Query 012914
Match_columns 453
No_of_seqs 204 out of 957
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 07:37:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012914.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012914hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166 Cullins [Cell cycle co 100.0 3.8E-89 8.2E-94 720.4 37.8 435 1-451 291-725 (725)
2 KOG2167 Cullins [Cell cycle co 100.0 5.4E-90 1.2E-94 683.2 28.1 431 1-453 225-661 (661)
3 COG5647 Cullin, a subunit of E 100.0 2.9E-84 6.4E-89 656.4 35.1 444 1-453 315-773 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 4E-76 8.6E-81 561.6 21.0 408 1-453 313-728 (728)
5 KOG2285 E3 ubiquitin ligase, C 100.0 1.7E-68 3.6E-73 513.8 31.8 444 1-453 292-777 (777)
6 PF00888 Cullin: Cullin family 100.0 3.8E-61 8.2E-66 515.0 36.5 344 1-357 243-588 (588)
7 smart00182 CULLIN Cullin. 100.0 3.2E-35 7E-40 256.6 17.8 141 137-278 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 8.4E-30 1.8E-34 258.4 26.9 301 131-443 442-758 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 1.4E-21 3E-26 147.5 2.0 68 380-447 1-68 (68)
10 TIGR01610 phage_O_Nterm phage 94.5 0.12 2.7E-06 41.4 6.4 66 284-357 20-93 (95)
11 PF09339 HTH_IclR: IclR helix- 94.1 0.1 2.2E-06 36.8 4.4 45 292-338 6-51 (52)
12 PF02082 Rrf2: Transcriptional 93.7 0.24 5.1E-06 38.6 6.2 59 290-355 11-70 (83)
13 PF12802 MarR_2: MarR family; 92.9 0.16 3.5E-06 36.8 4.0 51 287-339 3-55 (62)
14 PF13412 HTH_24: Winged helix- 92.6 0.28 6E-06 33.7 4.7 42 288-329 2-43 (48)
15 PF08220 HTH_DeoR: DeoR-like h 91.2 0.34 7.4E-06 34.8 3.9 46 291-338 2-47 (57)
16 PF01047 MarR: MarR family; I 90.9 0.2 4.4E-06 36.0 2.5 50 287-338 1-50 (59)
17 PF13463 HTH_27: Winged helix 90.2 0.55 1.2E-05 34.6 4.5 50 287-338 1-51 (68)
18 TIGR02337 HpaR homoprotocatech 89.9 0.72 1.6E-05 38.4 5.4 52 286-339 25-76 (118)
19 PRK11512 DNA-binding transcrip 88.7 1 2.2E-05 39.0 5.6 53 285-339 36-88 (144)
20 PF12840 HTH_20: Helix-turn-he 88.6 0.71 1.5E-05 33.5 3.9 48 288-337 9-56 (61)
21 PF01022 HTH_5: Bacterial regu 88.6 1.3 2.7E-05 30.3 5.0 44 290-336 3-46 (47)
22 PF09012 FeoC: FeoC like trans 87.3 0.31 6.7E-06 36.5 1.3 44 393-444 6-49 (69)
23 PF08279 HTH_11: HTH domain; 86.7 1.4 3.1E-05 31.0 4.5 37 293-329 4-41 (55)
24 COG3682 Predicted transcriptio 86.5 0.68 1.5E-05 38.7 3.0 62 387-453 6-67 (123)
25 smart00550 Zalpha Z-DNA-bindin 85.5 1.3 2.9E-05 33.0 4.0 47 290-338 7-55 (68)
26 TIGR02698 CopY_TcrY copper tra 85.1 1.1 2.4E-05 38.1 3.8 60 389-453 6-65 (130)
27 PRK11920 rirA iron-responsive 84.9 3.1 