12525 RNA polymerase sigma 25.8 1.2E+02 0.0026 26.0 4.6 33 254-288 124-156 (168)
237 TIGR01764 excise DNA binding d 25.7 89 0.0019 20.0 3.0 21 267-287 2-22 (49)
238 PRK09647 RNA polymerase sigma 25.7 1E+02 0.0022 27.6 4.3 34 254-289 144-177 (203)
239 PF01475 FUR: Ferric uptake re 25.7 85 0.0018 25.3 3.4 57 355-414 13-70 (120)
240 PHA02701 ORF020 dsRNA-binding 25.7 1.8E+02 0.0038 25.8 5.4 44 255-300 7-51 (183)
241 PRK11512 DNA-binding transcrip 25.5 54 0.0012 27.5 2.3 38 361-406 51-88 (144)
242 PRK00118 putative DNA-binding 25.5 1.1E+02 0.0025 24.4 3.9 38 251-290 19-57 (104)
243 PRK09642 RNA polymerase sigma 25.4 1.1E+02 0.0024 25.7 4.3 38 250-289 107-145 (160)
244 PRK11179 DNA-binding transcrip 25.4 54 0.0012 27.9 2.3 46 351-404 10-55 (153)
245 COG2512 Predicted membrane-ass 25.2 1E+02 0.0022 29.0 4.2 47 253-301 197-243 (258)
246 TIGR02337 HpaR homoprotocatech 25.2 75 0.0016 25.5 3.0 45 354-406 32-76 (118)
247 COG1846 MarR Transcriptional r 25.0 50 0.0011 26.1 1.9 27 381-407 45-71 (126)
248 PF03551 PadR: Transcriptional 24.9 68 0.0015 23.5 2.5 45 363-407 8-52 (75)
249 PRK09639 RNA polymerase sigma 24.8 1.3E+02 0.0028 25.5 4.6 32 254-288 118-149 (166)
250 PRK12522 RNA polymerase sigma 24.6 1.2E+02 0.0025 26.1 4.3 24 265-288 134-157 (173)
251 PF12728 HTH_17: Helix-turn-he 24.4 95 0.0021 20.6 2.9 21 267-287 2-22 (51)
252 PF05043 Mga: Mga helix-turn-h 24.3 99 0.0021 23.3 3.4 29 263-291 27-55 (87)
253 PRK08295 RNA polymerase factor 24.2 98 0.0021 27.4 3.9 38 251-290 157-194 (208)
254 COG5090 TFG2 Transcription ini 24.1 1E+02 0.0022 28.3 3.8 36 256-291 199-234 (297)
255 PRK12547 RNA polymerase sigma 23.9 1.3E+02 0.0028 25.6 4.4 41 249-290 112-152 (164)
256 TIGR02952 Sig70_famx2 RNA poly 23.9 1.3E+02 0.0028 25.5 4.5 39 249-289 122-161 (170)
257 PRK02363 DNA-directed RNA poly 23.8 1.1E+02 0.0024 25.5 3.7 35 357-395 11-46 (129)
258 cd07153 Fur_like Ferric uptake 23.6 1.8E+02 0.004 23.0 5.0 57 256-317 5-67 (116)
259 PRK09483 response regulator; P 23.6 1.4E+02 0.0031 26.1 4.8 41 249-291 148-188 (217)
260 PRK08301 sporulation sigma fac 23.5 1.4E+02 0.003 27.2 4.8 39 250-288 179-220 (234)
261 PRK12536 RNA polymerase sigma 23.4 1.2E+02 0.0027 26.2 4.3 39 251-290 131-169 (181)
262 PRK10046 dpiA two-component re 23.4 1.3E+02 0.0027 27.2 4.5 42 256-299 166-208 (225)
263 TIGR02999 Sig-70_X6 RNA polyme 23.4 1.3E+02 0.0028 26.0 4.4 39 250-289 135-173 (183)
264 PRK15431 ferrous iron transpor 23.4 73 0.0016 24.0 2.3 30 377-406 21-50 (78)
265 COG2865 Predicted transcriptio 23.2 57 0.0012 33.4 2.2 57 352-416 404-460 (467)
266 PF07638 Sigma70_ECF: ECF sigm 23.2 86 0.0019 27.6 3.2 26 265-290 150-175 (185)
267 PF09862 DUF2089: Protein of u 23.1 1.8E+02 0.0039 23.6 4.7 44 248-292 32-75 (113)
268 PF14493 HTH_40: Helix-turn-he 23.1 1.8E+02 0.0039 22.2 4.7 33 257-291 6-38 (91)
269 PF13314 DUF4083: Domain of un 23.0 2.2E+02 0.0048 20.1 4.4 33 66-98 23-55 (58)
270 PRK09047 RNA polymerase factor 22.8 1.4E+02 0.003 25.0 4.4 37 251-288 108-144 (161)
271 PRK10100 DNA-binding transcrip 22.6 1.4E+02 0.003 27.1 4.6 40 250-291 156-195 (216)
272 TIGR02985 Sig70_bacteroi1 RNA 22.6 1.5E+02 0.0033 24.5 4.6 38 251-290 115-153 (161)
273 smart00529 HTH_DTXR Helix-turn 22.6 67 0.0014 24.6 2.1 30 378-407 5-34 (96)
274 PF00538 Linker_histone: linke 22.5 58 0.0013 24.2 1.7 55 351-406 9-65 (77)
275 PF02334 RTP: Replication term 22.3 1.1E+02 0.0024 24.6 3.2 53 351-404 19-72 (122)
276 PRK12527 RNA polymerase sigma 22.2 1.2E+02 0.0027 25.5 4.0 38 250-288 106-143 (159)
277 PRK05472 redox-sensing transcr 22.2 1.3E+02 0.0029 27.1 4.3 40 252-291 16-57 (213)
278 COG1378 Predicted transcriptio 22.1 1.1E+02 0.0025 28.4 3.9 51 248-300 12-62 (247)
279 PF13518 HTH_28: Helix-turn-he 22.1 2.1E+02 0.0047 18.7 4.4 23 268-290 14-36 (52)
280 PRK13919 putative RNA polymera 22.0 1.3E+02 0.0028 26.1 4.2 38 250-288 136-173 (186)
281 PF09681 Phage_rep_org_N: N-te 22.0 31 0.00067 28.4 0.1 48 360-407 41-88 (121)
282 cd04762 HTH_MerR-trunc Helix-T 21.8 1.2E+02 0.0025 19.3 3.0 21 267-287 1-21 (49)
283 PF08461 HTH_12: Ribonuclease 21.7 1E+02 0.0022 22.2 2.8 49 355-406 3-52 (66)
284 smart00342 HTH_ARAC helix_turn 21.6 1.2E+02 0.0026 21.8 3.3 26 266-291 1-26 (84)
285 PF10078 DUF2316: Uncharacteri 21.4 1.1E+02 0.0023 23.8 2.9 24 265-288 22-45 (89)
286 PRK12423 LexA repressor; Provi 21.3 1.7E+02 0.0036 26.3 4.7 52 250-303 4-61 (202)
287 TIGR02835 spore_sigmaE RNA pol 21.1 1.6E+02 0.0034 27.0 4.6 25 264-288 196-220 (234)
288 PRK12530 RNA polymerase sigma 21.1 1.5E+02 0.0032 26.1 4.3 37 251-288 136-172 (189)
289 PRK09651 RNA polymerase sigma 21.0 1.2E+02 0.0026 26.1 3.6 25 264-288 133-157 (172)
290 COG4367 Uncharacterized protei 20.9 1.2E+02 0.0026 23.3 3.0 24 265-288 22-45 (97)
291 PRK14165 winged helix-turn-hel 20.8 80 0.0017 28.9 2.5 49 358-414 15-63 (217)
292 PF04297 UPF0122: Putative hel 20.7 1.9E+02 0.0041 23.0 4.3 38 250-288 18-55 (101)
293 TIGR02392 rpoH_proteo alternat 20.7 1.6E+02 0.0035 27.6 4.8 36 251-286 220-256 (270)
294 PRK12534 RNA polymerase sigma 20.5 1.4E+02 0.003 25.9 4.0 38 251-289 139-176 (187)
295 COG4565 CitB Response regulato 20.5 2.1E+02 0.0045 26.2 4.9 50 248-299 155-204 (224)
296 PRK06759 RNA polymerase factor 20.5 1.7E+02 0.0037 24.3 4.4 38 250-289 107-145 (154)
297 PRK06704 RNA polymerase factor 20.4 1.4E+02 0.003 27.5 4.0 40 249-289 116-155 (228)
298 PRK12542 RNA polymerase sigma 20.4 1.7E+02 0.0036 25.4 4.5 37 250-288 123-160 (185)
299 PRK10870 transcriptional repre 20.3 80 0.0017 27.7 2.4 36 363-406 70-105 (176)
300 PRK09646 RNA polymerase sigma 20.2 1.6E+02 0.0034 25.9 4.3 40 249-289 142-181 (194)
301 smart00529 HTH_DTXR Helix-turn 20.1 1.4E+02 0.003 22.7 3.5 31 269-301 2-32 (96)
302 COG0735 Fur Fe2+/Zn2+ uptake r 20.1 1.5E+02 0.0033 25.0 4.0 58 354-414 25-83 (145)
303 TIGR01610 phage_O_Nterm phage 20.1 70 0.0015 24.9 1.7 38 361-406 44-81 (95)
No 1
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.3e-84 Score=631.95 Aligned_cols=396 Identities=41% Similarity=0.712 Sum_probs=374.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhcCCC--HHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHhhcCCCCCCChHHHHH
Q 014910 12 QEQVLIRKIIELHDKYMEYVTNCFINH--TLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEE 89 (416)
Q Consensus 12 ~~~~~i~~l~~l~~~~~~l~~~~F~~~--~~f~~~l~~af~~~~N~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~e~~~ 89 (416)
.++.+|+.++.++++.+-++..||..+ ..|..++++||+.|+|... .++||+||+|.|.+|+.|. +..++++++.
T Consensus 260 kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~ 336 (661)
T KOG2167|consen 260 KDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEF 336 (661)
T ss_pred hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHH
Confidence 478999999999999999999999998 9999999999999999765 5799999999999999865 5667888999
Q ss_pred HHHHHHHHhhccCChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHHHHHHHHHHHH
Q 014910 90 TLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY 169 (416)
Q Consensus 90 ~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~ 169 (416)
.++.++.||+|+..||+|+.+|++.||+|||.++|++.|+|.+|+.+|+.+||..||++|++|++|+..|++++..|+++
T Consensus 337 ~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~ 416 (661)
T KOG2167|consen 337 VLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQS 416 (661)
T ss_pred HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HhcCCCCCCCcceEEEEeecCCCCCCCCCCccCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecceeEEEE
Q 014910 170 LSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELI 249 (416)
Q Consensus 170 ~~~~~~~~~~~~~~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~lg~~~l~~~~~~~~~~l~ 249 (416)
...+.....++ +.+.|++.++||.+++.++.||++|..+++-|..||..+|.||+|.|.+++|+|.+++.|..|+.++.
T Consensus 417 ~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~ 495 (661)
T KOG2167|consen 417 KGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQ 495 (661)
T ss_pred HHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHH
Confidence 55444333445 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCcceeeec
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIP 329 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~~~~~ki~i~ 329 (416)
+|++|++||++||+.+.+|++||.++|++.+.+|.+.|++|.|+|.++|.+.|.|+.+.+++.|.+|..|+++..||+|+
T Consensus 496 ~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikin 575 (661)
T KOG2167|consen 496 VSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKIN 575 (661)
T ss_pred HHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCc----hhhhhHHHhHHHhhhhhhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc
Q 014910 330 LPPV----DERKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 405 (416)
Q Consensus 330 ~~~~----~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~ 405 (416)
.+.+ +|.+.+.++|.+||++.||||||||||.||+|+|+.|+.++.++++ |+..+ ++|+|||+||+|||++||
T Consensus 576 qi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd 652 (661)
T KOG2167|consen 576 QIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD 652 (661)
T ss_pred hhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc
Confidence 8754 4567788999999999999999999999999999999999999997 98888 999999999999999999
Q ss_pred CCCCCceEecC
Q 014910 406 KENPNMFRYLA 416 (416)
Q Consensus 406 ~~~~~~y~Yia 416 (416)
+| +.|.|||
T Consensus 653 -~n-~~y~yva 661 (661)
T KOG2167|consen 653 -DN-NIYNYVA 661 (661)
T ss_pred -cc-ccccccC
Confidence 44 9999998
No 2
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.2e-82 Score=655.76 Aligned_cols=396 Identities=71% Similarity=1.120 Sum_probs=375.1
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHhhcCCCCCCChHHHHHH
Q 014910 11 VQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEET 90 (416)
Q Consensus 11 ~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~e~~~~ 90 (416)
.+|..+|+.+++++++|..++..||+++..|..+++.||..|+|.+.. ..+|+||+|||.+||++ ..+.++++++..
T Consensus 330 ~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~--~~~E~la~y~D~~lkk~-~k~~~e~~ie~~ 406 (725)
T KOG2166|consen 330 TNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA--TSAELLATYCDDILKKG-SKKLSDEAIEDT 406 (725)
T ss_pred cchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC--CcHHHHHHHhHHHhccc-ccCCchhHHHhH
Confidence 899999999999999999999999999999999999999999999863 23699999999999995 467789999999
Q ss_pred HHHHHHHhhccCChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHHHHHHHHHHHHH
Q 014910 91 LEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYL 170 (416)
Q Consensus 91 l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~ 170 (416)
+++++.+|+|+.+||+|+.+|+++||+|||+++|.|++.|+.||.+|+++||.+||.+|++|++|+..|+++...|.++
T Consensus 407 l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~- 485 (725)
T KOG2166|consen 407 LEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADY- 485 (725)
T ss_pred hhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhh-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999977
Q ss_pred hcCCCCCCCcceEEEEeecCCCCCCCCCCccCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecceeEEEEE
Q 014910 171 SNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIV 250 (416)
Q Consensus 171 ~~~~~~~~~~~~~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~lg~~~l~~~~~~~~~~l~~ 250 (416)
.+.....+++|.|.||+.|+||.+++.++.||++|.++++.|.+||..+|+||+|.|+|++|+|+|.++|.+++++++|
T Consensus 486 -~~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~v 564 (725)
T KOG2166|consen 486 -ANYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQV 564 (725)
T ss_pred -hchhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEE
Confidence 1222246799999999999999988778999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCcceeeecC
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPL 330 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~~~~~ki~i~~ 330 (416)
|++||+||++||+.+.+|+++|.++|+++.+++.++|+||.+.|.+++.. |.++. .+++.|.+|.+|+++.+|++++.
T Consensus 565 st~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~ 642 (725)
T KOG2166|consen 565 STYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPL 642 (725)
T ss_pred EhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCC
Confidence 99999999999999999999999999999999999999998888667666 66666 78999999999999999999998
Q ss_pred CCchhhhhHHHhHHHhhhhhhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCC
Q 014910 331 PPVDERKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPN 410 (416)
Q Consensus 331 ~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~ 410 (416)
++..+.+++.+.+++||+..|+||||||||+||.+.|.+|+.+|.+|++++|.|++.+||+|||.|||||||+|| +|++
T Consensus 643 ~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~ 721 (725)
T KOG2166|consen 643 PPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPN 721 (725)
T ss_pred CCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 888888889999999999999999999999999999999999999999999999999999999999999999999 8999
Q ss_pred ceEe
Q 014910 411 MFRY 414 (416)
Q Consensus 411 ~y~Y 414 (416)
+|+|
T Consensus 722 ~Y~Y 725 (725)
T KOG2166|consen 722 IYRY 725 (725)
T ss_pred cccC
Confidence 9998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5e-79 Score=607.46 Aligned_cols=401 Identities=36% Similarity=0.630 Sum_probs=363.4
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCC-CCChHHHHHHHHHHHhhcCCCCCCChHHH
Q 014910 9 GAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVG-GSSSSELLATFCDNILKKGGNEKLSDEAI 87 (416)
Q Consensus 9 ~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~~-~~~~~e~La~y~d~~l~~~~~~~~~~~e~ 87 (416)
....|..+++.++++++.+..++.+.|.+|..+..++++||..|+|.+.+ ...++|+||+|+|.+|++++ +..-...+
T Consensus 364 ~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~-k~s~~~~i 442 (773)
T COG5647 364 RECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFINGNESADSGPSEYLAKYIDGLLKKDG-KQSFIGKI 442 (773)
T ss_pred hhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhccccccccccHHHHHHHhHHHhhccc-cccccccH
Confidence 44689999999999999999999999999999999999999999998542 35689999999999999965 22233457
Q ss_pred HHHHHHHHHHhhccCChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHHHHHHHHHH
Q 014910 88 EETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFE 167 (416)
Q Consensus 88 ~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~ 167 (416)
+..+.+++.||+|+.+||+|+++|+++||+|||+++|.+.+.|..||++|++.||.+||+|+++|++||..|.++...|+
T Consensus 443 ~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~ 522 (773)
T COG5647 443 KDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQ 522 (773)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHh
Confidence 77889999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred HHHhcCCCCCCCcceEEEEeecCCCCCCC-CCCccCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecceeE
Q 014910 168 EYLSNNQNAHPGIDLSVTVLTTGFWPSYK-SSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNI 246 (416)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~VLs~~~WP~~~-~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~lg~~~l~~~~~~~~~ 246 (416)
+... + ..+.+++.|.||++.+||..+ ...++||++|.+.++.|++||..||+||+|.|.|+||+|+|+++|+.+++
T Consensus 523 ~s~~-s--~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~ 599 (773)
T COG5647 523 HSPQ-S--YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQK 599 (773)
T ss_pred hCch-h--hccccchhHHHHHHhcCCCCccccccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCcc
Confidence 6431 1 135789999999999999654 46899999999999999999999999999999999999999999998765
Q ss_pred EEE---EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCc
Q 014910 247 ELI---VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRM 323 (416)
Q Consensus 247 ~l~---~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~~~~ 323 (416)
.+. ++++|+.|+++||+++++|+++|.+.|+++.+++++.|+||++.|..++.+ +++.++|++.|.+|.+|+++.
T Consensus 600 ~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~ 677 (773)
T COG5647 600 YLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKL 677 (773)
T ss_pred ceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhhheeeecc--ccccCCCCceEEEcccccccc
Confidence 554 557899999999999999999999999999999999999999876555554 477889999999999999999
Q ss_pred ceeeecCCCc----hhhhhHHHhHHHhhhhhhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhh
Q 014910 324 RRIKIPLPPV----DERKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITR 399 (416)
Q Consensus 324 ~ki~i~~~~~----~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Lier 399 (416)
.+|+++.+.. ++...+++.+++||+..+|||||||||++|.|+|.+|+++|+.+++.||.|++.+||++|+.||||
T Consensus 678 ~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEK 757 (773)
T COG5647 678 ERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEK 757 (773)
T ss_pred ceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHH
Confidence 9999997653 445567788999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCCCCceEecC
Q 014910 400 DYLERDKENPNMFRYLA 416 (416)
Q Consensus 400 eyi~r~~~~~~~y~Yia 416 (416)
|||+|.++| .+|+|+|
T Consensus 758 eYLeR~~dd-~iY~YLa 773 (773)
T COG5647 758 EYLERQADD-EIYVYLA 773 (773)
T ss_pred HHHHhccCC-ceeeecC
Confidence 999999988 8999997
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.2e-70 Score=510.48 Aligned_cols=377 Identities=30% Similarity=0.542 Sum_probs=350.0
Q ss_pred CCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCC---CCChHHHHHHHHHHHhhcCCCCC
Q 014910 5 GGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVG---GSSSSELLATFCDNILKKGGNEK 81 (416)
Q Consensus 5 ~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~~---~~~~~e~La~y~d~~l~~~~~~~ 81 (416)
++..+...|..||+.++.+|+||.+++...|.+|..|..+++.|+..++|...+ ..+.+|.||+|||.+|+++. ++
T Consensus 344 s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~-kg 422 (728)
T KOG2284|consen 344 SRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKST-KG 422 (728)
T ss_pred hhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhh-cC
Confidence 345667899999999999999999999999999999999999999999998764 35789999999999999975 68
Q ss_pred CChHHHHHHHHHHHHHhhccCChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHHHH
Q 014910 82 LSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARE 161 (416)
Q Consensus 82 ~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~ 161 (416)
+++.+++.+|+..+.+|+|++|||+|.++|.++||+||+.+.|.|.|.|..||++|++.||.+||+++- +.|+..|.+
T Consensus 423 ~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~ 500 (728)
T KOG2284|consen 423 LSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTN 500 (728)
T ss_pred CChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccc
Confidence 899999999999999999999999999999999999999999999999999999999999999999998 999999999
Q ss_pred HHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEe
Q 014910 162 NQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKF 241 (416)
Q Consensus 162 l~~~f~~~~~~~~~~~~~~~~~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~lg~~~l~~~~ 241 (416)
+|.+|.+.+. ++.+|.+|+...+.|+.||..+|+||+|+|++.++++++++++
T Consensus 501 lnn~f~~~i~---------------------------nf~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~y 553 (728)
T KOG2284|consen 501 LNNQFAQDIA---------------------------NFHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTY 553 (728)
T ss_pred cchhHHHHHH---------------------------hccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeee
Confidence 9999987654 2789999999999999999999999999999999999999999
Q ss_pred cceeEEEEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCC
Q 014910 242 EQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTD 321 (416)
Q Consensus 242 ~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~~ 321 (416)
-++.|.-.+.++||++||+||..+.+++.+|.+.+|++.+.|.+.+.++.+ .++|.. ++..+..+..|++|.+|++
T Consensus 554 l~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~tild--v~~~~~--d~~~~~a~s~~~lnm~~ts 629 (728)
T KOG2284|consen 554 LDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTILD--VTLLTC--DDQNLTADSLVRLNMSMTS 629 (728)
T ss_pred cCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHHh--ceeecc--cccccChhhhhhccccccc
Confidence 999999999999999999999999999999999999999999999999985 467754 3446777889999999999
Q ss_pred CcceeeecCCCc-----hhhhhHHHhHHHhhhhhhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhh
Q 014910 322 RMRRIKIPLPPV-----DERKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDL 396 (416)
Q Consensus 322 ~~~ki~i~~~~~-----~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~L 396 (416)
+..++++..|.+ +|.+.+...+.+||++.++||||||||+||.+.|+.|+.+|+.|.+++|.|++..||++||.|
T Consensus 630 kr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~l 709 (728)
T KOG2284|consen 630 KRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDL 709 (728)
T ss_pred cceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHH
Confidence 999999987654 345566778899999999999999999999999999999999999999999999999999999
Q ss_pred hhhccccccCCCCCceEecC
Q 014910 397 ITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 397 iereyi~r~~~~~~~y~Yia 416 (416)
|++.||+|.+.+ +.|.|+|
T Consensus 710 i~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 710 IEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHhhcccc-ccchhcC
Confidence 999999999876 9999997
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.5e-65 Score=480.80 Aligned_cols=410 Identities=29% Similarity=0.491 Sum_probs=363.4
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC------------------CCCChHHHHH
Q 014910 6 GSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAV------------------GGSSSSELLA 67 (416)
Q Consensus 6 ~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~------------------~~~~~~e~La 67 (416)
++.-+.|+..||++|+.++++|..++.+.|++|+.|..|.+.||+.++|+.. +..++||+||
T Consensus 326 aE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLA 405 (777)
T KOG2285|consen 326 AENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLA 405 (777)
T ss_pred hhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHHH
Confidence 3445689999999999999999999999999999999999999999999864 1357999999
Q ss_pred HHHHHHhhcC-CCCCCChHHHHHHHHHHHHHhhccCChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhC--Ch
Q 014910 68 TFCDNILKKG-GNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCG--GQ 144 (416)
Q Consensus 68 ~y~d~~l~~~-~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G--~~ 144 (416)
+|||.+||+. .+++++.++++.+|++++-+++|+.+||+|+.|++.+|++||+...|++.+.|..|++.|+ +|| .+
T Consensus 406 NYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaD 484 (777)
T KOG2285|consen 406 NYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPAD 484 (777)
T ss_pred HHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHH
Confidence 9999999994 4678899999999999999999999999999999999999999999999999999999998 577 57
Q ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCccCCHHHHHHHHHHHHHHhhcCCC
Q 014910 145 FTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKS-SDLNLPSEMVKCVEVFKGFYETKTKH 223 (416)
Q Consensus 145 ~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLs~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~k~~~ 223 (416)
|.+++.+|++|++.|++++.+|+..+...+.....-.+++.||+.|.|...+. ..+.||.+|++.+-..++||+++|.|
T Consensus 485 yVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsg 564 (777)
T KOG2285|consen 485 YVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSG 564 (777)
T ss_pred HHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccCc
Confidence 99999999999999999999999988766544556678999999999997643 46889999999999999999999999
Q ss_pred ceEEeccCCceEEEEeEecceeEEEEEcHHHHHHHHhhhCC--CCcCHHHHHHHcCCCHHHHHHHHHhhhc---ccceee
Q 014910 224 RKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTS--DRLSYSEIMTQLNLTHDDLVRLLHSLSC---AKYKIL 298 (416)
Q Consensus 224 R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~--~~~t~~ei~~~~~i~~~~l~~~L~~L~~---~k~~iL 298 (416)
|+|+|.|+++.++|++..+-|.|.++|+++||+||.+||+. +.+|++.+.-+|.+|..++.+.|.||+. .|+.||
T Consensus 565 rkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiL 644 (777)
T KOG2285|consen 565 RKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQIL 644 (777)
T ss_pred cchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhhee
Confidence 99999999999998876555789999999999999999975 6899999999999999999999999974 367888
Q ss_pred ecCCC----CCCCCCCCeEEEccCCCC-----CcceeeecCCCc----hh--hhhHHHhHHHhhhhhhceeeeehhccCC
Q 014910 299 LKEPN----TKTISQSDHFEFNSKFTD-----RMRRIKIPLPPV----DE--RKKIVEDVDKDRRYAIDAALVRIMKSRK 363 (416)
Q Consensus 299 ~~~~~----~~~i~~~~~~~lN~~f~~-----~~~ki~i~~~~~----~e--~~~~~~~~~~~r~~~i~A~IVRimK~~k 363 (416)
..+|+ .+++.+++.|.+|.+|.- ..++-+++...- .| .++.++.+.+-|-...|-+|++|||.||
T Consensus 645 L~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK 724 (777)
T KOG2285|consen 645 LCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRK 724 (777)
T ss_pred eecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHH
Confidence 87763 356778899999999973 122444443321 11 2334567888999999999999999999
Q ss_pred CCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 364 VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 364 ~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
+++..+|-.++++.|+..|.|+..+||+.||.|||..|++||++|.++|.|+|
T Consensus 725 ~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 725 TYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 99999999999999999999999999999999999999999999999999997
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=2.7e-56 Score=468.70 Aligned_cols=308 Identities=44% Similarity=0.750 Sum_probs=268.0
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHhhcCCCCCCChHHHHH
Q 014910 10 AVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEE 89 (416)
Q Consensus 10 ~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~e~~~ 89 (416)
..+|..||+.++++|++|+.++.+||++++.|..++++||+.++|.. ...++++||+|||.+|+++. ++.++++++.
T Consensus 279 ~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~--~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~ 355 (588)
T PF00888_consen 279 SSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKN--NNKIPELLAKYCDSLLRKSN-KKLSEEEIEQ 355 (588)
T ss_dssp GGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCS--TSHHHHHHHHHHHHHHBSSC-CCS-HCCHHH
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcC--CcchHHHHHHHhhHhhhhcc-cccchHHHHH
Confidence 46788999999999999999999999999999999999999999988 35899999999999999975 5667888999
Q ss_pred HHHHHHHHhhccCChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHHHHHHHHHHHH
Q 014910 90 TLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY 169 (416)
Q Consensus 90 ~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~ 169 (416)
.++.++.+|+|+++||+|+.+|+++||+|||..++.+.+.|..+|++|+.+||.+++++|++|++|+..|++++..|++.
T Consensus 356 ~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~ 435 (588)
T PF00888_consen 356 KLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQK 435 (588)
T ss_dssp HHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HhcCCCCC-CCcceEEEEeecCCCCCCCCCC-ccCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecceeEE
Q 014910 170 LSNNQNAH-PGIDLSVTVLTTGFWPSYKSSD-LNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIE 247 (416)
Q Consensus 170 ~~~~~~~~-~~~~~~~~VLs~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~lg~~~l~~~~~~~~~~ 247 (416)
....+... .+++|++.||++++||..+... +.+|++|+.+++.|++||+.+|++|+|+|.+++|+|+|++++++++++
T Consensus 436 ~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~ 515 (588)
T PF00888_consen 436 QSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYE 515 (588)
T ss_dssp HHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEE
T ss_pred hhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCcee
Confidence 87654322 2789999999999999988766 999999999999999999999999999999999999999999999999
Q ss_pred EEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 014910 248 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 320 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~ 320 (416)
+.||++||+||++||+.+++|+++|++.||++.++++++|.+|+..+..++.+.++++++++++.|++|.+|+
T Consensus 516 l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 516 LTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp EEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred EEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 9999999999999999999999999999999999999999999865433333677888999999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=4.1e-35 Score=251.36 Aligned_cols=141 Identities=48% Similarity=0.896 Sum_probs=132.3
Q ss_pred ccCChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 014910 100 YISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPG 179 (416)
Q Consensus 100 ~l~~KD~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 179 (416)
|+++||+|+.+|+++||+|||..++++.+.|..+|++|+.+||.+++++|++|++|+..|+++++.|++.+.+++ ...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~-~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNS-NKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 689999999999999999999999999999999999999999999999999999999999999999998876532 2356
Q ss_pred cceEEEEeecCCCCCCCC-CCccCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEe
Q 014910 180 IDLSVTVLTTGFWPSYKS-SDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKF 241 (416)
Q Consensus 180 ~~~~~~VLs~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~lg~~~l~~~~ 241 (416)
++|+|.|||+++||..+. .++.||++|+.+++.|++||..+|++|+|+|+|++|+|+|+++|
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 899999999999999877 78999999999999999999999999999999999999999864
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.5e-30 Score=257.71 Aligned_cols=302 Identities=24% Similarity=0.324 Sum_probs=241.0
Q ss_pred HHHHHhhccCChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHHHHHHHHHHHH--H
Q 014910 93 KVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY--L 170 (416)
Q Consensus 93 ~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~--~ 170 (416)
-+-.|++.+.+|+.|++.||.+||.||+....++.+.|..-++.||-++|.+..+.|+.|++|+..|+++++.++.. .
T Consensus 441 i~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~ 520 (765)
T KOG2165|consen 441 IFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESEL 520 (765)
T ss_pred HHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhh
Confidence 35667888999999999999999999999999999999999999999999999999999999999999999999874 2
Q ss_pred hcCCCCCCCcceEEEEeecCCCCCCCCCCccCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecceeEEEEE
Q 014910 171 SNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIV 250 (416)
Q Consensus 171 ~~~~~~~~~~~~~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~lg~~~l~~~~~~~~~~l~~ 250 (416)
.......+.+.+++.+||+.+||......+.+|.+++..++.|.+.|.+.+++|+|.|.+++|+|++++.|.+++..++|
T Consensus 521 ~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tV 600 (765)
T KOG2165|consen 521 SRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTV 600 (765)
T ss_pred hcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEee
Confidence 22112234678899999999999988888999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCcceeeecC
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPL 330 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~~~~~ki~i~~ 330 (416)
|+.||+|+.+|.+.++||++++++.+|+|...+.+.|..|+ +.++|..+|. ++++.+|++++.=.+.-+- -.+
T Consensus 601 sp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~d~~q~--~~~ 673 (765)
T KOG2165|consen 601 SPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEMDFDQA--EGT 673 (765)
T ss_pred CHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeecccccccccc--CCC
Confidence 99999999999999999999999999999999999999997 4588887653 2667889998854332210 111
Q ss_pred CCc--h-hh--hhHHHhHHHhh--hhhhceeeeehhccCCCCChhHHHHHHHHHhccCCCC-------ChHHHHHHHHhh
Q 014910 331 PPV--D-ER--KKIVEDVDKDR--RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKP-------DIKAIKKRMEDL 396 (416)
Q Consensus 331 ~~~--~-e~--~~~~~~~~~~r--~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~-------~~~~ik~~Ie~L 396 (416)
+.. + +. ......+.+-+ -..-...||-.+-.-+.|..+.+.+... .|.| +-++++.-+..+
T Consensus 674 ~~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLk-----mF~~~~~~~~~TlqeL~~fLq~k 748 (765)
T KOG2165|consen 674 VLLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLK-----MFVPPDGSAEITLQELQGFLQRK 748 (765)
T ss_pred cccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHe-----eeecCCCCCcccHHHHHHHHHHH
Confidence 111 1 11 11111222211 1233448888888889999988877543 4544 345666666666
Q ss_pred hhhccccccC
Q 014910 397 ITRDYLERDK 406 (416)
Q Consensus 397 iereyi~r~~ 406 (416)
+..|-++-.+
T Consensus 749 V~e~kL~f~~ 758 (765)
T KOG2165|consen 749 VREGKLEFIA 758 (765)
T ss_pred hhccceEEec
Confidence 6666555544
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.81 E-value=3e-21 Score=143.03 Aligned_cols=68 Identities=50% Similarity=0.963 Sum_probs=62.4
Q ss_pred HHHhhhhhhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCC
Q 014910 343 VDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPN 410 (416)
Q Consensus 343 ~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~ 410 (416)
++++|...|+|+||||||++|+++|++|+.+|.+.++++|.|+..+||++||+||++|||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 36799999999999999999999999999999999999999999999999999999999999999876
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=95.60 E-value=0.042 Score=43.35 Aligned_cols=65 Identities=17% Similarity=0.237 Sum_probs=52.9
Q ss_pred EEEcHHHHHHHHhhh--------CCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCC
Q 014910 248 LIVSTYQAATLLLFN--------TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 319 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn--------~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f 319 (416)
..+++-|+.+|+... ....+|-.||++.+|++.+.+.++|..|. +.++|.+.. ....|.+|.++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~~ 92 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTPL 92 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCCc
Confidence 467888999888665 45789999999999999999999999997 567887542 24789999887
Q ss_pred C
Q 014910 320 T 320 (416)
Q Consensus 320 ~ 320 (416)
+
T Consensus 93 ~ 93 (95)
T TIGR01610 93 S 93 (95)
T ss_pred c
Confidence 5
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=94.36 E-value=0.072 Score=36.81 Aligned_cols=45 Identities=27% Similarity=0.325 Sum_probs=36.6
Q ss_pred HHHHHhhhCCC-CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 255 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 255 ~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+.||..|.+.+ .+|+.||++.+|++...+.+.|..|. ..+++.+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~--~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLV--EEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCcCeecC
Confidence 45788888776 58999999999999999999999997 35777653
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=94.15 E-value=0.11 Score=35.12 Aligned_cols=41 Identities=20% Similarity=0.331 Sum_probs=34.6
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
+..+..||..+.+++.+|..||++.+|++...+.+.|..|.
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45677888888888899999999999999999999999996
No 13
>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=93.98 E-value=0.08 Score=37.74 Aligned_cols=51 Identities=20% Similarity=0.337 Sum_probs=42.6
Q ss_pred EcHHHHHHHHhhhCCCC--cCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 250 VSTYQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~--~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|. +.+++.+.+
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 47789999988877776 9999999999999999999999997 457777653
No 14
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=93.90 E-value=0.19 Score=38.44 Aligned_cols=60 Identities=15% Similarity=0.208 Sum_probs=41.7
Q ss_pred HHHHHHHhhhCCC-CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCC
Q 014910 253 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 319 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f 319 (416)
+++.+.+..+..+ .+|.++|++.++++...+.+.++.|. +.+++.... .+++-|.++.+-
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 3444444444433 49999999999999999999999997 568876542 145778887653
No 15
>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=93.03 E-value=0.078 Score=37.46 Aligned_cols=51 Identities=18% Similarity=0.344 Sum_probs=43.2
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+|..|+.+|....+.+.++..+|++.++++...+.+.+..|. +.+++.+.+
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 367899999988888899999999999999999999999997 457777653
No 16
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=92.78 E-value=0.19 Score=35.46 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=38.9
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
|..|+...++.+.+|+++|++.+|++...+.+-|..|.. .+++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~--~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEK--QGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 456788888899999999999999999999999999973 4566554
No 17
>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=92.15 E-value=0.25 Score=35.79 Aligned_cols=50 Identities=16% Similarity=0.307 Sum_probs=38.5
Q ss_pred EcHHHHHHHHhhh-CCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 250 VSTYQAATLLLFN-TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn-~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+|..|..||..+. ....++..+|++.++++...+-+.++.|. ..+++.+.
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~--~~glv~~~ 51 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLE--EKGLVEKE 51 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEec
Confidence 3667899998888 77899999999999999999999999997 35777654
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=91.82 E-value=0.36 Score=39.45 Aligned_cols=52 Identities=12% Similarity=0.201 Sum_probs=45.4
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
.++..|+.||..+..++.+|..+|++.+|++...+-+.+..|. +.+++.+.+
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 4578899999988888899999999999999999999999997 458887653
No 19
>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=91.18 E-value=0.53 Score=31.65 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=34.7
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
...-||.++-+ +..++.||++.+|++...+.++|..|. +.+++.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLVE 46 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCee
Confidence 45567777766 689999999999999999999999996 345553
No 20
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=91.12 E-value=0.47 Score=40.28 Aligned_cols=53 Identities=19% Similarity=0.183 Sum_probs=45.7
Q ss_pred EEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 248 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
..++..|+.||......+.+|..+|++.++++...+-+.+..|. +.+++.+.+
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 35678899999877767789999999999999999999999997 568888764
No 21
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=90.96 E-value=0.35 Score=34.49 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=40.0
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
++.-..||.++...+++|+.+|++.+|++...+..+|..|. +.+++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~--~aGli~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLE--EAGLIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEe
Confidence 45667788888667899999999999999999999999997 45777643
No 22
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=90.48 E-value=0.87 Score=33.38 Aligned_cols=47 Identities=21% Similarity=0.276 Sum_probs=38.3
Q ss_pred HHHHHHHhhhCCCC--cCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 253 YQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~--~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
..-.||.++.+.+. +|..||++.+|++...+.++|..|. +.+++.+.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~--~~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE--KKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 44567777777765 9999999999999999999999996 45677654
No 23
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=89.49 E-value=0.35 Score=39.73 Aligned_cols=62 Identities=21% Similarity=0.302 Sum_probs=52.6
Q ss_pred hhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 350 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 350 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
..++-||+||=.++..+.+|++.++.. .+.++...|+.-|..|..||.|.+.-+ ...|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~----~~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPA----DREWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhh----cccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence 356778999999999999999888765 477899999999999999999999874 57787754
No 24
>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=89.16 E-value=0.46 Score=39.75 Aligned_cols=60 Identities=17% Similarity=0.201 Sum_probs=45.0
Q ss_pred ceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 352 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 352 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
+..|++++-..+.++..+++... .....++...+...|..|.+||||+|..+ ...|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l----~~~~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRIL----AEKKDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHH----hhccCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 34467777677778777666654 33456788899999999999999999854 45788864
No 25
>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=88.82 E-value=0.99 Score=31.23 Aligned_cols=36 Identities=17% Similarity=0.351 Sum_probs=29.0
Q ss_pred HHHHhh-hCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 256 ATLLLF-NTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 256 ~iLl~F-n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.||.++ +..+.+|.++|++.+|++...+.+.|..|.
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 445444 666679999999999999999999999985
No 26
>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=88.67 E-value=1.2 Score=35.84 Aligned_cols=52 Identities=25% Similarity=0.367 Sum_probs=43.7
Q ss_pred EEcHHHHHHHHhhh----CCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 249 IVSTYQAATLLLFN----TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn----~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
.+|..|..||.... ..+.+|..+|++.++++...+-+.+..|. +.+++.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~ 77 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKER 77 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccC
Confidence 45788888887665 55689999999999999999999999997 568888754
No 27
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=88.14 E-value=1.5 Score=33.74 Aligned_cols=45 Identities=22% Similarity=0.345 Sum_probs=37.4
Q ss_pred HHHHHhhhCC-CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 255 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 255 ~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
..||..+... +.+|+.||++.+|++...+.+.|..|. ..+++.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeec
Confidence 4566677766 689999999999999999999999997 45788754
No 28
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=87.99 E-value=0.28 Score=36.09 Aligned_cols=44 Identities=18% Similarity=0.321 Sum_probs=34.3
Q ss_pred eehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 014910 356 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 356 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
-.+|+.++.++.++|-. +|..+++.+...|+.|+.+|||++.+.
T Consensus 6 ~~~l~~~~~~S~~eLa~--------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAR--------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHS-SEEHHHHHH--------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHcCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 34677888888877766 588999999999999999999998753
No 29
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=87.09 E-value=1.3 Score=34.38 Aligned_cols=52 Identities=23% Similarity=0.299 Sum_probs=44.7
Q ss_pred EEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 248 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+.++..+..||..+.....++..+|++.++++...+.+.|..|. +.+++.+.
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 45778899999988877889999999999999999999999997 45777653
No 30
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=86.60 E-value=0.74 Score=37.53 Aligned_cols=59 Identities=12% Similarity=0.216 Sum_probs=42.3
Q ss_pred eeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 353 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 353 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
..|++++=..+.++..|++.. +.....+....|...+..|.+||||++... ...|.|-|
T Consensus 6 ~~IM~~lW~~~~~t~~eI~~~----l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 6 LEIMEILWESGEATVREIHEA----LPEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHSSEEHHHHHHH----HCTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHhCCCCCHHHHHHH----HHhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 345566656666776666665 444466889999999999999999999874 46788864
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=86.58 E-value=0.59 Score=34.08 Aligned_cols=49 Identities=22% Similarity=0.274 Sum_probs=39.5
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
|-.++-|+..+-..+..|..+|++.+|++...+.+.|..|.. .+++.+.
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~--~GlV~~~ 55 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEE--KGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHH--TTSEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 455666776555667899999999999999999999999973 4677654
No 32
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=86.25 E-value=1.7 Score=40.84 Aligned_cols=45 Identities=11% Similarity=0.282 Sum_probs=39.2
Q ss_pred HHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 255 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+.||.+|.....+|+.||++.+|++...+.+.|..|. ..++|.+.
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~--~~G~l~~~ 61 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMK--TLGYVAQE 61 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEc
Confidence 4678889887789999999999999999999999997 45788764
No 33
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=86.01 E-value=2.4 Score=36.48 Aligned_cols=57 Identities=11% Similarity=0.080 Sum_probs=41.6
Q ss_pred HHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 014910 255 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 318 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~ 318 (416)
+.+.+..+..+.+|..+|++..++|...|.+.|..|. +.+++..... .++-|.++..
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~rG-----~~GGy~La~~ 69 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVRG-----RNGGVRLGRP 69 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeecC-----CCCCeeecCC
Confidence 3344445555678999999999999999999999996 6788875421 3455666544
No 34
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=85.62 E-value=1.9 Score=29.07 Aligned_cols=44 Identities=20% Similarity=0.263 Sum_probs=34.9
Q ss_pred HHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 255 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
-.|+..+.+...++..+|++.++++...+.+.|..|.. .+++.+
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~ 46 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTR 46 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 34566666667899999999999999999999999963 355554
No 35
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=85.47 E-value=2.7 Score=36.64 Aligned_cols=45 Identities=16% Similarity=0.216 Sum_probs=36.1
Q ss_pred HHHHHHhhhCC-CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 254 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 254 Q~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.+.+.+.|+.. ..+|.++|++.+++|...+.+.|..|. +.+|+..
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s 57 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSS 57 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 33444556643 589999999999999999999999996 5688874
No 36
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=85.36 E-value=2.3 Score=35.22 Aligned_cols=39 Identities=21% Similarity=0.296 Sum_probs=34.0
Q ss_pred hCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 262 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 262 n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+.++..|+++|++.++.+...+.++|+.|. ..+++.+..
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~--~~GlV~Rek 76 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLL--EAGLVEREK 76 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHH--HcCCeeeee
Confidence 367899999999999999999999999997 468887653
No 37
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=85.09 E-value=1.9 Score=36.41 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=44.4
Q ss_pred EEEcHHHHHHHHhhhCC-CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 248 LIVSTYQAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+.++..|..+|...... +.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 45678899999877654 568999999999999999999999997 568887754
No 38
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=85.07 E-value=2 Score=38.19 Aligned_cols=53 Identities=13% Similarity=-0.011 Sum_probs=45.8
Q ss_pred EEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 248 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+.++..|..||......+.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 45678899999999888899999999999999999999999996 457887653
No 39
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=84.54 E-value=2.3 Score=30.60 Aligned_cols=56 Identities=21% Similarity=0.227 Sum_probs=37.3
Q ss_pred HHHhhhC-CCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEc
Q 014910 257 TLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFN 316 (416)
Q Consensus 257 iLl~Fn~-~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN 316 (416)
||..++. +.+++..||++.+|++.......|..|. +.+.+.+.|.++. ....|.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~rG--~~~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRRG--KSTYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SSS--SS-EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCCC--cceeeeec
Confidence 4555555 6789999999999999999999999997 4455555443221 12356665
No 40
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=83.08 E-value=3.6 Score=34.50 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=34.6
Q ss_pred HHHHHhhhCC-CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 255 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 255 ~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
+.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 3344445443 479999999999999999999999996 5688764
No 41
>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=82.88 E-value=3.6 Score=32.71 Aligned_cols=62 Identities=24% Similarity=0.393 Sum_probs=46.3
Q ss_pred EEcHHHHHHHHh-------hhC-CCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 014910 249 IVSTYQAATLLL-------FNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 320 (416)
Q Consensus 249 ~~s~~Q~~iLl~-------Fn~-~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~ 320 (416)
.++.-|.-|++. ||. .+.+|..++++.||++...+.+++..|+ +.++|... +..+-+|.+++
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i~ 98 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNIS 98 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeecccc
Confidence 445566666655 343 3589999999999999999999999997 56888653 35666676653
No 42
>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=82.61 E-value=2.5 Score=36.85 Aligned_cols=49 Identities=18% Similarity=0.281 Sum_probs=40.9
Q ss_pred CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCc
Q 014910 266 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRM 323 (416)
Q Consensus 266 ~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~~~~ 323 (416)
.+|..+|++.+|++...+.+++..|. +.++|.+. ..+.|.+|+++-.+-
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~-------~~G~Y~iNP~~~~kG 123 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKI-------RNGAYMINPNFFFKG 123 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEc-------cCCeEEECcHHheeC
Confidence 57899999999999999999999997 45788764 356899999976543
No 43
>PRK10870 transcriptional repressor MprA; Provisional
Probab=81.92 E-value=3.6 Score=36.27 Aligned_cols=52 Identities=13% Similarity=0.185 Sum_probs=43.0
Q ss_pred EEcHHHHHHHHhhhC--CCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 249 IVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~--~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
-+|..|..||..... ..++|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~ 105 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRE 105 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 356779888887754 4579999999999999999999999997 568888764
No 44
>PHA00738 putative HTH transcription regulator
Probab=81.57 E-value=4 Score=32.67 Aligned_cols=68 Identities=18% Similarity=0.089 Sum_probs=52.0
Q ss_pred EEEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 014910 247 ELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 320 (416)
Q Consensus 247 ~l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~ 320 (416)
++...+.=-.||.++.+++.+++.+|++.++++...+-++|.-|. ..+|+.....|. .-.|++|.+..
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 455666666777777777789999999999999999999999996 468887654432 34577777643
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=81.22 E-value=2.6 Score=27.68 Aligned_cols=36 Identities=28% Similarity=0.451 Sum_probs=27.2
Q ss_pred HHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 255 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
-.||-.+......++.+|++.+|++...+.+-+..|
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 356666777788999999999999999998877654
No 46
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=80.25 E-value=4.7 Score=34.56 Aligned_cols=59 Identities=15% Similarity=0.208 Sum_probs=42.8
Q ss_pred HHHHHHHhhhCCC-CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 014910 253 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 318 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~ 318 (416)
+++.+.+.-+..+ ..|.++|++..|++...|.+.|..|. |.+++..... +++-|.++..
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~rG-----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVRG-----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeecC-----CCCCccCCCC
Confidence 3444555555444 68899999999999999999999996 6788875421 3455766654
No 47
>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=80.04 E-value=4.9 Score=29.73 Aligned_cols=42 Identities=17% Similarity=0.326 Sum_probs=33.5
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.||+..... +.|+++|.+.||++.+.+...|..|. +.+++.+
T Consensus 9 ~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 9 KILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred HHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 344444444 99999999999999999999999996 4577764
No 48
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=79.65 E-value=4.8 Score=28.97 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=38.1
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
+..+..|+..+.+.. ++..+|++.+|++...+.+.|..|.. .+++..
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~--~g~i~~ 52 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEE--AGLVES 52 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHH--CCCeEE
Confidence 446777887777666 99999999999999999999999963 466654
No 49
>PRK11569 transcriptional repressor IclR; Provisional
Probab=79.61 E-value=4.1 Score=38.66 Aligned_cols=46 Identities=17% Similarity=0.212 Sum_probs=38.7
Q ss_pred HHHHHhhhCC-CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 255 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 255 ~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
..||.+|.+. ..+|+.||++.+|++...+.+.|.+|. ..++|.+.+
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~ 77 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVG 77 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 4578889874 479999999999999999999999997 457887643
No 50
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=79.61 E-value=1.9 Score=32.72 Aligned_cols=44 Identities=25% Similarity=0.354 Sum_probs=33.6
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
...||...+..+.+++.+|.+.+|++...+-++|..|.. .+++.
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~--~GyV~ 45 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEE--AGYVE 45 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEE
Confidence 345666666678899999999999999999999999963 45554
No 51
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=79.33 E-value=4.6 Score=38.26 Aligned_cols=45 Identities=27% Similarity=0.324 Sum_probs=38.4
Q ss_pred HHHHHhhhCC-CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 255 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 255 ~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
..||.+|... ..+|+.||++.+|++...+.+.|..|. ..+.|.+.
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~--~~G~l~~~ 73 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQ--AADFVYQD 73 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEc
Confidence 4688889765 479999999999999999999999997 45788764
No 52
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=79.27 E-value=4.7 Score=26.51 Aligned_cols=33 Identities=30% Similarity=0.413 Sum_probs=28.8
Q ss_pred CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 266 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 266 ~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.+|..+|++.+|++...+.+.|..|. +.+++..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 57899999999999999999999997 4577764
No 53
>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=78.92 E-value=3.1 Score=29.44 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=30.1
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
|.-+|-++.+.+.+|+++|++.+|++...++..+.-|-
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 55566555447899999999999999999999888774
No 54
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=78.84 E-value=4.8 Score=37.57 Aligned_cols=46 Identities=28% Similarity=0.416 Sum_probs=39.0
Q ss_pred HHHHHhhhCCCC-cCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 255 AATLLLFNTSDR-LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 255 ~~iLl~Fn~~~~-~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+.||.+|..... +++.||++.+|+|...+.+.|..|. ..+++.+.+
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 457888887654 7899999999999999999999997 468888764
No 55
>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=78.11 E-value=4 Score=32.30 Aligned_cols=44 Identities=23% Similarity=0.306 Sum_probs=37.2
Q ss_pred EEcHHHHHHHHhhhC----CCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 249 IVSTYQAATLLLFNT----SDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~----~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
.++..|-.||-.+.. .+.+++++|++.++++..+++.+|..|+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSN 91 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 578899999988887 35899999999999999999999999974
No 56
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=77.98 E-value=2.7 Score=30.54 Aligned_cols=47 Identities=13% Similarity=0.328 Sum_probs=34.3
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEec
Q 014910 361 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYL 415 (416)
Q Consensus 361 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yi 415 (416)
..+.++..+|... ...+...+-..++.|.++|+|+|.++++..|..+
T Consensus 19 ~~~~~t~~eIa~~--------l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 19 KNGPATAEEIAEE--------LGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHCHEEHHHHHHH--------HTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HcCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 4555555555443 2357788999999999999999998765555554
No 57
>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=77.91 E-value=4 Score=36.85 Aligned_cols=51 Identities=18% Similarity=0.193 Sum_probs=44.7
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
.++..|..||..+.+++.++..+|++.+|++...+.+.|..|. +.+++.+.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~ 190 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQK 190 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 5677899999999887889999999999999999999999997 45788765
No 58
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=77.83 E-value=6.1 Score=32.72 Aligned_cols=45 Identities=20% Similarity=0.278 Sum_probs=34.3
Q ss_pred HHHHHHhhhCC-CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 254 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 254 Q~~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
++.+++.-++. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~ 57 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVES 57 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 34444443333 389999999999999999999999997 4577764
No 59
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=76.63 E-value=5.4 Score=37.53 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=38.4
Q ss_pred HHHHHhhhCCC-CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 255 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 255 ~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+.||.+|.+.. .+|..||++.+|++...+.+.|..|. ..++|.+.+
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~ 60 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSA 60 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 45778887654 59999999999999999999999997 468887654
No 60
>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=76.62 E-value=6.1 Score=36.77 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=37.3
Q ss_pred HHHHHhhhC-CCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 255 AATLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 255 ~~iLl~Fn~-~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
..||.+|.. ...+|+.||++.+|+|...+.+.|..|.. .+.|.+
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 457888986 45899999999999999999999999974 577764
No 61
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=75.77 E-value=6.3 Score=27.16 Aligned_cols=39 Identities=21% Similarity=0.339 Sum_probs=31.8
Q ss_pred hhCCCCc-CHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 261 FNTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 261 Fn~~~~~-t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+.....+ |..+|++.+|++...+.++|..|. +.+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 4445567 899999999999999999999997 45777654
No 62
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=75.75 E-value=6 Score=31.71 Aligned_cols=51 Identities=20% Similarity=0.303 Sum_probs=43.5
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+++.|+.+|.........+..+|++.++++...+.+.+..|. +.+++.+.+
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 788999999888877766669999999999999999999997 557887654
No 63
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=75.50 E-value=4.1 Score=29.77 Aligned_cols=53 Identities=9% Similarity=0.201 Sum_probs=40.4
Q ss_pred ceeeeehhccCCC--CChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCce
Q 014910 352 DAALVRIMKSRKV--LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 412 (416)
Q Consensus 352 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y 412 (416)
+..|...|+.++. ++..+|-.+ ...+...+.+.+..|.++|||.+++..+..|
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~--------lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKN--------LGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 3456777888776 887777664 3356778999999999999999988665554
No 64
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=74.48 E-value=7.9 Score=32.07 Aligned_cols=43 Identities=26% Similarity=0.260 Sum_probs=34.2
Q ss_pred HHHHhhhC--CCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 256 ATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 256 ~iLl~Fn~--~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.+|..+.. .+.+|+.+|++.+|++...+.+.|..|. +.+++..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~ 57 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTS 57 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 34444443 3579999999999999999999999997 4678864
No 65
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=73.69 E-value=6.4 Score=31.26 Aligned_cols=45 Identities=13% Similarity=0.198 Sum_probs=37.7
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
..-.||..+......|+.+|++.+|++...+.+.+..|.. .+++.
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 3456777787778899999999999999999999999973 46665
No 66
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=73.55 E-value=3 Score=29.94 Aligned_cols=53 Identities=11% Similarity=0.224 Sum_probs=33.2
Q ss_pred eeeeehhc-cCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc--CCCCCceE
Q 014910 353 AALVRIMK-SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD--KENPNMFR 413 (416)
Q Consensus 353 A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~--~~~~~~y~ 413 (416)
..|.+.+. ..+.++..+|... +..+...+-+.|+.|+++|||++. +.|.....
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~--------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~ 61 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAER--------LGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKR 61 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHH--------TT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEE
T ss_pred HHHHHHHHccCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeE
Confidence 34455555 5566666665553 556778899999999999999664 44555333
No 67
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=73.51 E-value=4.2 Score=30.22 Aligned_cols=28 Identities=21% Similarity=0.177 Sum_probs=24.7
Q ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 264 SDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 264 ~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
...+|+.||++.+|++...++..+..+.
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 3578999999999999999999888764
No 68
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=72.97 E-value=8.3 Score=31.58 Aligned_cols=62 Identities=21% Similarity=0.331 Sum_probs=44.6
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 318 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~ 318 (416)
++.-..||.++-+.+..++.||++.+|++...+-++|.-|. ..+++.....|. .-.|.+|.+
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 34445566655455679999999999999999999999996 468887654332 234777653
No 69
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=71.86 E-value=2.3 Score=29.92 Aligned_cols=45 Identities=13% Similarity=0.343 Sum_probs=39.1
Q ss_pred eeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 354 ALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 354 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
.|+..++.++.++..+|.+ .|..+...|..-+..|.+.|+|.|.-
T Consensus 4 ~Il~~l~~~~~~s~~ela~--------~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 4 QILELLKEKGKVSVKELAE--------EFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHcCCEEHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 4677888899999888877 37889999999999999999999865
No 70
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=71.83 E-value=5.6 Score=36.27 Aligned_cols=43 Identities=21% Similarity=0.253 Sum_probs=36.0
Q ss_pred HHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 255 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
..||.+.+....+|.+||++.+|++...++++|..|.. -+++.
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~--~Glv~ 56 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA--EGLVE 56 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh--Cccee
Confidence 45677777788999999999999999999999999973 35554
No 71
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=71.54 E-value=8.6 Score=26.61 Aligned_cols=35 Identities=17% Similarity=0.258 Sum_probs=29.9
Q ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 264 SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 264 ~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.+..|..+|++.+|++...+.+.|..|. +.+++..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~--~~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR--EAGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 5678999999999999999999999997 3466654
No 72
>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=70.21 E-value=7.5 Score=28.22 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=32.5
Q ss_pred HHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 255 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
..|-.++++...+|+.+|++.+|++..++..++..|..
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar 48 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR 48 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 34666788888999999999999999999999999974
No 73
>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=69.71 E-value=2.6 Score=37.57 Aligned_cols=58 Identities=17% Similarity=0.330 Sum_probs=40.7
Q ss_pred hhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 350 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 350 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
.++.+ |...|.+|.+..+||-. .|..+.+++-.+|..|...|-|.---+|++.|+||.
T Consensus 100 lL~~F-i~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEF-INYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHH-HHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHH-HHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 55554 58889999999888766 488899999999999999998888778899999984
No 74
>PF13730 HTH_36: Helix-turn-helix domain
Probab=69.62 E-value=11 Score=25.77 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=22.9
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 268 SYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 268 t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
|.+.|++.+|++...+.+++..|.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 899999999999999999999996
No 75
>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=68.35 E-value=14 Score=26.20 Aligned_cols=35 Identities=26% Similarity=0.340 Sum_probs=30.4
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
..+|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE--EEGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 479999999999999999999999997 45777654
No 76
>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=68.25 E-value=12 Score=26.60 Aligned_cols=43 Identities=14% Similarity=0.212 Sum_probs=33.8
Q ss_pred HHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 257 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 257 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
|..+-.+...++..+|++.+|++...+...+..|. +.+++...
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~ 55 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYE 55 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEec
Confidence 44444577899999999999999999999999996 45677654
No 77
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=66.46 E-value=19 Score=30.33 Aligned_cols=40 Identities=15% Similarity=0.262 Sum_probs=33.0
Q ss_pred hhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 261 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 261 Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+.....++..+|++.+|+|...+.++|..|. +.+++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEec
Confidence 3444578999999999999999999999996 568887543
No 78
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=65.90 E-value=8.5 Score=36.11 Aligned_cols=47 Identities=19% Similarity=0.200 Sum_probs=40.7
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
-|..||.+.++++.+++.||++.+|++...+++-|..|- +.++|.+.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~ 52 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEE
Confidence 467889999999999999999999999999999999996 45666654
No 79
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=65.44 E-value=9.3 Score=35.83 Aligned_cols=47 Identities=19% Similarity=0.287 Sum_probs=40.7
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
-|-.||.+.++.+.++++||++.+|+++..++|=|..|. +.++|.+.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEE
Confidence 356788899999999999999999999999999999996 45667664
No 80
>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=65.23 E-value=9.2 Score=25.29 Aligned_cols=31 Identities=23% Similarity=0.389 Sum_probs=21.9
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
.|+-++.+. +|+.+|++.+|++...+.+.|.
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 344455553 8999999999999999988774
No 81
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=64.64 E-value=10 Score=26.23 Aligned_cols=44 Identities=11% Similarity=0.209 Sum_probs=31.4
Q ss_pred eehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCC
Q 014910 356 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 408 (416)
Q Consensus 356 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~ 408 (416)
++.+. .+.++..++... +..+...+.+.|+.|.++|++......
T Consensus 3 l~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~ 46 (66)
T smart00418 3 LKLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREG 46 (66)
T ss_pred HHHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecC
Confidence 34444 556666665443 346778899999999999999987643
No 82
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=64.18 E-value=10 Score=27.14 Aligned_cols=35 Identities=20% Similarity=0.295 Sum_probs=26.8
Q ss_pred CCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 263 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 263 ~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
.++..|+.+|...++++...++.+|-.|.. .+++.
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQ--h~~v~ 58 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQ--HNLVQ 58 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHH--TTSEE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--cCCee
Confidence 456899999999999999999999999973 45553
No 83
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=64.07 E-value=19 Score=31.54 Aligned_cols=54 Identities=20% Similarity=0.174 Sum_probs=40.3
Q ss_pred EEEEcHHHHHHHHhhhCCCC-cCHHHHHHHc--CCCHHHHHHHHHhhhcccceeeecCC
Q 014910 247 ELIVSTYQAATLLLFNTSDR-LSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 247 ~l~~s~~Q~~iLl~Fn~~~~-~t~~ei~~~~--~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
++--+.+..+|+.+..-.+. .+.++|++.+ +++.++++.+|..|. +.++|.+.+
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 33334455566655554433 3899999999 999999999999997 679998753
No 84
>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=63.66 E-value=18 Score=24.23 Aligned_cols=32 Identities=22% Similarity=0.403 Sum_probs=23.7
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
.|-+.| ...+|++||++.+|++...+.+....
T Consensus 12 vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 12 VIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 344555 45789999999999999988776543
No 85
>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=63.26 E-value=9 Score=27.92 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=27.4
Q ss_pred HHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 258 LLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 258 Ll~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
.-...++..+|++||+..++++.+.+...|..|..
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33455677899999999999999999999999974
No 86
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=62.70 E-value=7.3 Score=31.00 Aligned_cols=45 Identities=13% Similarity=0.143 Sum_probs=31.1
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
-.+.|+..+..++.++-++|++.+|++..++.+.|..|.. .+++.
T Consensus 14 ~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv~ 58 (105)
T PF02002_consen 14 EAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLVS 58 (105)
T ss_dssp TTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-E
T ss_pred hHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeE
Confidence 3456666666667899999999999999999999999974 45553
No 87
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=62.70 E-value=13 Score=28.12 Aligned_cols=35 Identities=3% Similarity=-0.031 Sum_probs=30.8
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
-++.|+-+... +.+|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 46778888888 899999999999999999988774
No 88
>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=61.87 E-value=18 Score=26.75 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=39.7
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhccccee
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKI 297 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~i 297 (416)
++=|+.++-++...+.-|+++|++.||-....+.-.|..+...|.++
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl 55 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGL 55 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCc
Confidence 55689999999888899999999999999999999998886434444
No 89
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=60.73 E-value=16 Score=32.30 Aligned_cols=64 Identities=16% Similarity=0.164 Sum_probs=48.9
Q ss_pred CceEEeccCCceEEEEeEecceeEEEEEcHHHHHHHHhhhCC--CCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 223 HRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTS--DRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 223 ~R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~--~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.|.-.|.+.+|.++.+- .+.| .||+.||.-|+.-... ..||.+-|++..+++.+++...|..+.
T Consensus 96 ~r~~~~~~~fg~~ep~~-vPkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEK-VPKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCCcccccccccCccc-CCCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 34445788888887753 3334 5788999888754433 489999999999999999999998874
No 90
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=60.45 E-value=13 Score=30.00 Aligned_cols=57 Identities=9% Similarity=0.108 Sum_probs=42.4
Q ss_pred eeehhcc-CCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 014910 355 LVRIMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 414 (416)
Q Consensus 355 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 414 (416)
|..+|.. .+-++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4445554 45699999999887652 357888899999999999999997644344444
No 91
>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=60.32 E-value=23 Score=31.84 Aligned_cols=45 Identities=13% Similarity=0.172 Sum_probs=36.1
Q ss_pred HHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 255 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
..||......+.+|..+|++.+|++...+.++|..|. +.+++.+.
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 3455555555679999999999999999999999997 45777654
No 92
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=60.19 E-value=15 Score=33.67 Aligned_cols=50 Identities=24% Similarity=0.313 Sum_probs=42.4
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
.|..-..||.++.....+.+.||++++|+|...+..+++.|. +.+++..+
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 355566788888888899999999999999999999999996 66888644
No 93
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=60.07 E-value=15 Score=34.27 Aligned_cols=48 Identities=15% Similarity=0.149 Sum_probs=40.4
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
-|..|+..+++++.+++.||++.+|++...+++-|..|. +.+++.+..
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~ 53 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVR 53 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 466788899999999999999999999999999999996 346666543
No 94
>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=59.29 E-value=25 Score=26.44 Aligned_cols=38 Identities=11% Similarity=0.213 Sum_probs=28.5
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.-.+|-++-....+|+++|+.++|.+.+++...|..+.
T Consensus 26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 44566777888999999999999999999999998875
No 95
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=58.75 E-value=19 Score=26.11 Aligned_cols=24 Identities=17% Similarity=0.499 Sum_probs=20.6
Q ss_pred ChHHHHHHHHhhhhhccccccCCC
Q 014910 385 DIKAIKKRMEDLITRDYLERDKEN 408 (416)
Q Consensus 385 ~~~~ik~~Ie~Liereyi~r~~~~ 408 (416)
+..-+...|+.|.++|||+|+++-
T Consensus 39 S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 39 STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred ChHHHHHHHHHHHHCcCccCCCCC
Confidence 467788899999999999999864
No 96
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=58.43 E-value=16 Score=31.71 Aligned_cols=48 Identities=13% Similarity=0.171 Sum_probs=40.6
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
+.-.-..||..+.+....|+.+|++.+|++...+.+-++.|.. .+++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~--~GvI~ 59 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLER--QGFIQ 59 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeE
Confidence 4556677888888889999999999999999999999999973 45654
No 97
>PRK00215 LexA repressor; Validated
Probab=58.00 E-value=24 Score=31.64 Aligned_cols=51 Identities=20% Similarity=0.259 Sum_probs=40.0
Q ss_pred EcHHHHHHHHhhhC-----CCCcCHHHHHHHcCC-CHHHHHHHHHhhhcccceeeecCC
Q 014910 250 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNL-THDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~-----~~~~t~~ei~~~~~i-~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
++.-|..+|..+.+ ....|+.||++.+|+ +...+.+.|..|. +.+++.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCC
Confidence 35678888866542 346899999999999 9999999999997 346776654
No 98
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=57.41 E-value=23 Score=23.71 Aligned_cols=39 Identities=18% Similarity=0.312 Sum_probs=29.8
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
+.-+..++.++. ..++..+|++.+|++...+...+..+.
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 445555665553 357999999999999999998887664
No 99
>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=57.00 E-value=13 Score=36.33 Aligned_cols=50 Identities=22% Similarity=0.286 Sum_probs=36.6
Q ss_pred EEEcHHHHHHHHhhhC--CCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 248 LIVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~--~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
-.++..+..|+.+..+ .+++-..+|...+|++...+.++|..|.. | +++.
T Consensus 80 ~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~-k-~lIK 131 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLES-K-KLIK 131 (327)
T ss_dssp -SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHH-T-TSEE
T ss_pred cCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHh-C-CCEE
Confidence 3557778888877654 45888999999999999999999999974 2 4554
No 100
>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=56.97 E-value=8.3 Score=25.65 Aligned_cols=43 Identities=7% Similarity=0.246 Sum_probs=32.3
Q ss_pred eeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccc
Q 014910 353 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLE 403 (416)
Q Consensus 353 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~ 403 (416)
-.|+..+.....++..+|-..+ ..+.+.+...|..|.+.|||+
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 3456677777888887776653 468888999999999999985
No 101
>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=56.94 E-value=14 Score=22.68 Aligned_cols=26 Identities=27% Similarity=0.482 Sum_probs=20.8
Q ss_pred CcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 266 RLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 266 ~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.+|-+||++.+|++.+.+-+.|..|.
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 36789999999999999999998885
No 102
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=56.45 E-value=21 Score=30.56 Aligned_cols=49 Identities=12% Similarity=0.207 Sum_probs=40.8
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
.++..--.||..+..+...|+.+|++.+|++...+.+-++.|.. .+++.
T Consensus 6 ~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~--~GvI~ 54 (153)
T PRK11179 6 QIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ--AGIIT 54 (153)
T ss_pred ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 34556677888888888999999999999999999999999974 35554
No 103
>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=56.01 E-value=22 Score=30.72 Aligned_cols=44 Identities=14% Similarity=0.148 Sum_probs=35.1
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
...|+..+-.+..+|-+||++.+|++..++.+.|..|.. .+++.
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 345565555566899999999999999999999999974 46664
No 104
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.91 E-value=19 Score=31.89 Aligned_cols=45 Identities=13% Similarity=0.086 Sum_probs=36.6
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
....||.++-.++.+|.++|++.+|++...++++|..|.. .+++.
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 3455666666667899999999999999999999999973 46665
No 105
>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=55.74 E-value=26 Score=23.55 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=28.6
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
+..|..++.++- ..+|..+|++.+|++...+...+..+.
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344455554443 468999999999999999988877653
No 106
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=55.39 E-value=18 Score=33.80 Aligned_cols=47 Identities=17% Similarity=0.300 Sum_probs=40.0
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
-+..|+.++++++.+++.||++.++++...++|-|..|. +.++|.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le--~~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLA--EQNKILRH 52 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 466788888999999999999999999999999999996 34666654
No 107
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=55.39 E-value=18 Score=33.80 Aligned_cols=39 Identities=21% Similarity=0.224 Sum_probs=36.2
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
-|..|+.+.+.++.+++.+|++.+|+++..++|-|..|-
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 477899999999999999999999999999999999885
No 108
>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=55.35 E-value=27 Score=23.68 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=17.6
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
..+|++||++.+|++...+...+.
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 478999999999999999887764
No 109
>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=55.04 E-value=7 Score=28.38 Aligned_cols=53 Identities=25% Similarity=0.263 Sum_probs=31.1
Q ss_pred eeeeehhccCC-CCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 353 AALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 353 A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
|.||..||++. .++.+||..++. +..+ ...++.|-+.+=|+.+++ .+.|.|.|
T Consensus 8 ~~~VeymK~r~~Plt~~eI~d~l~------~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 8 AKAVEYMKKRDHPLTLEEILDYLS------LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHH-S-B-HHHHHHHHT------SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHhcCCCcCHHHHHHHHc------CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 56788899874 477777776543 3333 235566668889999874 47999975
No 110
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=54.55 E-value=41 Score=23.37 Aligned_cols=33 Identities=15% Similarity=0.217 Sum_probs=27.7
Q ss_pred cCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 267 LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 267 ~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
.|..+|++.+|++...+.+.|..|. +.++|...
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~--~~G~i~~~ 58 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELE--AEGLVERR 58 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 3599999999999999999999997 35777643
No 111
>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=53.63 E-value=20 Score=24.86 Aligned_cols=40 Identities=15% Similarity=0.233 Sum_probs=32.0
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.|.-+..||.++.. +.+..+|++.+|+++..+..++..+.
T Consensus 4 LT~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 4 LTERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp S-HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 35567778877765 56899999999999999999998886
No 112
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=53.37 E-value=20 Score=33.97 Aligned_cols=48 Identities=8% Similarity=0.106 Sum_probs=40.5
Q ss_pred HHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 252 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 252 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
--|..|+.+++.++.+++.||++.+|++...++|-|..|- ..+++.+.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le--~~G~l~r~ 64 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLE--KQGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHH--hCCCeEEE
Confidence 3577889899999899999999999999999999999995 34555554
No 113
>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=53.17 E-value=14 Score=32.91 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=22.3
Q ss_pred CcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 266 RLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 266 ~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
.+|+++|++.||+..+++..+|+.|
T Consensus 150 ~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 150 SISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp -EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred eEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 6999999999999999999999988
No 114
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=52.06 E-value=45 Score=25.20 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=32.0
Q ss_pred HhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 259 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 259 l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
+..++.+..|-++|++.+|++...+-++++.|-..-+.|..
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEe
Confidence 44556678999999999999999999999999643344443
No 115
>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=51.06 E-value=22 Score=25.75 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=35.2
Q ss_pred EcHHHHHHHHhhhC-----CCCcCHHHHHHHcCCC-HHHHHHHHHhhhcccceeeecCC
Q 014910 250 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~-----~~~~t~~ei~~~~~i~-~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+|.-|.-||..+-+ .-.-|+.||++.+|+. ...+..+|..|. +.+.|.+.+
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 45567777765432 2256999999999997 899999999997 457777654
No 116
>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=50.91 E-value=11 Score=34.56 Aligned_cols=34 Identities=9% Similarity=0.215 Sum_probs=28.9
Q ss_pred ccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 014910 379 SRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 413 (416)
Q Consensus 379 ~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 413 (416)
..+|..+...|+++|+.|++.|+|.|..+ .++|+
T Consensus 31 a~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 31 MDQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 33699999999999999999999999875 46664
No 117
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=50.37 E-value=27 Score=36.14 Aligned_cols=50 Identities=12% Similarity=0.133 Sum_probs=43.5
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.++..|..||..+...+.+|..+|++.+|++...+.+.+.+|.. .+++..
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 46789999999998888999999999999999999999999973 366654
No 118
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=50.20 E-value=25 Score=24.37 Aligned_cols=30 Identities=17% Similarity=0.424 Sum_probs=24.7
Q ss_pred hhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 261 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 261 Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
|+.-...|.+||++.+|++...+-.+|..=
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 555568999999999999999888877653
No 119
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=50.11 E-value=23 Score=31.48 Aligned_cols=46 Identities=11% Similarity=0.049 Sum_probs=39.0
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
-+..|+.+.+.+..+++++|++.+|++...++|-|..|.. .+++.+
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~--~g~~~r 53 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI--PELRER 53 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc--chHHHH
Confidence 5678888899999999999999999999999999999963 344443
No 120
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.01 E-value=17 Score=33.42 Aligned_cols=53 Identities=23% Similarity=0.374 Sum_probs=44.5
Q ss_pred eehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 356 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 356 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
|-..|+.|.+..+||-. .|....++.-.+|..|+..|.|.-.-+|++.|+||.
T Consensus 206 v~YIk~nKvV~ledLas--------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 206 VEYIKKNKVVPLEDLAS--------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHhcCeeeHHHHHH--------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 56678888888888766 377777788889999999999999888999999984
No 121
>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=49.65 E-value=1.5e+02 Score=25.75 Aligned_cols=59 Identities=22% Similarity=0.241 Sum_probs=42.7
Q ss_pred HHHHHHhhhCC-CCcCHHHHHHHc--CCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 014910 254 QAATLLLFNTS-DRLSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 318 (416)
Q Consensus 254 Q~~iLl~Fn~~-~~~t~~ei~~~~--~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~ 318 (416)
...|+-.|... .++++.+|...+ +++...+.++|..|+. +.+|..+. +...-+|..|.+
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 45677766654 599999999998 5899999999999984 34565543 223456777755
No 122
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=49.21 E-value=29 Score=32.23 Aligned_cols=39 Identities=26% Similarity=0.321 Sum_probs=35.0
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
-|..|+..+++++.++++||++.+|++...+++-|..|.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~ 43 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQ 43 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356688888888899999999999999999999999986
No 123
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=49.15 E-value=34 Score=28.90 Aligned_cols=49 Identities=16% Similarity=0.318 Sum_probs=40.6
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
++-.-.-||..+......++.+|++.+|++...+.+.+..|. +.+++..
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 344566788888888889999999999999999999999996 4566653
No 124
>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=48.82 E-value=21 Score=31.92 Aligned_cols=50 Identities=18% Similarity=0.180 Sum_probs=40.2
Q ss_pred EcHHHHHHHHhhhCC-----CCcCHHHHHHHcCCC-HHHHHHHHHhhhcccceeeecC
Q 014910 250 VSTYQAATLLLFNTS-----DRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~-----~~~t~~ei~~~~~i~-~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
++..|..||....+. -..|+.||++.+|++ ...+.++|..|. +.++|.+.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~ 59 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERD 59 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecC
Confidence 467888888766532 258899999999998 999999999996 45777764
No 125
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=48.59 E-value=28 Score=30.37 Aligned_cols=50 Identities=30% Similarity=0.349 Sum_probs=37.2
Q ss_pred cCCCceEEeccCCceEEEEeEecceeEEEEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 220 KTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 220 k~~~R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+++.+.|+|.+++- -|+-.+.-+ .-..|+++|++.+|.++.+++++|..=
T Consensus 36 ~~~~~~lTWvdSLa--------------------vAAga~are-kag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 36 KDPYERLTWVDSLA--------------------VAAGALARE-KAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred hCcccccchhhHHH--------------------HHHHHHHHH-HccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 46889999998552 222222233 457899999999999999999998754
No 126
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=48.38 E-value=13 Score=34.38 Aligned_cols=32 Identities=22% Similarity=0.298 Sum_probs=27.5
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 014910 381 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 413 (416)
Q Consensus 381 ~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 413 (416)
.|..+...++++|+.|++.|+|.|..+ +++|+
T Consensus 42 ~~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 42 QYNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 578899999999999999999999875 56654
No 127
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=47.98 E-value=26 Score=22.46 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=20.5
Q ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 264 SDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 264 ~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
...+++++|++..|++...+.+..+...
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4579999999999999999988876653
No 128
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=47.85 E-value=13 Score=29.56 Aligned_cols=47 Identities=11% Similarity=0.198 Sum_probs=38.0
Q ss_pred hceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc
Q 014910 351 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 405 (416)
Q Consensus 351 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~ 405 (416)
+|-.|++.+.....++..+|-.. +..+...+.++|..|.++|+|+|-
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~--------l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK--------VGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeece
Confidence 34567788888888888877765 457889999999999999999853
No 129
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=47.61 E-value=67 Score=26.79 Aligned_cols=68 Identities=16% Similarity=0.222 Sum_probs=49.3
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCC---CeEEEccCCC
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQS---DHFEFNSKFT 320 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~---~~~~lN~~f~ 320 (416)
|+--..+|-+..+.+..|+.|+++.+|-+...+.+.|..|. .++++..+.+|+...+. +.+.++-.|.
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 34444567778888999999999999999999999999996 47888776555443322 3344555554
No 130
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=47.40 E-value=33 Score=32.60 Aligned_cols=38 Identities=18% Similarity=0.299 Sum_probs=31.2
Q ss_pred HHHHHHHhhhC-CCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 253 YQAATLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 253 ~Q~~iLl~Fn~-~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+...|+-.+.+ ...+|+++|++.|||..+++..+|+.|
T Consensus 209 W~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 209 WTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 55566655443 568999999999999999999999987
No 131
>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=47.29 E-value=11 Score=26.45 Aligned_cols=26 Identities=12% Similarity=0.332 Sum_probs=20.9
Q ss_pred CCCChHHHHHHHHhhhhhccccccCC
Q 014910 382 FKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 382 F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
+..+...+...|..|.++|||+|..+
T Consensus 31 l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 31 LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 33577889999999999999999754
No 132
>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=46.71 E-value=13 Score=26.49 Aligned_cols=32 Identities=13% Similarity=0.280 Sum_probs=25.6
Q ss_pred cCCCCChHHHHHHHHhhhhhccccccCCCCCce
Q 014910 380 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 412 (416)
Q Consensus 380 ~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y 412 (416)
++|..+...+.+++..|.+.|+|.+.++ .+++
T Consensus 32 ~~~~vsr~tvr~al~~L~~~g~i~~~~~-~G~~ 63 (64)
T PF00392_consen 32 ERYGVSRTTVREALRRLEAEGLIERRPG-RGTF 63 (64)
T ss_dssp HHHTS-HHHHHHHHHHHHHTTSEEEETT-TEEE
T ss_pred HHhccCCcHHHHHHHHHHHCCcEEEECC-ceEE
Confidence 3578899999999999999999999874 3443
No 133
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=46.69 E-value=24 Score=23.51 Aligned_cols=33 Identities=18% Similarity=0.313 Sum_probs=21.7
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
.++.++.+ .+|..+|++.+|++...+.+-+..+
T Consensus 9 ~ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 9 QIIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 34444544 7899999999999999998877655
No 134
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=46.04 E-value=16 Score=25.01 Aligned_cols=27 Identities=7% Similarity=0.186 Sum_probs=23.9
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCC
Q 014910 381 MFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 381 ~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
.|..+...+.+.+..|.+.|+|.+..+
T Consensus 29 ~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 29 QLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 577899999999999999999988764
No 135
>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=45.59 E-value=15 Score=33.74 Aligned_cols=32 Identities=16% Similarity=0.380 Sum_probs=27.8
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 014910 381 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 413 (416)
Q Consensus 381 ~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 413 (416)
+|..+...++++|+.|.+.|||.|..+ .++|+
T Consensus 41 ~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 41 RFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 588999999999999999999999875 46654
No 136
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=45.25 E-value=15 Score=33.88 Aligned_cols=35 Identities=9% Similarity=0.427 Sum_probs=29.0
Q ss_pred hccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 014910 378 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 413 (416)
Q Consensus 378 l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 413 (416)
|...|..+...++++|+.|++.|+|.|..+ .++|+
T Consensus 41 La~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 41 LAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 334688999999999999999999999875 46654
No 137
>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=45.07 E-value=36 Score=28.04 Aligned_cols=36 Identities=8% Similarity=0.035 Sum_probs=31.2
Q ss_pred CCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 263 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 263 ~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
..-+.|.++||..++-+.+.++.+|..|. +.+++..
T Consensus 50 ~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~ 85 (121)
T PF09681_consen 50 GNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEI 85 (121)
T ss_pred CCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 34589999999999999999999999996 6778765
No 138
>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=44.53 E-value=23 Score=25.23 Aligned_cols=52 Identities=12% Similarity=0.133 Sum_probs=34.4
Q ss_pred eeehhccCCCCChhHHHHHHHHH--hccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 355 LVRIMKSRKVLGHQQLVSECVEQ--LSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 355 IVRimK~~k~l~~~~L~~~v~~~--l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
|+..+..-..++.+.+.....-. ....+.++.++++.-++.+++.|-|+-++
T Consensus 2 I~gMLtN~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~~ 55 (60)
T PF08672_consen 2 IVGMLTNLGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECSG 55 (60)
T ss_dssp HHHHHHHH-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--T
T ss_pred HhHHhhcCCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEecC
Confidence 44555566677887777765544 23568899999999999999999998874
No 139
>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=44.41 E-value=58 Score=21.13 Aligned_cols=40 Identities=25% Similarity=0.373 Sum_probs=28.6
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
++..+..++.++- ...++..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3444555554442 246899999999999999998877654
No 140
>PRK06474 hypothetical protein; Provisional
Probab=44.22 E-value=69 Score=28.22 Aligned_cols=52 Identities=15% Similarity=0.221 Sum_probs=40.6
Q ss_pred EEEcHHHHHHHHhhhCCC-CcCHHHHHHHc-CCCHHHHHHHHHhhhcccceeeecC
Q 014910 248 LIVSTYQAATLLLFNTSD-RLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~-~~t~~ei~~~~-~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+-.++.-..||..+...+ .+|..+|++.+ +++...+-++|..|. +.+++...
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~ 60 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVV 60 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 345666777887665544 49999999999 799999999999997 46787754
No 141
>PHA02591 hypothetical protein; Provisional
Probab=44.10 E-value=29 Score=26.04 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=22.3
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
.++|.++|++.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3789999999999999999988765
No 142
>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=43.55 E-value=13 Score=25.69 Aligned_cols=43 Identities=14% Similarity=0.309 Sum_probs=29.6
Q ss_pred eehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 356 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 356 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
..++-..+.++..+|-. .+..+...+-..+..|.++|||+|..
T Consensus 9 L~~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 9 LRILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 33444455555555444 34468888999999999999999864
No 143
>PRK13239 alkylmercury lyase; Provisional
Probab=43.51 E-value=46 Score=30.14 Aligned_cols=40 Identities=15% Similarity=0.257 Sum_probs=35.2
Q ss_pred HHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 252 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 252 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.+...||.++-++...|+++|++.+|.+.+.+.+.|+.|.
T Consensus 22 ~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 22 TLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 3566777778888999999999999999999999999884
No 144
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.42 E-value=30 Score=29.42 Aligned_cols=30 Identities=13% Similarity=0.207 Sum_probs=27.2
Q ss_pred CCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 263 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 263 ~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
.++.+|-++|++.+|++...+++.|..|..
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 456899999999999999999999999974
No 145
>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=43.10 E-value=37 Score=26.68 Aligned_cols=53 Identities=8% Similarity=0.156 Sum_probs=42.5
Q ss_pred hceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccc
Q 014910 351 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 404 (416)
Q Consensus 351 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 404 (416)
++-+|..++. .+.+.=-+|.+++.+...+.+.++...+=..+..|-++|+|++
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 3445555665 4678888999998887665678888999999999999999998
No 146
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=43.01 E-value=63 Score=21.59 Aligned_cols=35 Identities=17% Similarity=0.360 Sum_probs=26.1
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
+...|+.+.-+. .|+.+++..+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 444555444332 69999999999999999988754
No 147
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=43.00 E-value=20 Score=27.52 Aligned_cols=36 Identities=22% Similarity=0.224 Sum_probs=32.1
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 381 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 381 ~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
++......-+++|..|.++|.|+.-..+....+|.|
T Consensus 50 rlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 50 KYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 577888999999999999999998888888899976
No 148
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=42.97 E-value=64 Score=23.99 Aligned_cols=43 Identities=21% Similarity=0.253 Sum_probs=30.7
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
-+.||.... .++.+..+|+..++++...+.+.|..|. +.+++.
T Consensus 8 i~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~--~~gLI~ 50 (77)
T PF14947_consen 8 IFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELE--EKGLIK 50 (77)
T ss_dssp HHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCcCee
Confidence 355676665 5678999999999999999999999997 346664
No 149
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=42.22 E-value=51 Score=27.24 Aligned_cols=41 Identities=15% Similarity=0.308 Sum_probs=36.5
Q ss_pred HHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 252 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 252 ~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
.+.+-|+-+--+++.+|+.|+...||++-..+++.+.-|+.
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa 52 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA 52 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35677888888889999999999999999999999999973
No 150
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=41.29 E-value=35 Score=33.96 Aligned_cols=63 Identities=22% Similarity=0.286 Sum_probs=41.5
Q ss_pred EEeccCCceEEEEeEecceeEEEEE-------cHHHHHHHHhhhC-CC-CcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 226 LTWIYSLGQCNINGKFEQKNIELIV-------STYQAATLLLFNT-SD-RLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 226 L~w~~~lg~~~l~~~~~~~~~~l~~-------s~~Q~~iLl~Fn~-~~-~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+.+.+.||..|=.+--+ ...|.= +-+-..||-++-+ .+ .+|+++|++.|||..+++...|++|
T Consensus 282 IdFSYeLSr~E~~~GsP--EKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L 353 (396)
T KOG2747|consen 282 IDFSYELSRREGKIGSP--EKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSL 353 (396)
T ss_pred hhhhhhhhcccCcCCCC--CCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhh
Confidence 56777788777554322 222211 2244445544433 22 3999999999999999999999998
No 151
>PRK14999 histidine utilization repressor; Provisional
Probab=41.23 E-value=18 Score=33.38 Aligned_cols=47 Identities=15% Similarity=0.289 Sum_probs=34.6
Q ss_pred hhccCCCC-ChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 014910 358 IMKSRKVL-GHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 413 (416)
Q Consensus 358 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 413 (416)
.++....+ +-.+|.+ .|..+...|+++|+.|.+.|+|.|..+ +++|+
T Consensus 29 ~~~~G~~LPsE~eLa~--------~~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSEAELVA--------QYGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 34444445 4444444 588999999999999999999999875 46664
No 152
>PF13730 HTH_36: Helix-turn-helix domain
Probab=40.75 E-value=19 Score=24.54 Aligned_cols=21 Identities=5% Similarity=0.325 Sum_probs=18.2
Q ss_pred CCCChHHHHHHHHhhhhhccc
Q 014910 382 FKPDIKAIKKRMEDLITRDYL 402 (416)
Q Consensus 382 F~~~~~~ik~~Ie~Liereyi 402 (416)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 346788899999999999987
No 153
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=40.43 E-value=19 Score=33.23 Aligned_cols=35 Identities=17% Similarity=0.384 Sum_probs=29.3
Q ss_pred hccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 014910 378 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 413 (416)
Q Consensus 378 l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 413 (416)
|...|..+.-.++++|..|.+.|+|.|-.+ .++|+
T Consensus 37 La~~f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 37 LAEQFGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred HHHHHCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 444699999999999999999999999875 46664
No 154
>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=40.31 E-value=51 Score=25.26 Aligned_cols=46 Identities=15% Similarity=0.260 Sum_probs=36.5
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHc-CCCHHHHHHHHHhhhcccceeeecC
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~-~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+-+.||..... +...+.||.+.+ |++...|.+.|..|. ..+++.+.
T Consensus 6 W~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~--~~GLv~r~ 52 (90)
T PF01638_consen 6 WTLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELE--EAGLVERR 52 (90)
T ss_dssp THHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred CHHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHH--Hcchhhcc
Confidence 34567766666 688999999999 999999999999997 45788654
No 155
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=39.88 E-value=43 Score=24.72 Aligned_cols=18 Identities=22% Similarity=0.434 Sum_probs=14.2
Q ss_pred HhhhhhccccccCCCCCce
Q 014910 394 EDLITRDYLERDKENPNMF 412 (416)
Q Consensus 394 e~Liereyi~r~~~~~~~y 412 (416)
..||+-||++|+++ .+.|
T Consensus 51 R~LVd~g~L~R~~d-g~~Y 68 (71)
T PF09860_consen 51 RYLVDYGLLERTRD-GSRY 68 (71)
T ss_pred HHHHHcCCeeecCC-CCee
Confidence 47899999999974 4555
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=39.72 E-value=50 Score=24.47 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=39.0
Q ss_pred HHHHHHHHhhhC--CCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 252 TYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 252 ~~Q~~iLl~Fn~--~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
..|.++|...-. ..+++-.+|...+|++...+-..++.|. +.+++.+.
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~ 51 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQ 51 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEE
Confidence 467888877754 4588999999999999999999999997 45777654
No 157
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=39.10 E-value=56 Score=27.41 Aligned_cols=43 Identities=19% Similarity=0.308 Sum_probs=34.2
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.|..+.+..+..++.+|++.++++...+.+.|..|. +.+++.+
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 344455666788999999999999999999999996 3466653
No 158
>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=39.00 E-value=1.3e+02 Score=21.50 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=27.5
Q ss_pred HHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 258 LLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 258 Ll~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
|..+.+. ..+..+|++.+|++...+.+.+..|..
T Consensus 6 l~~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 6 LALLADN-PFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3344444 578999999999999999999999853
No 159
>PLN03239 histone acetyltransferase; Provisional
Probab=38.87 E-value=48 Score=32.46 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=30.4
Q ss_pred HHHHHHHhhhCC----CCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 253 YQAATLLLFNTS----DRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 253 ~Q~~iLl~Fn~~----~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+...|+-.+-+. ..+|+++|+..|||..+++..+|+.|
T Consensus 267 W~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 267 WGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred HHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 555666544322 46999999999999999999999988
No 160
>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=38.84 E-value=66 Score=21.95 Aligned_cols=41 Identities=20% Similarity=0.257 Sum_probs=32.6
Q ss_pred HhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 259 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 259 l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
-+|.+++.+|+.++.+.+|++-......|+-|= +.++..+.
T Consensus 3 ~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD--~~g~T~R~ 43 (50)
T PF09107_consen 3 ELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLD--REGITRRV 43 (50)
T ss_dssp HHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHh--ccCCEEEe
Confidence 457788899999999999999999988888883 45666554
No 161
>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=38.44 E-value=66 Score=24.90 Aligned_cols=33 Identities=12% Similarity=0.319 Sum_probs=23.2
Q ss_pred HhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 259 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 259 l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
.+..+... ++..|.+.||||.-.++.+|.+|..
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 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=38.20 E-value=49 Score=27.14 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=37.3
Q ss_pred cHHHHHHHHhhhCC--------CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 251 STYQAATLLLFNTS--------DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~--------~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
..+.-..|+..|.. -+.+.++|+..++-+.+.++.+|..|. +.+++..
T Consensus 28 ~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~ 83 (119)
T TIGR01714 28 IIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEK 83 (119)
T ss_pred HHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 34555555555543 478999999999999999999999996 6778764
No 163
>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=37.77 E-value=23 Score=26.47 Aligned_cols=58 Identities=19% Similarity=0.236 Sum_probs=34.3
Q ss_pred hhhceeeeehhccCC--CCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccc---cccCCCCCceEecC
Q 014910 349 YAIDAALVRIMKSRK--VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYL---ERDKENPNMFRYLA 416 (416)
Q Consensus 349 ~~i~A~IVRimK~~k--~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi---~r~~~~~~~y~Yia 416 (416)
...=|.||..||++. .++.+|+..++.. +... ..++ +.|-+-.-+ +.+.. .++|.|.|
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 334577899999987 5888888877653 2222 2222 333333333 44443 47999975
No 164
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=37.73 E-value=1.5e+02 Score=26.39 Aligned_cols=111 Identities=16% Similarity=0.158 Sum_probs=59.7
Q ss_pred CHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeE--e-------cceeEEEEEcHHHHHHHHhhhCCCCcCHHHHH
Q 014910 203 PSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGK--F-------EQKNIELIVSTYQAATLLLFNTSDRLSYSEIM 273 (416)
Q Consensus 203 P~~l~~~~~~f~~~Y~~k~~~R~L~w~~~lg~~~l~~~--~-------~~~~~~l~~s~~Q~~iLl~Fn~~~~~t~~ei~ 273 (416)
|.++..+++...+-|.... |-+.-...-|...+..+ + ......-.+|...+-+|-..--+.++|-.+|.
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 3678899999999998653 33333222222222221 1 01112224455555555555445689999999
Q ss_pred HHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 014910 274 TQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 320 (416)
Q Consensus 274 ~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~ 320 (416)
+..|++...+ +..|. ..+++...+..........|.++..|-
T Consensus 112 ~irGv~~~~i---i~~L~--~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNSDGA---LQTLL--AKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCHHHH---HHHHH--HCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999997544 44443 235665322111111334566666664
No 165
>PRK11050 manganese transport regulator MntR; Provisional
Probab=36.92 E-value=75 Score=27.11 Aligned_cols=43 Identities=12% Similarity=0.161 Sum_probs=34.9
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.|+.++...+.++..+|++.++++...+.+.|..|.. .+++.+
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 4555667777899999999999999999999999973 366654
No 166
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=36.89 E-value=25 Score=32.42 Aligned_cols=32 Identities=13% Similarity=0.275 Sum_probs=27.6
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 014910 381 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 413 (416)
Q Consensus 381 ~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 413 (416)
.|..+...|+++|+.|...|+|.|..+ .++|+
T Consensus 38 ~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 69 (240)
T PRK09764 38 EFGVSRVTVRQALRQLVEQQILESIQG-SGTYV 69 (240)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 588999999999999999999999875 46654
No 167
>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=36.87 E-value=24 Score=32.31 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=27.8
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 014910 381 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 413 (416)
Q Consensus 381 ~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 413 (416)
.|..+...|+++|+.|.+.|+|.|..+ .++|+
T Consensus 34 ~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 65 (230)
T TIGR02018 34 QYGCSRMTVNRALRELTDAGLLERRQG-VGTFV 65 (230)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 588999999999999999999999875 46553
No 168
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=36.74 E-value=60 Score=30.51 Aligned_cols=43 Identities=21% Similarity=0.383 Sum_probs=34.3
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
-+|++.-+ ++-|++||...++++...+..+|.-|. +.+++.+.
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 34555554 688999999999999999999999996 45777654
No 169
>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=35.98 E-value=24 Score=24.19 Aligned_cols=22 Identities=18% Similarity=0.511 Sum_probs=19.2
Q ss_pred CcCHHHHHHHcCCCHHHHHHHH
Q 014910 266 RLSYSEIMTQLNLTHDDLVRLL 287 (416)
Q Consensus 266 ~~t~~ei~~~~~i~~~~l~~~L 287 (416)
.+++.||++.+|++..++.+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999998888
No 170
>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=35.86 E-value=29 Score=24.17 Aligned_cols=27 Identities=11% Similarity=0.251 Sum_probs=23.4
Q ss_pred cCCCCChHHHHHHHHhhhhhccccccC
Q 014910 380 RMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 380 ~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
..|..+...+.+.|..|.+.|||.+.+
T Consensus 33 ~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 33 EELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 356678899999999999999998875
No 171
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=35.71 E-value=49 Score=27.41 Aligned_cols=40 Identities=15% Similarity=0.304 Sum_probs=30.7
Q ss_pred hccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 359 MKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 359 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
|..++.++.++|-+.+ .-+.+.+-+++.+|++.|++.|..
T Consensus 37 L~~~~~~tvdelae~l--------nr~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 37 LEENGPLTVDELAEIL--------NRSRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HhhcCCcCHHHHHHHH--------CccHHHHHHHHHHHHHcCCeeeee
Confidence 3366777777766543 347788999999999999999964
No 172
>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=35.61 E-value=44 Score=22.34 Aligned_cols=22 Identities=14% Similarity=0.379 Sum_probs=19.2
Q ss_pred CHHHHHHHcCCCHHHHHHHHHh
Q 014910 268 SYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 268 t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
|+.||++..|++...+-++|+.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 6899999999999999888753
No 173
>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=35.58 E-value=69 Score=24.61 Aligned_cols=40 Identities=23% Similarity=0.257 Sum_probs=31.8
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
....+..++.....+++++|++.++++.+++...+..++.
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~ 86 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLIS 86 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHH
Confidence 3444555556788999999999999999999999888863
No 174
>PHA02943 hypothetical protein; Provisional
Probab=35.16 E-value=74 Score=27.27 Aligned_cols=54 Identities=22% Similarity=0.249 Sum_probs=36.2
Q ss_pred HHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEcc
Q 014910 257 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 317 (416)
Q Consensus 257 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~ 317 (416)
||-.+ ..+.-|..||++.+|++-..+.-+|.-|- |-+.+.+..- .....|.+|.
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLE--rEG~VkrV~~----G~~tyw~l~~ 69 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLA--KEGMVLKVEI----GRAAIWCLDE 69 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCceEEEee----cceEEEEECh
Confidence 45555 55678899999999999999988887774 3344443321 1234566655
No 175
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=35.14 E-value=80 Score=24.65 Aligned_cols=53 Identities=15% Similarity=0.207 Sum_probs=43.4
Q ss_pred EEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 248 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+..+.....||..+...+.=...-|+..+++|.+++...|..|. ..++|.+..
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 34566778888888877777788899999999999999999997 468887653
No 176
>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=35.10 E-value=61 Score=30.77 Aligned_cols=57 Identities=14% Similarity=0.274 Sum_probs=31.8
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCC
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 319 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f 319 (416)
+--.|.-+|.++..|++.+|.+.|+=|+..|+.+|...+ ++.+.+. -...|.|=.+|
T Consensus 217 L~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 217 LLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 444667789999999999999999999999999998874 4555431 22556665544
No 177
>PF08820 DUF1803: Domain of unknown function (DUF1803); InterPro: IPR014924 This small protein is found in one or two copies in bacteria. The function of this is unknown.
Probab=35.01 E-value=30 Score=27.00 Aligned_cols=27 Identities=33% Similarity=0.615 Sum_probs=20.0
Q ss_pred hccCCCCChHHHHHHHHhhhhhcccccc
Q 014910 378 LSRMFKPDIKAIKKRMEDLITRDYLERD 405 (416)
Q Consensus 378 l~~~F~~~~~~ik~~Ie~Liereyi~r~ 405 (416)
+++.| |...-+...||.||.-|||.|.
T Consensus 34 iKk~f-~~qk~~D~fie~li~~GYI~re 60 (93)
T PF08820_consen 34 IKKDF-PKQKRLDIFIEALIKLGYIERE 60 (93)
T ss_pred HHHhh-ccccchhHHHHHHHHcCCeEec
Confidence 34445 3445577899999999999994
No 178
>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=34.84 E-value=32 Score=27.42 Aligned_cols=41 Identities=17% Similarity=0.340 Sum_probs=30.0
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccc--cCCCC
Q 014910 361 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER--DKENP 409 (416)
Q Consensus 361 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r--~~~~~ 409 (416)
..+.++..+|... ...+...+-..|..|.++|||.| ++.|.
T Consensus 40 ~~~~~t~~eL~~~--------l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 40 NEGKLTLKEIIKE--------ILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred cCCcCcHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 3456777666654 34577889999999999999997 45554
No 179
>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=34.60 E-value=1.1e+02 Score=25.40 Aligned_cols=49 Identities=16% Similarity=0.161 Sum_probs=37.5
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHc----CCCHHHHHHHHHhhhcccceeeec
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQL----NLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~----~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
+|..+..|+..+=+.+..|..+|.+.+ +.+...+...|..|. +.+++.+
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~--~KG~v~~ 54 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLV--DKGCLTT 54 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHH--HCCceee
Confidence 466788888766566788999977665 788899999999997 3467754
No 180
>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=34.32 E-value=74 Score=26.81 Aligned_cols=40 Identities=23% Similarity=0.225 Sum_probs=31.8
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
.+|.-|..|+.++ ...+|.+||++.+|++...+...+...
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 3567788888876 368899999999999998887655543
No 181
>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=34.30 E-value=65 Score=24.88 Aligned_cols=46 Identities=17% Similarity=0.200 Sum_probs=34.0
Q ss_pred HHHHHhhhCCCCcCHHHHHHHc--CCCHHHHHHHHHhhhcccceeeecCC
Q 014910 255 AATLLLFNTSDRLSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~--~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+.||...-+++-+|..++.+.+ .+....+...+.-|. |.+++.+++
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 4556566677788999999977 788899999999996 668888764
No 182
>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=33.97 E-value=72 Score=26.81 Aligned_cols=39 Identities=21% Similarity=0.262 Sum_probs=29.5
Q ss_pred EEcHHHHHHHHh-hhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 249 IVSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 249 ~~s~~Q~~iLl~-Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
.+|+.|..|+.+ +- .+++.+||++.+|++...+...+.-
T Consensus 111 ~L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 111 KLPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HCCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 446666666655 43 4789999999999999988877654
No 183
>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=33.95 E-value=56 Score=23.13 Aligned_cols=37 Identities=19% Similarity=0.315 Sum_probs=29.4
Q ss_pred CCCCc-CHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 263 TSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 263 ~~~~~-t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
..+.+ |..+|++.+|++...+.++|..|.. .+++...
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~--~g~i~~~ 57 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEA--EGLIERR 57 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHH--CCcEEEE
Confidence 44678 9999999999999999999999973 5777654
No 184
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=33.89 E-value=63 Score=24.35 Aligned_cols=44 Identities=16% Similarity=0.226 Sum_probs=33.4
Q ss_pred eehhccC-CCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 014910 356 VRIMKSR-KVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 356 VRimK~~-k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
...+... ..++..+|..++ ..+...+.+.+..|.+.|||.+++.
T Consensus 11 l~~l~~~~~~~t~~~ia~~l--------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 11 LRALAEEPGGLTLAELAERL--------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHhCCCCcCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 3444444 578888887764 3577889999999999999999753
No 185
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=33.82 E-value=73 Score=29.07 Aligned_cols=41 Identities=22% Similarity=0.288 Sum_probs=36.5
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.+|+-+..||.+.-+ +.|.+||++.++++...++.++..+.
T Consensus 143 ~LS~RE~eVL~Lia~--G~SnkEIA~~L~IS~~TVk~hvs~I~ 183 (217)
T PRK13719 143 KVTKYQNDVFILYSF--GFSHEYIAQLLNITVGSSKNKISEIL 183 (217)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 568899999998876 67999999999999999999988875
No 186
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=33.72 E-value=22 Score=33.35 Aligned_cols=44 Identities=16% Similarity=0.354 Sum_probs=39.6
Q ss_pred eeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc
Q 014910 354 ALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 405 (416)
Q Consensus 354 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~ 405 (416)
.|+..+++++.++.+||.. +|..+...|++=|..|-++|++.|.
T Consensus 9 ~Il~~l~~~g~v~v~eLa~--------~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 9 KILELLKEKGKVSVEELAE--------LFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHcCcEEHHHHHH--------HhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 5788899999999988877 5889999999999999999999995
No 187
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=33.71 E-value=67 Score=29.04 Aligned_cols=41 Identities=22% Similarity=0.327 Sum_probs=36.9
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..|.-|..||.++-+ ++|..||++.+++++.+++.++..+.
T Consensus 148 ~LT~RE~eVL~lla~--G~snkeIA~~L~iS~~TVk~h~~~i~ 188 (211)
T COG2197 148 LLTPRELEVLRLLAE--GLSNKEIAEELNLSEKTVKTHVSNIL 188 (211)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 578899999999975 67999999999999999999998876
No 188
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=33.43 E-value=1.2e+02 Score=30.70 Aligned_cols=38 Identities=24% Similarity=0.266 Sum_probs=33.3
Q ss_pred hhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 261 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 261 Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
+...+.+|.++|++.++++...+.+.|..|. +.+++.+
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 5666799999999999999999999999997 5688875
No 189
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.39 E-value=25 Score=29.66 Aligned_cols=50 Identities=12% Similarity=0.232 Sum_probs=41.4
Q ss_pred hhhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 349 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 349 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
..+|..|.+++.....++..+|-..+- .+...+..+|+.|.+.|.|++..
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg--------lS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG--------LSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCceeeEE
Confidence 345777888999988899888877652 68888999999999999998864
No 190
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=33.37 E-value=71 Score=28.73 Aligned_cols=41 Identities=12% Similarity=0.159 Sum_probs=37.0
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..|.-+.-||.+.-+ ++|..||++.+++++..++.++..+.
T Consensus 137 ~LT~RE~eVL~lla~--G~snkeIA~~L~iS~~TVk~h~~~I~ 177 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQGTIQISDQMNIKAKTVSSHKGNIK 177 (207)
T ss_pred cCCHHHHHHHHHHHc--CCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 489999999998875 67999999999999999999998876
No 191
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=33.33 E-value=59 Score=25.80 Aligned_cols=48 Identities=15% Similarity=0.239 Sum_probs=26.0
Q ss_pred HHHHHhcCCCHHHHHHHHHHHHHHHhcCC----CCCChHHHHHHHHHHHhhc
Q 014910 29 EYVTNCFINHTLFHKALKEAFEIFCNKAV----GGSSSSELLATFCDNILKK 76 (416)
Q Consensus 29 ~l~~~~F~~~~~f~~~l~~af~~~~N~~~----~~~~~~e~La~y~d~~l~~ 76 (416)
.++..+...+......+..||+.+++.-+ +.+..++++|+++..++..
T Consensus 58 ~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~ 109 (113)
T PF02847_consen 58 KLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIAD 109 (113)
T ss_dssp HHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHT
T ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHc
Confidence 33333333444444555566666665422 2345677777777777765
No 192
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=33.19 E-value=59 Score=29.99 Aligned_cols=57 Identities=11% Similarity=0.222 Sum_probs=42.2
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 320 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~~f~ 320 (416)
-..+.-+|.++..||+.+|.+.|+=|...|+.+|..++ ++.+.+. -..+|+|-.+|.
T Consensus 188 ld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-----v~NkKg~-----~k~tyeLKPEYK 244 (254)
T KOG2905|consen 188 LDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-----VLNKKGP-----YKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-----HHhccCc-----ccCceecCHHHh
Confidence 33455689999999999999999999999999999885 3443221 235677666554
No 193
>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=33.18 E-value=63 Score=24.32 Aligned_cols=30 Identities=17% Similarity=0.280 Sum_probs=26.5
Q ss_pred hCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 262 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 262 n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..+..+++++|++.++++.+++...+..++
T Consensus 20 ~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i 49 (88)
T smart00088 20 EPYSSISLSDLAKLLGLSVPEVEKLVSKAI 49 (88)
T ss_pred HHhceeeHHHHHHHhCcCHHHHHHHHHHHH
Confidence 346789999999999999999999888886
No 194
>smart00753 PAM PCI/PINT associated module.
Probab=33.18 E-value=63 Score=24.32 Aligned_cols=30 Identities=17% Similarity=0.280 Sum_probs=26.5
Q ss_pred hCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 262 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 262 n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..+..+++++|++.++++.+++...+..++
T Consensus 20 ~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i 49 (88)
T smart00753 20 EPYSSISLSDLAKLLGLSVPEVEKLVSKAI 49 (88)
T ss_pred HHhceeeHHHHHHHhCcCHHHHHHHHHHHH
Confidence 346789999999999999999999888886
No 195
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=33.03 E-value=49 Score=25.15 Aligned_cols=47 Identities=13% Similarity=0.224 Sum_probs=34.2
Q ss_pred ceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 352 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 352 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
+..|...+...+.++..+|... +..+...+.+.|..|.++|+|++..
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 3445556666667777776554 3456777999999999999998764
No 196
>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=32.65 E-value=1.7e+02 Score=22.13 Aligned_cols=48 Identities=15% Similarity=0.240 Sum_probs=36.5
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecCC
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
+++.|=+.-.....+.-.+|++.++++...++..+..|- ..++|.+.|
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 344444445566789999999999999999999999995 468886543
No 197
>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=32.38 E-value=86 Score=22.68 Aligned_cols=33 Identities=24% Similarity=0.363 Sum_probs=28.3
Q ss_pred CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 266 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 266 ~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.+|-++|+..+|++...+.+.|..|. +.+++..
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 57899999999999999999999996 4467654
No 198
>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=32.27 E-value=48 Score=24.41 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=20.4
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
..-|.+||++.+|++.+.+...+...
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 35699999999999999999988754
No 199
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=32.21 E-value=41 Score=27.78 Aligned_cols=52 Identities=21% Similarity=0.366 Sum_probs=44.3
Q ss_pred hhhhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 014910 348 RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 348 ~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
...|.+.||-..+.++.++..+|... +..+...++..+..|+++|.|-+.+.
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~--------TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAK--------TGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHH--------HCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 36788999999999999999999885 44678889999999999998888763
No 200
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=32.16 E-value=1.2e+02 Score=20.80 Aligned_cols=41 Identities=17% Similarity=0.198 Sum_probs=35.1
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.++.-+..++.++... .+..||+..++++...+..++....
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 4577888889888775 7999999999999999999888774
No 201
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=31.66 E-value=36 Score=28.49 Aligned_cols=26 Identities=8% Similarity=0.266 Sum_probs=22.0
Q ss_pred CCCCChHHHHHHHHhhhhhccccccC
Q 014910 381 MFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 381 ~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 34567778999999999999999964
No 202
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=31.50 E-value=42 Score=29.41 Aligned_cols=56 Identities=16% Similarity=0.150 Sum_probs=36.7
Q ss_pred HHHhhhhhhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 014910 343 VDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 343 ~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
...+.-.+|-+ ++.+|.... +. ..+.+.+.. ..+.++++++|+.|.+-|+|+++++
T Consensus 21 ~~~W~~~~ir~-l~~l~~~~~--d~----~~iak~l~p--~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 21 YSSWYHPAIRE-LLPLMPFAP--DP----EWIAKRLRP--KISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred HhhhHHHHHHH-HhhcCCCCC--CH----HHHHHHhcC--CCCHHHHHHHHHHHHHCCCeEECCC
Confidence 44555555655 455655543 22 233332211 4578999999999999999999985
No 203
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=31.41 E-value=80 Score=28.11 Aligned_cols=41 Identities=22% Similarity=0.214 Sum_probs=36.4
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..|.-+.-||.+.-+ ++|..||++.++++...++.++..+.
T Consensus 150 ~Lt~rE~evl~~~~~--G~s~~eIA~~l~iS~~TV~~h~~~i~ 190 (216)
T PRK10840 150 RLSPKESEVLRLFAE--GFLVTEIAKKLNRSIKTISSQKKSAM 190 (216)
T ss_pred cCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 378899999988864 68999999999999999999998886
No 204
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=31.21 E-value=22 Score=33.36 Aligned_cols=45 Identities=18% Similarity=0.222 Sum_probs=39.1
Q ss_pred eeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc
Q 014910 353 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 405 (416)
Q Consensus 353 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~ 405 (416)
..|+..+++++.++..||.+ .|..+...|.+-|+.|-++|.|.|.
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~--------~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQ--------YFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 45678889999999988877 4789999999999999999999884
No 205
>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=30.69 E-value=61 Score=26.12 Aligned_cols=48 Identities=17% Similarity=0.201 Sum_probs=36.8
Q ss_pred CChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 014910 365 LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 414 (416)
Q Consensus 365 l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 414 (416)
.....++.+|+.... .+ ++...+--||+.||..|.++-.++-.++-+|
T Consensus 62 ~~~arvIg~vl~~~~-~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 62 QKAARVIGEVLGHSD-QG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred cHHHHHHHHHHHhcC-cC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 456678888988764 34 6678899999999999999988765554443
No 206
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=30.66 E-value=98 Score=26.59 Aligned_cols=44 Identities=14% Similarity=0.233 Sum_probs=35.0
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+|..++.+.......+|++.++++...+...++-|. +.+++...
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~ 57 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYE 57 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEe
Confidence 344455567789999999999999999999999996 45777654
No 207
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=30.51 E-value=93 Score=26.36 Aligned_cols=39 Identities=18% Similarity=0.204 Sum_probs=30.6
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
.+|.-|..||.++. ..+|.+||++.+|++...+......
T Consensus 6 ~Lt~rqreVL~lr~--~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 6 FLTERQIEVLRLRE--RGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred CCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45778888887763 6799999999999999776655443
No 208
>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=30.35 E-value=56 Score=24.24 Aligned_cols=33 Identities=18% Similarity=0.196 Sum_probs=23.4
Q ss_pred HhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 259 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 259 l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
....+...+|+.+|++.+|++...+.|..+.|-
T Consensus 27 ~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG 59 (77)
T PF01418_consen 27 ENPDEIAFMSISELAEKAGVSPSTIVRFCKKLG 59 (77)
T ss_dssp H-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCT
T ss_pred hCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhC
Confidence 333444589999999999999999999887773
No 209
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=30.03 E-value=98 Score=20.21 Aligned_cols=24 Identities=25% Similarity=0.343 Sum_probs=16.3
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
..+|..+|++.+|.+...+.+.|.
T Consensus 19 ~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 468999999999999998877663
No 210
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=29.87 E-value=62 Score=30.47 Aligned_cols=33 Identities=15% Similarity=0.227 Sum_probs=28.4
Q ss_pred CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 266 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 266 ~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
.-|-++|.+..||+....+++|..|. |.+.+..
T Consensus 246 KSsPEdIk~~FgiSKg~FKrAiGgL~--K~g~I~q 278 (287)
T COG2996 246 KSSPEDIKATFGISKGQFKRAIGGLM--KAGKIKQ 278 (287)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHH--hCCeEEE
Confidence 45899999999999999999999997 5566654
No 211
>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=29.63 E-value=78 Score=26.74 Aligned_cols=40 Identities=18% Similarity=0.204 Sum_probs=28.5
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
++.-|-.++.+.- ...+|.+||++.+|++...++..+..-
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 3455555554432 347899999999999999888776543
No 212
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=29.63 E-value=1.2e+02 Score=26.96 Aligned_cols=43 Identities=14% Similarity=0.240 Sum_probs=34.5
Q ss_pred HHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 257 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 257 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
++.-+..++..|..+|+..+|++..++.++|=.|. +.+.+...
T Consensus 18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~--~~~~v~~~ 60 (183)
T PHA03103 18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQ--REGMVYMS 60 (183)
T ss_pred HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHH--hcCceecC
Confidence 45556777899999999999999999999999986 34555443
No 213
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=29.61 E-value=1e+02 Score=27.27 Aligned_cols=41 Identities=22% Similarity=0.203 Sum_probs=36.2
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.+|+-+.-||.+..+ +.|..||++.++++...++..+..+.
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L~IS~rTVkth~srIm 173 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALLSLSEEQTKSLRRSIM 173 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 378899999998876 67999999999999999999888876
No 214
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=29.58 E-value=1.5e+02 Score=23.47 Aligned_cols=50 Identities=12% Similarity=0.159 Sum_probs=31.9
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC----CCCChHHHHHHHHHHHhhc
Q 014910 27 YMEYVTNCFINHTLFHKALKEAFEIFCNKAV----GGSSSSELLATFCDNILKK 76 (416)
Q Consensus 27 ~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~----~~~~~~e~La~y~d~~l~~ 76 (416)
|..++......+......+..||..+++.-+ ..+..+.++|.++..++..
T Consensus 56 ~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~ 109 (113)
T smart00544 56 YSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLISD 109 (113)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHHc
Confidence 4444555555555666677777777776533 2235677888888877765
No 215
>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=29.54 E-value=77 Score=22.59 Aligned_cols=24 Identities=8% Similarity=0.398 Sum_probs=19.7
Q ss_pred hCCCCcCHHHHHHHcCCCHHHHHH
Q 014910 262 NTSDRLSYSEIMTQLNLTHDDLVR 285 (416)
Q Consensus 262 n~~~~~t~~ei~~~~~i~~~~l~~ 285 (416)
...+.++..+|++.+|+++..+..
T Consensus 18 ~~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 18 ESNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred HhCCCccHHHHHHHHCCCHHHHHH
Confidence 345689999999999999987743
No 216
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.47 E-value=87 Score=28.36 Aligned_cols=41 Identities=17% Similarity=0.297 Sum_probs=33.3
Q ss_pred EEcHHHHHHHH-hh-----hCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 249 IVSTYQAATLL-LF-----NTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 249 ~~s~~Q~~iLl-~F-----n~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
.+|.-|..+|. .+ +.-..++..||++.+||++..+..+|..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr 201 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR 201 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 78899999885 33 4445899999999999999887777765
No 217
>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=29.19 E-value=39 Score=26.56 Aligned_cols=42 Identities=7% Similarity=0.169 Sum_probs=28.9
Q ss_pred eeeeehhcc----CCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccc
Q 014910 353 AALVRIMKS----RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYL 402 (416)
Q Consensus 353 A~IVRimK~----~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi 402 (416)
..|..++|. ...++.++|.+.+ ..+..+|+++|+.|++.|+|
T Consensus 50 ~~Vl~~i~~~~~~~~Gv~v~~I~~~l--------~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 50 DKVLNFIKQQPNSEEGVHVDEIAQQL--------GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHC----TTTEEHHHHHHHS--------TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHh--------CcCHHHHHHHHHHHHhCCeE
Confidence 334445555 4457777766543 35789999999999999966
No 218
>PRK09462 fur ferric uptake regulator; Provisional
Probab=29.18 E-value=81 Score=26.65 Aligned_cols=50 Identities=4% Similarity=0.176 Sum_probs=38.8
Q ss_pred eeeehhcc--CCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 354 ALVRIMKS--RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 354 ~IVRimK~--~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
+|.+++.. .+-++.++|...+.+.. ..++...|=+.|+.|.+.|.|.+-.
T Consensus 21 ~Il~~l~~~~~~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 21 KILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 34455554 35899999999987643 4467888999999999999998864
No 219
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=28.87 E-value=87 Score=31.86 Aligned_cols=38 Identities=21% Similarity=0.367 Sum_probs=30.4
Q ss_pred HHHHHHHhh-hCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 253 YQAATLLLF-NTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 253 ~Q~~iLl~F-n~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+-..||-.+ +....+|+++|++.|||..+++..+|+.|
T Consensus 360 W~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l 398 (450)
T PLN00104 360 WTRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL 398 (450)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 444555433 44468999999999999999999999988
No 220
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=28.47 E-value=51 Score=28.47 Aligned_cols=47 Identities=11% Similarity=0.208 Sum_probs=40.2
Q ss_pred hhceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccc
Q 014910 350 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 404 (416)
Q Consensus 350 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 404 (416)
.+|-.|.++|.....+++.+|-..| ..+...+.+||..|.+.|.|++
T Consensus 14 ~~D~~IL~~Lq~d~R~s~~eiA~~l--------glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKDGRISNVELSKRV--------GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEE
Confidence 3577889999999999998877754 3688889999999999999985
No 221
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=28.35 E-value=1.1e+02 Score=27.95 Aligned_cols=44 Identities=20% Similarity=0.238 Sum_probs=35.2
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+.+-..++...+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 11 allg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LE--e~GlI~R~ 54 (217)
T PRK14165 11 ALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLE--DEGYITRT 54 (217)
T ss_pred HHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 344445555679999999999999999999999996 45777654
No 222
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=28.28 E-value=99 Score=28.14 Aligned_cols=47 Identities=19% Similarity=0.197 Sum_probs=35.1
Q ss_pred EcHHHHHHHHh-h--hCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceee
Q 014910 250 VSTYQAATLLL-F--NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKIL 298 (416)
Q Consensus 250 ~s~~Q~~iLl~-F--n~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL 298 (416)
.+.-+.-+++. . +...++|.++|++.++++...++.++..|++ +.++
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~--~~~~ 208 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN--CHIL 208 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh--CCEE
Confidence 34555444432 2 2346899999999999999999999999974 4666
No 223
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=28.20 E-value=1e+02 Score=27.86 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=36.7
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..|+-+.-||.++-+ +.|..||++.+++++.+++.++..+.
T Consensus 134 ~LT~RE~eVL~ll~~--G~snkeIA~~L~iS~~TV~~h~~~I~ 174 (207)
T PRK11475 134 MLSPTEREILRFMSR--GYSMPQIAEQLERNIKTIRAHKFNVM 174 (207)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 378899999999876 57999999999999999999998876
No 224
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=27.95 E-value=34 Score=32.01 Aligned_cols=45 Identities=20% Similarity=0.443 Sum_probs=39.3
Q ss_pred eeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc
Q 014910 353 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 405 (416)
Q Consensus 353 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~ 405 (416)
..|..++++++.++..||.+ .|..+...|.+-|..|-++|+|.|-
T Consensus 8 ~~Il~~l~~~~~~~~~ela~--------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 8 DAIIELVKQQGYVSTEELVE--------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHcCCEeHHHHHH--------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45678889999999988877 4779999999999999999999985
No 225
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.79 E-value=1.1e+02 Score=23.78 Aligned_cols=35 Identities=23% Similarity=0.364 Sum_probs=27.4
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.+|+++.+... |..++++.+|++...+.+.+..+.
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35555655433 799999999999999999888775
No 226
>PRK04217 hypothetical protein; Provisional
Probab=27.78 E-value=1.1e+02 Score=24.67 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=28.6
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
.++.-|..++.+.. .+.+|++||++.+|++...+.+.|...
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 34445554443332 246799999999999999888877654
No 227
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=27.22 E-value=1.6e+02 Score=27.94 Aligned_cols=35 Identities=11% Similarity=0.158 Sum_probs=29.7
Q ss_pred CcCHHHHHHHcC--CCHHHHHHHHHhhhcccceeeecCC
Q 014910 266 RLSYSEIMTQLN--LTHDDLVRLLHSLSCAKYKILLKEP 302 (416)
Q Consensus 266 ~~t~~ei~~~~~--i~~~~l~~~L~~L~~~k~~iL~~~~ 302 (416)
..+.++|++.++ ++.++++.+|..|. +.++|.+.+
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~--~~glikk~~ 173 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLLE--RLGLIKKNE 173 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHHH--HCCCeeECC
Confidence 346889999998 89999999999997 679998753
No 228
>TIGR03076 near_not_gcvH Chlamydial GcvH-like protein upstream region protein. The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia but lack the P and T proteins, and have a single homolog of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The protein family modeled here is observed so far only in the Chlamydiae, always as part of a two-gene operon, upstream of the homolog of GcvH. Its function is unknown.
Probab=26.86 E-value=5.4e+02 Score=26.83 Aligned_cols=104 Identities=18% Similarity=0.300 Sum_probs=65.4
Q ss_pred chHHHHHHHHHHHHHHHHH-------------------HHHhcCCCHHHHHHHHHHHHHHHhcCCCC---CChHHHHHHH
Q 014910 12 QEQVLIRKIIELHDKYMEY-------------------VTNCFINHTLFHKALKEAFEIFCNKAVGG---SSSSELLATF 69 (416)
Q Consensus 12 ~~~~~i~~l~~l~~~~~~l-------------------~~~~F~~~~~f~~~l~~af~~~~N~~~~~---~~~~e~La~y 69 (416)
-|+..+.+++++...+..| |++.|+ +.|..+.-+|+-.+++..... ....|.++-+
T Consensus 174 fphy~LrqmLeYrrqmfnLp~D~~L~~g~dL~LFGY~~i~DWFg--~~yvs~v~e~ll~fi~EQkk~v~mps~~EA~~Df 251 (686)
T TIGR03076 174 FPHYVLRQMLEYRRQMFNLPVDGSLAQGKDLRLFGYRNIKDWFG--DAYVSAAVEALLRFIDEQKKNIAMPSLKEAQQDF 251 (686)
T ss_pred CCHHHHHHHHHHHHHhccCCCChhHhhcccceeeccccHHHhhh--HHHHHHHHHHHHHHHHHhcccccCCcHHHHHHHH
Confidence 4566677888887766332 344555 467777788888888765432 2456888888
Q ss_pred HHHHhhc------CCCCCCChHHHHHHHHHHHHHhhccC-ChhHHHHHHHH-HHHHHHcCCC
Q 014910 70 CDNILKK------GGNEKLSDEAIEETLEKVVKLLAYIS-DKDLFAEFYRK-KLARRLLFDR 123 (416)
Q Consensus 70 ~d~~l~~------~~~~~~~~~e~~~~l~~i~~lf~~l~-~KD~F~~~Y~~-~La~RLL~~~ 123 (416)
+|.-=.. +..-+++-++ -+...|+++. +...|.+.||. +|++|.+..-
T Consensus 252 ~dkaq~af~~~sk~~~~~ls~~e------~v~s~~~fmgv~esef~~myReiLL~kRafl~l 307 (686)
T TIGR03076 252 YDKAKQAFTKLSKHAEFNLTFDQ------FVSSYFSFMGVSESEFFNMYREILLCKRALLAL 307 (686)
T ss_pred HHHHHHHHHHhccCCCcCcCHHH------HHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHh
Confidence 8873221 1111334333 3566777776 56678888875 6789977644
No 229
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=26.83 E-value=45 Score=26.01 Aligned_cols=26 Identities=23% Similarity=0.368 Sum_probs=23.1
Q ss_pred CCCChHHHHHHHHhhhhhccccccCC
Q 014910 382 FKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 382 F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
+..+.++|..+++.|.+.|+|+|..+
T Consensus 31 l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 31 LKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred HCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 45678899999999999999999875
No 230
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.78 E-value=80 Score=27.43 Aligned_cols=37 Identities=14% Similarity=0.284 Sum_probs=27.5
Q ss_pred EcHHHHHHHHh-hhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 250 VSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 250 ~s~~Q~~iLl~-Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
++.-|-.|+.+ +- +++|++||++.+|++...++..|.
T Consensus 128 Lp~~~R~v~~L~~~--~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 128 LRPRVKQAFLMATL--DGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45555555544 33 478999999999999998887664
No 231
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.76 E-value=80 Score=27.28 Aligned_cols=37 Identities=19% Similarity=0.331 Sum_probs=26.2
Q ss_pred EcHHHHHHH-HhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 250 VSTYQAATL-LLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 250 ~s~~Q~~iL-l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
++.-+-.|+ +.+- +++|++||++.+|++...++..|.
T Consensus 130 L~~~~r~i~~l~~~--~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 130 LEKDRAAAVRRAYL--EGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHHCCChHHHHHHHH
Confidence 344454434 4442 468999999999999988877654
No 232
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=26.63 E-value=67 Score=28.11 Aligned_cols=40 Identities=20% Similarity=0.374 Sum_probs=30.1
Q ss_pred HHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 258 LLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 258 Ll~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
++.++ .+++|++||+++||++...+-..+.-|.. .+|..+
T Consensus 34 ilyls-~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~--~~lV~~ 73 (177)
T COG1510 34 ILYLS-RKPLTLDEIAEALGMSKSNVSMGLKKLQD--WNLVKK 73 (177)
T ss_pred hheec-CCCccHHHHHHHHCCCcchHHHHHHHHHh--cchHHh
Confidence 34444 46999999999999999888888777753 455544
No 233
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=26.30 E-value=95 Score=27.70 Aligned_cols=33 Identities=30% Similarity=0.516 Sum_probs=29.0
Q ss_pred HhhhCCCC-cCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 259 LLFNTSDR-LSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 259 l~Fn~~~~-~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
++|-..++ +|+++|++.++++..++..+|..|.
T Consensus 12 ~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~ 45 (188)
T PRK00135 12 LLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQ 45 (188)
T ss_pred HHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56777775 9999999999999999999999885
No 234
>PRK09954 putative kinase; Provisional
Probab=26.13 E-value=1.3e+02 Score=29.57 Aligned_cols=38 Identities=13% Similarity=0.208 Sum_probs=33.7
Q ss_pred HHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 255 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 255 ~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
.-||..+.++..+|..||++.+|++...+.+.|..|..
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34777788888999999999999999999999999964
No 235
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=25.94 E-value=85 Score=27.16 Aligned_cols=32 Identities=28% Similarity=0.493 Sum_probs=25.1
Q ss_pred HhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 259 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 259 l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
++|-..+++|+++|++.++ +.+.+...|..|.
T Consensus 6 lLF~s~~pvs~~~La~~l~-~~~~v~~~l~~L~ 37 (159)
T PF04079_consen 6 LLFASGEPVSIEELAEILG-SEDEVEEALEELQ 37 (159)
T ss_dssp HHHH-SS-B-HHHHHHHCT--HHHHHHHHHHHH
T ss_pred hHHHcCCCCCHHHHHHHhC-CHHHHHHHHHHHH
Confidence 4677778899999999999 9999999999886
No 236
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=25.83 E-value=1.2e+02 Score=25.98 Aligned_cols=33 Identities=24% Similarity=0.323 Sum_probs=23.9
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
+.++.|.+- +.+|++||++.+|++...++..|.
T Consensus 124 r~v~~L~~~--eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 124 RAAFLMSQL--EGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334444343 478999999999999988776653
No 237
>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=25.71 E-value=89 Score=20.04 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=18.1
Q ss_pred cCHHHHHHHcCCCHHHHHHHH
Q 014910 267 LSYSEIMTQLNLTHDDLVRLL 287 (416)
Q Consensus 267 ~t~~ei~~~~~i~~~~l~~~L 287 (416)
+|++|+++.+|++...+.+-+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 689999999999998887654
No 238
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=25.70 E-value=1e+02 Score=27.58 Aligned_cols=34 Identities=29% Similarity=0.376 Sum_probs=24.4
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
+..++|.+ ...++++||++.+|++...++..|.-
T Consensus 144 r~v~~L~~--~~g~s~~EIA~~Lgis~~tV~~~l~R 177 (203)
T PRK09647 144 RAAVVLCD--IEGLSYEEIAATLGVKLGTVRSRIHR 177 (203)
T ss_pred HHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33344443 34789999999999999887776543
No 239
>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=25.68 E-value=85 Score=25.32 Aligned_cols=57 Identities=9% Similarity=0.175 Sum_probs=40.3
Q ss_pred eeehhcc-CCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 014910 355 LVRIMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 414 (416)
Q Consensus 355 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 414 (416)
|..+|++ .+-++.++|...+.+. ...++...|=+.|+.|.+.|.|.+-..+.+...|
T Consensus 13 Il~~l~~~~~~~ta~ei~~~l~~~---~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 13 ILELLKESPEHLTAEEIYDKLRKK---GPRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp HHHHHHHHSSSEEHHHHHHHHHHT---TTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred HHHHHHcCCCCCCHHHHHHHhhhc---cCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 3444454 4578899999888753 3457888999999999999999997655444444
No 240
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=25.66 E-value=1.8e+02 Score=25.83 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=33.1
Q ss_pred HHHHHhhhCCC-CcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 255 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 255 ~~iLl~Fn~~~-~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
..||..+...+ .+|.-+|+..+|++...+.++|-.|. +.+.+..
T Consensus 7 ~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~--~~~~v~~ 51 (183)
T PHA02701 7 SLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLL--ESDAVSC 51 (183)
T ss_pred HHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHh--hcCcEec
Confidence 34555555544 69999999999999999999998886 3344443
No 241
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=25.51 E-value=54 Score=27.50 Aligned_cols=38 Identities=16% Similarity=0.331 Sum_probs=29.0
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 361 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 361 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
....++..+|-.. +..+...+-..|+.|.++|||+|..
T Consensus 51 ~~~~~t~~eLa~~--------l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 51 CAACITPVELKKV--------LSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HcCCCCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEecc
Confidence 3455666666553 4467888999999999999999964
No 242
>PRK00118 putative DNA-binding protein; Validated
Probab=25.49 E-value=1.1e+02 Score=24.38 Aligned_cols=38 Identities=16% Similarity=0.233 Sum_probs=27.0
Q ss_pred cHHHHHHHH-hhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 251 STYQAATLL-LFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 251 s~~Q~~iLl-~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+.-|-.++. .+. ...|+.+|++.+|++...+.+.+..-
T Consensus 19 ~ekqRevl~L~y~--eg~S~~EIAe~lGIS~~TV~r~L~RA 57 (104)
T PRK00118 19 TEKQRNYMELYYL--DDYSLGEIAEEFNVSRQAVYDNIKRT 57 (104)
T ss_pred CHHHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444444443 333 37899999999999999888876543
No 243
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.40 E-value=1.1e+02 Score=25.73 Aligned_cols=38 Identities=16% Similarity=0.136 Sum_probs=26.2
Q ss_pred EcHHHHHHH-HhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 250 VSTYQAATL-LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 250 ~s~~Q~~iL-l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
++.-|-.++ +.+- .++|++||++.+|++...++..|.-
T Consensus 107 Lp~~~r~v~~l~~~--~g~s~~EIA~~lgis~~tV~~~l~R 145 (160)
T PRK09642 107 LPENYRDVVLAHYL--EEKSYQEIALQEKIEVKTVEMKLYR 145 (160)
T ss_pred CCHHHHHHHHHHHH--hCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 444444444 3333 4789999999999999988766543
No 244
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=25.40 E-value=54 Score=27.93 Aligned_cols=46 Identities=11% Similarity=0.159 Sum_probs=38.1
Q ss_pred hceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccc
Q 014910 351 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 404 (416)
Q Consensus 351 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 404 (416)
+|-.|.+.|.....+++.+|-.++ ..+.+.+..||+.|.+.|+|++
T Consensus 10 ~D~~Il~~Lq~d~R~s~~eiA~~l--------glS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 10 LDRGILEALMENARTPYAELAKQF--------GVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeee
Confidence 455677888888889988887754 3688999999999999999985
No 245
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=25.19 E-value=1e+02 Score=28.96 Aligned_cols=47 Identities=23% Similarity=0.338 Sum_probs=38.1
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 253 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 253 ~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
-|..+-..-+..+.++-+||.+++|+|...+-|+|..|- |.+++.+.
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE--k~GlIe~~ 243 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE--KRGLIEKE 243 (258)
T ss_pred HHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH--hCCceEEE
Confidence 444444556666789999999999999999999999996 67887654
No 246
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=25.18 E-value=75 Score=25.51 Aligned_cols=45 Identities=16% Similarity=0.156 Sum_probs=31.6
Q ss_pred eeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 354 ALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 354 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
.|...+.....++..+|-.. ...+...+-..|..|.++|||+|..
T Consensus 32 ~iL~~l~~~~~~t~~ela~~--------~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 32 RILRILAEQGSMEFTQLANQ--------ACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHHcCCcCHHHHHHH--------hCCCchhHHHHHHHHHHCCCEEecc
Confidence 34455556667776665553 2345567889999999999999954
No 247
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=24.99 E-value=50 Score=26.12 Aligned_cols=27 Identities=15% Similarity=0.297 Sum_probs=23.0
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCC
Q 014910 381 MFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 381 ~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
....+...+...|+.|.++|||+|..+
T Consensus 45 ~l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 45 RLGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred HHCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 445788889999999999999999754
No 248
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=24.88 E-value=68 Score=23.49 Aligned_cols=45 Identities=13% Similarity=0.124 Sum_probs=36.2
Q ss_pred CCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 014910 363 KVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 363 k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
+.++=-+|.+.+.+...+.+.++...|=..|..|.++|+|+....
T Consensus 8 ~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~ 52 (75)
T PF03551_consen 8 GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWE 52 (75)
T ss_dssp S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEE
T ss_pred CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeee
Confidence 455667888888776655678999999999999999999987643
No 249
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.79 E-value=1.3e+02 Score=25.49 Aligned_cols=32 Identities=28% Similarity=0.405 Sum_probs=23.9
Q ss_pred HHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 254 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 254 Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
+.++.+.+ ..++.+||++.+|++...++..+.
T Consensus 118 r~il~l~~---~g~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 118 RTVLLLRF---SGYSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred HHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 33444444 478999999999999988777654
No 250
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=24.63 E-value=1.2e+02 Score=26.10 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=20.4
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
++++++||++.+|++...++..|.
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 367999999999999988877664
No 251
>PF12728 HTH_17: Helix-turn-helix domain
Probab=24.40 E-value=95 Score=20.63 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=17.9
Q ss_pred cCHHHHHHHcCCCHHHHHHHH
Q 014910 267 LSYSEIMTQLNLTHDDLVRLL 287 (416)
Q Consensus 267 ~t~~ei~~~~~i~~~~l~~~L 287 (416)
+|++|+++.+|++...+.+.+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~ 22 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWI 22 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 689999999999998876644
No 252
>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=24.29 E-value=99 Score=23.28 Aligned_cols=29 Identities=14% Similarity=0.338 Sum_probs=22.7
Q ss_pred CCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 263 TSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 263 ~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..+..|++++++.++++...+.+.+..+-
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 34578999999999999999999888774
No 253
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.19 E-value=98 Score=27.40 Aligned_cols=38 Identities=29% Similarity=0.362 Sum_probs=27.7
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+..+..|+.++- ..+|.+||++.+|++...++..+.-.
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 444555554443 47899999999999999888766543
No 254
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=24.12 E-value=1e+02 Score=28.26 Aligned_cols=36 Identities=8% Similarity=0.068 Sum_probs=31.9
Q ss_pred HHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 256 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 256 ~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.+.-+|.+++.||+..|++.+|-|+..|+.+|...+
T Consensus 199 ~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~ia 234 (297)
T COG5090 199 MLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIA 234 (297)
T ss_pred HHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHH
Confidence 345689999999999999999999999999998764
No 255
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.90 E-value=1.3e+02 Score=25.60 Aligned_cols=41 Identities=12% Similarity=0.213 Sum_probs=28.5
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
.++.-|-.++.+.- .+++|++||++.+|++...++..|.--
T Consensus 112 ~L~~~~r~v~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~Ra 152 (164)
T PRK12547 112 LLSADQREAIILIG-ASGFSYEDAAAICGCAVGTIKSRVSRA 152 (164)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 33555555554432 147899999999999998887766543
No 256
>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=23.87 E-value=1.3e+02 Score=25.46 Aligned_cols=39 Identities=23% Similarity=0.298 Sum_probs=28.5
Q ss_pred EEcHHHHHHHHh-hhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 249 IVSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 249 ~~s~~Q~~iLl~-Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
.+|+-|-.|+.+ +- .++|++||++.+|++...++..+..
T Consensus 122 ~L~~~~r~vl~l~~~--~g~s~~eIA~~l~is~~tv~~~l~r 161 (170)
T TIGR02952 122 ILTPKQQHVIALRFG--QNLPIAEVARILGKTEGAVKILQFR 161 (170)
T ss_pred hCCHHHHHHHHHHHh--cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345556666654 33 3689999999999999888876654
No 257
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=23.77 E-value=1.1e+02 Score=25.47 Aligned_cols=35 Identities=23% Similarity=0.396 Sum_probs=25.8
Q ss_pred ehhccC-CCCChhHHHHHHHHHhccCCCCChHHHHHHHHh
Q 014910 357 RIMKSR-KVLGHQQLVSECVEQLSRMFKPDIKAIKKRMED 395 (416)
Q Consensus 357 RimK~~-k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~ 395 (416)
-||+.+ +.|++.+|+++|.+.+. .+.+.+..+|-.
T Consensus 11 ~iL~~~~~~m~f~dL~~ev~~~~~----~s~e~~~~~iaq 46 (129)
T PRK02363 11 EILKEKKEPMSFYDLVNEIQKYLG----KSDEEIRERIAQ 46 (129)
T ss_pred HHHHHcCCcccHHHHHHHHHHHhC----CCHHHHHHHHHH
Confidence 356555 67999999999999765 466667666655
No 258
>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=23.65 E-value=1.8e+02 Score=23.02 Aligned_cols=57 Identities=19% Similarity=0.264 Sum_probs=39.3
Q ss_pred HHHHhhhC-CCCcCHHHHHHHc-----CCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEcc
Q 014910 256 ATLLLFNT-SDRLSYSEIMTQL-----NLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 317 (416)
Q Consensus 256 ~iLl~Fn~-~~~~t~~ei~~~~-----~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~lN~ 317 (416)
.||..+.. ...+|.+||.+.+ +++...+-++|..|. ..+++.+...+. ....|.++.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~--~~Gli~~~~~~~---~~~~y~~~~ 67 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLE--EAGLVREIELGD---GKARYELNT 67 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHH--hCCCEEEEEeCC---CceEEEeCC
Confidence 45555544 4579999999988 689999999999997 457776542111 124566654
No 259
>PRK09483 response regulator; Provisional
Probab=23.57 E-value=1.4e+02 Score=26.05 Aligned_cols=41 Identities=20% Similarity=0.203 Sum_probs=35.2
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..|.-+.-||.++.. +.|..+|++.++++...++.++..+.
T Consensus 148 ~Lt~rE~~vl~~~~~--G~~~~~Ia~~l~is~~TV~~~~~~i~ 188 (217)
T PRK09483 148 SLSERELQIMLMITK--GQKVNEISEQLNLSPKTVNSYRYRMF 188 (217)
T ss_pred ccCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 468888888887764 57999999999999999999998886
No 260
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=23.51 E-value=1.4e+02 Score=27.22 Aligned_cols=39 Identities=18% Similarity=0.279 Sum_probs=27.3
Q ss_pred EcHHHHHHHH-hh--hCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 250 VSTYQAATLL-LF--NTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 250 ~s~~Q~~iLl-~F--n~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
++.-|-.|+. .| +..+.+|++||++.+|++...++..+.
T Consensus 179 Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~ 220 (234)
T PRK08301 179 LSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3444444444 33 335689999999999999988876543
No 261
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=23.44 E-value=1.2e+02 Score=26.21 Aligned_cols=39 Identities=15% Similarity=0.112 Sum_probs=27.8
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+.-|-.++.++- .+.+|++||++.+|++...++..|..-
T Consensus 131 ~~~~r~v~~l~~-~~g~s~~EIA~~l~is~~tV~~~l~ra 169 (181)
T PRK12536 131 PDRQRLPIVHVK-LEGLSVAETAQLTGLSESAVKVGIHRG 169 (181)
T ss_pred CHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 555555543321 246899999999999999988877543
No 262
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=23.43 E-value=1.3e+02 Score=27.16 Aligned_cols=42 Identities=14% Similarity=0.230 Sum_probs=33.1
Q ss_pred HHHHhhhCC-CCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 256 ATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 256 ~iLl~Fn~~-~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
.||.++.+. ...|.+||++.++++...+++++..|.. .+++.
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~--~~~~~ 208 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCAS--RHLII 208 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHh--CCeEE
Confidence 566666543 2689999999999999999999999973 45554
No 263
>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=23.39 E-value=1.3e+02 Score=26.02 Aligned_cols=39 Identities=23% Similarity=0.112 Sum_probs=26.9
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
++.-|-.|+.+.- .+++|++||++.+|++...++..|.-
T Consensus 135 Lp~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 135 VDPRQAEVVELRF-FAGLTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3444444444332 24689999999999999988876643
No 264
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=23.37 E-value=73 Score=24.01 Aligned_cols=30 Identities=17% Similarity=0.159 Sum_probs=26.1
Q ss_pred HhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 377 QLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 377 ~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
+|+.+|..+.+.|..-++.|+.+|-|+|-+
T Consensus 21 ~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 21 QISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 344568889999999999999999999886
No 265
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=23.25 E-value=57 Score=33.45 Aligned_cols=57 Identities=14% Similarity=0.278 Sum_probs=48.2
Q ss_pred ceeeeehhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 014910 352 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 416 (416)
Q Consensus 352 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 416 (416)
+.+|++.++..+.++-.+|-+. |..+...+.+.|..|+.+|++++-+.+..-+.||.
T Consensus 404 ~~~il~~~~en~~~T~~~L~~~--------l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v~ 460 (467)
T COG2865 404 QEKILELIKENGKVTARELREI--------LGISSETIRRRIANLVKRGLLKQLGSSGRGTWYVK 460 (467)
T ss_pred HHHHHHHHhhccccCHHHHHHH--------hCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEec
Confidence 4789999999999998887763 44788889999999999999999987777777763
No 266
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=23.17 E-value=86 Score=27.57 Aligned_cols=26 Identities=27% Similarity=0.381 Sum_probs=23.0
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
.++|.+||++.+|+++..+.+.|...
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 47899999999999999999988654
No 267
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=23.15 E-value=1.8e+02 Score=23.64 Aligned_cols=44 Identities=16% Similarity=0.144 Sum_probs=35.1
Q ss_pred EEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhc
Q 014910 248 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 292 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~ 292 (416)
..++.-|..-+..|=...+ ++.++++.+|+++..++.-|..++.
T Consensus 32 ~~L~~E~~~Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rLd~ii~ 75 (113)
T PF09862_consen 32 ARLSPEQLEFIKLFIKNRG-NLKEMEKELGISYPTVRNRLDKIIE 75 (113)
T ss_pred hcCCHHHHHHHHHHHHhcC-CHHHHHHHHCCCcHHHHHHHHHHHH
Confidence 3567777777777765433 8999999999999999999998863
No 268
>PF14493 HTH_40: Helix-turn-helix domain
Probab=23.13 E-value=1.8e+02 Score=22.23 Aligned_cols=33 Identities=30% Similarity=0.293 Sum_probs=28.4
Q ss_pred HHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 257 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 257 iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.+.+|++ ++|++||++.-|++...+..+|..++
T Consensus 6 T~~l~~~--G~si~eIA~~R~L~~sTI~~HL~~~~ 38 (91)
T PF14493_consen 6 TYELFQK--GLSIEEIAKIRGLKESTIYGHLAELI 38 (91)
T ss_pred HHHHHHc--CCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4567774 68999999999999999999998775
No 269
>PF13314 DUF4083: Domain of unknown function (DUF4083)
Probab=23.04 E-value=2.2e+02 Score=20.06 Aligned_cols=33 Identities=24% Similarity=0.519 Sum_probs=21.9
Q ss_pred HHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHh
Q 014910 66 LATFCDNILKKGGNEKLSDEAIEETLEKVVKLL 98 (416)
Q Consensus 66 La~y~d~~l~~~~~~~~~~~e~~~~l~~i~~lf 98 (416)
+..++-.++.++.-++-+.++++.+||.|+.|+
T Consensus 23 Ftl~IRri~~~s~~kkq~~~~~eqKLDrIIeLL 55 (58)
T PF13314_consen 23 FTLFIRRILINSNAKKQDVDSMEQKLDRIIELL 55 (58)
T ss_pred HHHHHHHHHHhccccccchhHHHHHHHHHHHHH
Confidence 444555566654323334568999999999986
No 270
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.79 E-value=1.4e+02 Score=25.02 Aligned_cols=37 Identities=11% Similarity=0.118 Sum_probs=25.1
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
+.-|-.|+.+.- ..++|++||++.+|++...++..+.
T Consensus 108 p~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 108 PARQREAFLLRY-WEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred CHHHHHHHHHHH-HhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 343444443321 2478999999999999988876554
No 271
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.60 E-value=1.4e+02 Score=27.09 Aligned_cols=40 Identities=18% Similarity=0.157 Sum_probs=35.5
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
+|.-|.-||.+.-. ++|..||++.+++++..++.++..+.
T Consensus 156 Lt~rE~~Vl~l~~~--G~s~~eIA~~L~iS~~TVk~~~~~i~ 195 (216)
T PRK10100 156 LTHREKEILNKLRI--GASNNEIARSLFISENTVKTHLYNLF 195 (216)
T ss_pred CCHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 68889999987776 68999999999999999999998875
No 272
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=22.58 E-value=1.5e+02 Score=24.55 Aligned_cols=38 Identities=16% Similarity=0.179 Sum_probs=27.4
Q ss_pred cHHHHHHHHh-hhCCCCcCHHHHHHHcCCCHHHHHHHHHhh
Q 014910 251 STYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 251 s~~Q~~iLl~-Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
+.-+..++.+ +- .++|++||++.+|++...+...+...
T Consensus 115 ~~~~r~il~l~~~--~~~~~~eIA~~lgis~~tv~~~~~ra 153 (161)
T TIGR02985 115 PEQCRKIFILSRF--EGKSYKEIAEELGISVKTVEYHISKA 153 (161)
T ss_pred CHHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4445555543 43 47899999999999999988776543
No 273
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=22.57 E-value=67 Score=24.58 Aligned_cols=30 Identities=7% Similarity=0.149 Sum_probs=24.9
Q ss_pred hccCCCCChHHHHHHHHhhhhhccccccCC
Q 014910 378 LSRMFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 378 l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
+...+..+...+-+.+..|.++|||.|.++
T Consensus 5 la~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 5 IAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 334566788889999999999999999874
No 274
>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=22.48 E-value=58 Score=24.20 Aligned_cols=55 Identities=18% Similarity=0.168 Sum_probs=39.9
Q ss_pred hceeeeehhccCCCCChhHHHHHHHHHhccCCCC--ChHHHHHHHHhhhhhccccccC
Q 014910 351 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKP--DIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 351 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~--~~~~ik~~Ie~Liereyi~r~~ 406 (416)
|..|| +-|+.++..+...|...+...-.-...| -...++.+|..++++|-+.+..
T Consensus 9 I~eAI-~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 9 ILEAI-KALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHH-HHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHH-HHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 33443 6789999999999999988753211222 1356999999999999888865
No 275
>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=22.33 E-value=1.1e+02 Score=24.62 Aligned_cols=53 Identities=13% Similarity=0.389 Sum_probs=29.4
Q ss_pred hceeeeehhccCCCCChhHHHHHHHHHhcc-CCCCChHHHHHHHHhhhhhccccc
Q 014910 351 IDAALVRIMKSRKVLGHQQLVSECVEQLSR-MFKPDIKAIKKRMEDLITRDYLER 404 (416)
Q Consensus 351 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~-~F~~~~~~ik~~Ie~Liereyi~r 404 (416)
+.-.|+.+.-+++.-.. ++..+..+..+. .|.|..++|=+++-.|++.|+++|
T Consensus 19 lKlYiitm~e~~r~Yg~-q~Ld~lr~EFk~~Gy~P~hsEvYraLHeL~~dGilk~ 72 (122)
T PF02334_consen 19 LKLYIITMVEQERGYGL-QLLDELRSEFKPLGYRPNHSEVYRALHELVDDGILKQ 72 (122)
T ss_dssp HHHHHHHHHHTT-EBCT-CHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHhhhhcccchHH-HHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhhhHHHH
Confidence 33444444444442111 334444444442 388999999999999999999965
No 276
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.24 E-value=1.2e+02 Score=25.45 Aligned_cols=38 Identities=16% Similarity=0.198 Sum_probs=26.7
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
+++-+..|+.+. ..+.+|++||++.+|++...++..|.
T Consensus 106 L~~~~r~v~~l~-~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 106 LPPACRDSFLLR-KLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 455555555443 23578999999999999987766543
No 277
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=22.19 E-value=1.3e+02 Score=27.07 Aligned_cols=40 Identities=15% Similarity=0.156 Sum_probs=34.2
Q ss_pred HHHHHHHHhhhCCC--CcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 252 TYQAATLLLFNTSD--RLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 252 ~~Q~~iLl~Fn~~~--~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
..+..||..+.+.+ .+|.++|++..|++...+++-|..|-
T Consensus 16 ~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~ 57 (213)
T PRK05472 16 PLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFG 57 (213)
T ss_pred HHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHH
Confidence 45667888888887 99999999999999999999887773
No 278
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=22.14 E-value=1.1e+02 Score=28.45 Aligned_cols=51 Identities=18% Similarity=0.171 Sum_probs=40.6
Q ss_pred EEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeeec
Q 014910 248 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 300 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 300 (416)
|-.|-++|-+-+..-..+..|..||++.+|+|..-+-..|.+|.. .+++..
T Consensus 12 lGlt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~--kG~v~~ 62 (247)
T COG1378 12 LGLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEK--KGLVEV 62 (247)
T ss_pred cCCCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHH--CCCEEe
Confidence 445667787777666667899999999999999999999999973 355543
No 279
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.10 E-value=2.1e+02 Score=18.65 Aligned_cols=23 Identities=17% Similarity=0.364 Sum_probs=19.9
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhh
Q 014910 268 SYSEIMTQLNLTHDDLVRLLHSL 290 (416)
Q Consensus 268 t~~ei~~~~~i~~~~l~~~L~~L 290 (416)
|+.+++..+|++...+.+-+...
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHH
Confidence 99999999999998887766655
No 280
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.98 E-value=1.3e+02 Score=26.07 Aligned_cols=38 Identities=13% Similarity=0.072 Sum_probs=27.6
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
++.-+-.|+.+.- .+.+|++||++.+|++...++..|.
T Consensus 136 L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 136 LSPEERRVIEVLY-YQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4555666665432 3478999999999999988876554
No 281
>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=21.97 E-value=31 Score=28.43 Aligned_cols=48 Identities=13% Similarity=0.147 Sum_probs=36.0
Q ss_pred ccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 014910 360 KSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 407 (416)
Q Consensus 360 K~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 407 (416)
+..+.+-.++.+....+.|+-.|.-+++.|+.+|..|.+-|.|+.+++
T Consensus 41 n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~ed 88 (121)
T PF09681_consen 41 NDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDED 88 (121)
T ss_pred CCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 444455555555555555655677899999999999999999999874
No 282
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=21.80 E-value=1.2e+02 Score=19.31 Aligned_cols=21 Identities=24% Similarity=0.303 Sum_probs=17.4
Q ss_pred cCHHHHHHHcCCCHHHHHHHH
Q 014910 267 LSYSEIMTQLNLTHDDLVRLL 287 (416)
Q Consensus 267 ~t~~ei~~~~~i~~~~l~~~L 287 (416)
+|..|+++.+|++...+.+-.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 478999999999998886644
No 283
>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=21.67 E-value=1e+02 Score=22.24 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=39.1
Q ss_pred eeehhccCC-CCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 355 LVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 355 IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
|.++++... .+...+|....... -+..+.+.|..++..|-++||+++..
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~---g~~~se~avRrrLr~me~~Glt~~~g 52 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLR---GEELSEEAVRRRLRAMERDGLTRKVG 52 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhc---ChhhhHHHHHHHHHHHHHCCCccccC
Confidence 556666654 59999998877653 47788899999999999999998765
No 284
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.60 E-value=1.2e+02 Score=21.79 Aligned_cols=26 Identities=19% Similarity=0.381 Sum_probs=21.9
Q ss_pred CcCHHHHHHHcCCCHHHHHHHHHhhh
Q 014910 266 RLSYSEIMTQLNLTHDDLVRLLHSLS 291 (416)
Q Consensus 266 ~~t~~ei~~~~~i~~~~l~~~L~~L~ 291 (416)
.+|+++|++.+|++...+.+.+....
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 37899999999999999888776653
No 285
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=21.41 E-value=1.1e+02 Score=23.82 Aligned_cols=24 Identities=25% Similarity=0.412 Sum_probs=21.6
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
..+|.++|+..+|++.+.+.++|.
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 479999999999999999998874
No 286
>PRK12423 LexA repressor; Provisional
Probab=21.25 E-value=1.7e+02 Score=26.25 Aligned_cols=52 Identities=17% Similarity=0.250 Sum_probs=38.4
Q ss_pred EcHHHHHHHHhhhCC---C--CcCHHHHHHHcCC-CHHHHHHHHHhhhcccceeeecCCC
Q 014910 250 VSTYQAATLLLFNTS---D--RLSYSEIMTQLNL-THDDLVRLLHSLSCAKYKILLKEPN 303 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~---~--~~t~~ei~~~~~i-~~~~l~~~L~~L~~~k~~iL~~~~~ 303 (416)
+|.-|-.||..+.+. . .-|+.||++.+|+ +...+.++|..|. +.++|...+.
T Consensus 4 lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~--~~G~l~~~~~ 61 (202)
T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALA--EAGLIEVVPN 61 (202)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEecCC
Confidence 356677777655432 2 3499999999995 8889999999996 4578876543
No 287
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=21.12 E-value=1.6e+02 Score=26.98 Aligned_cols=25 Identities=16% Similarity=0.262 Sum_probs=21.5
Q ss_pred CCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 264 SDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 264 ~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
.+++|++||++.+|++...+...+.
T Consensus 196 ~eg~s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 196 GTEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4689999999999999998877653
No 288
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.08 E-value=1.5e+02 Score=26.06 Aligned_cols=37 Identities=22% Similarity=0.252 Sum_probs=25.6
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
+.-|-.|+.+.- ...+|++||++.+|++...++..|.
T Consensus 136 p~~~R~v~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 136 PAQQARVFMMRE-YLELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred CHHHHHHHhHHH-HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 444444444332 2378999999999999988876654
No 289
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.04 E-value=1.2e+02 Score=26.12 Aligned_cols=25 Identities=28% Similarity=0.477 Sum_probs=20.9
Q ss_pred CCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 264 SDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 264 ~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
...+|++||++.+|++...++..|.
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 133 LDGLTYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3578999999999999988777654
No 290
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.91 E-value=1.2e+02 Score=23.35 Aligned_cols=24 Identities=42% Similarity=0.405 Sum_probs=21.7
Q ss_pred CCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 265 DRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 265 ~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
..+|.++|+..+|.++..+.+.|+
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHHH
Confidence 379999999999999999999884
No 291
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=20.75 E-value=80 Score=28.85 Aligned_cols=49 Identities=8% Similarity=0.130 Sum_probs=34.8
Q ss_pred hhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 014910 358 IMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 414 (416)
Q Consensus 358 imK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 414 (416)
.++..-.++..+|-.. ...+.+.+-+.|..|.++|||+|..+..+.+.+
T Consensus 15 ~l~~~~~IS~~eLA~~--------L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~ 63 (217)
T PRK14165 15 AVNNTVKISSSEFANH--------TGTSSKTAARILKQLEDEGYITRTIVPRGQLIT 63 (217)
T ss_pred ccCCCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEE
Confidence 3444445666666654 346888899999999999999998654454444
No 292
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=20.73 E-value=1.9e+02 Score=23.02 Aligned_cols=38 Identities=24% Similarity=0.372 Sum_probs=22.7
Q ss_pred EcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 250 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 250 ~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
+|--|-.++.++-. +.+|+.||++..|++...+...+.
T Consensus 18 LT~kQ~~~l~lyy~-eDlSlsEIAe~~~iSRqaV~d~ik 55 (101)
T PF04297_consen 18 LTEKQREILELYYE-EDLSLSEIAEELGISRQAVYDSIK 55 (101)
T ss_dssp S-HHHHHHHHHHCT-S---HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHc-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34557777765543 368999999999999865544443
No 293
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=20.72 E-value=1.6e+02 Score=27.60 Aligned_cols=36 Identities=8% Similarity=0.262 Sum_probs=25.6
Q ss_pred cHHHHHHHH-hhhCCCCcCHHHHHHHcCCCHHHHHHH
Q 014910 251 STYQAATLL-LFNTSDRLSYSEIMTQLNLTHDDLVRL 286 (416)
Q Consensus 251 s~~Q~~iLl-~Fn~~~~~t~~ei~~~~~i~~~~l~~~ 286 (416)
+.-|-.||. .|-..+.+|..||++.+|++...+.+.
T Consensus 220 ~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~ 256 (270)
T TIGR02392 220 DARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQI 256 (270)
T ss_pred CHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHH
Confidence 444444554 343345799999999999999888743
No 294
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.53 E-value=1.4e+02 Score=25.94 Aligned_cols=38 Identities=5% Similarity=0.102 Sum_probs=26.8
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 251 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 251 s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
+.-|-.++.+.- ...+|++||++.+|++...+...|..
T Consensus 139 ~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~~v~~~l~R 176 (187)
T PRK12534 139 EPPRSELIRTAF-FEGITYEELAARTDTPIGTVKSWIRR 176 (187)
T ss_pred CHHHHHHHHHHH-HcCCCHHHHHHHhCCChhHHHHHHHH
Confidence 444444443321 35789999999999999888776654
No 295
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=20.52 E-value=2.1e+02 Score=26.20 Aligned_cols=50 Identities=24% Similarity=0.173 Sum_probs=36.8
Q ss_pred EEEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHhhhcccceeee
Q 014910 248 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 299 (416)
Q Consensus 248 l~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~ 299 (416)
+.-.|+|...-..=.....+|.+|+++++|++....++.|..|.. .++|.
T Consensus 155 i~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~--~~~l~ 204 (224)
T COG4565 155 LDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVS--NGILE 204 (224)
T ss_pred cCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHh--cCeee
Confidence 455566654333222346899999999999999999999999974 45664
No 296
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=20.50 E-value=1.7e+02 Score=24.34 Aligned_cols=38 Identities=11% Similarity=0.054 Sum_probs=26.6
Q ss_pred EcHHHHHHH-HhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 250 VSTYQAATL-LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 250 ~s~~Q~~iL-l~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
+++-|-.|+ +.+- +.+|.+||++.+|++...++..+..
T Consensus 107 L~~~~r~ii~l~~~--~~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 107 LDEKEKYIIFERFF--VGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344444444 3332 3689999999999999988877654
No 297
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=20.42 E-value=1.4e+02 Score=27.51 Aligned_cols=40 Identities=20% Similarity=0.193 Sum_probs=27.8
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
.++.-|-.|+++.- ...+|++||++.+|++...++..|.-
T Consensus 116 ~Lp~~~R~v~lL~~-~eg~S~~EIAe~LgiS~~tVksrL~R 155 (228)
T PRK06704 116 SLNVQQSAILLLKD-VFQYSIADIAKVCSVSEGAVKASLFR 155 (228)
T ss_pred hCCHHHhhHhhhHH-hhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34555555555432 23689999999999999888776543
No 298
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=20.42 E-value=1.7e+02 Score=25.43 Aligned_cols=37 Identities=14% Similarity=0.261 Sum_probs=26.6
Q ss_pred EcHHHHHHHHh-hhCCCCcCHHHHHHHcCCCHHHHHHHHH
Q 014910 250 VSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLH 288 (416)
Q Consensus 250 ~s~~Q~~iLl~-Fn~~~~~t~~ei~~~~~i~~~~l~~~L~ 288 (416)
+++-|-.|+.+ +- ..+|++||++.+|++...++..+.
T Consensus 123 L~~~~r~i~~l~~~--~g~s~~EIA~~lgis~~tVk~~l~ 160 (185)
T PRK12542 123 LNESNRQVFKYKVF--YNLTYQEISSVMGITEANVRKQFE 160 (185)
T ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44445555543 33 368999999999999988877654
No 299
>PRK10870 transcriptional repressor MprA; Provisional
Probab=20.30 E-value=80 Score=27.68 Aligned_cols=36 Identities=14% Similarity=0.290 Sum_probs=27.1
Q ss_pred CCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 363 KVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 363 k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
..++..+|-.. +..+...+-..|+.|.++|||+|..
T Consensus 70 ~~it~~eLa~~--------l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 70 HSIQPSELSCA--------LGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred CCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEecC
Confidence 45666655543 4467788999999999999999954
No 300
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=20.16 E-value=1.6e+02 Score=25.92 Aligned_cols=40 Identities=15% Similarity=0.236 Sum_probs=28.4
Q ss_pred EEcHHHHHHHHhhhCCCCcCHHHHHHHcCCCHHHHHHHHHh
Q 014910 249 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 289 (416)
Q Consensus 249 ~~s~~Q~~iLl~Fn~~~~~t~~ei~~~~~i~~~~l~~~L~~ 289 (416)
.++.-|-.|+.+.- .+.+|++||++.+|++...++..+..
T Consensus 142 ~L~~~~r~vl~l~~-~~~~s~~EIA~~Lgis~~tVk~~l~r 181 (194)
T PRK09646 142 ALTDTQRESVTLAY-YGGLTYREVAERLAVPLGTVKTRMRD 181 (194)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCChHhHHHHHHH
Confidence 34556666664421 24689999999999999888776543
No 301
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=20.13 E-value=1.4e+02 Score=22.73 Aligned_cols=31 Identities=29% Similarity=0.383 Sum_probs=26.5
Q ss_pred HHHHHHHcCCCHHHHHHHHHhhhcccceeeecC
Q 014910 269 YSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 301 (416)
Q Consensus 269 ~~ei~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 301 (416)
+.+|++.+|++...+.+.|..|. +.+++.+.
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~--~~glI~r~ 32 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLE--KDGLVEYE 32 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHH--HCCCEEEc
Confidence 46899999999999999999997 45787764
No 302
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=20.11 E-value=1.5e+02 Score=25.04 Aligned_cols=58 Identities=16% Similarity=0.159 Sum_probs=43.7
Q ss_pred eeeehhccC-CCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 014910 354 ALVRIMKSR-KVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 414 (416)
Q Consensus 354 ~IVRimK~~-k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 414 (416)
+|.++|... ..++..+|..++.+. ....+...|=+.++.|.+.|+|.+-+...+...|
T Consensus 25 ~vl~~L~~~~~~~sAeei~~~l~~~---~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y 83 (145)
T COG0735 25 AVLELLLEADGHLSAEELYEELREE---GPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRY 83 (145)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHh---CCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEE
Confidence 455666644 559999999998874 2446788899999999999999998765444444
No 303
>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=20.10 E-value=70 Score=24.89 Aligned_cols=38 Identities=8% Similarity=0.087 Sum_probs=30.1
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 014910 361 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 406 (416)
Q Consensus 361 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 406 (416)
....+++.+|-..+ ..+.+.+.+.|..|.++|+|+|..
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 45567777776643 357788999999999999999876
Done!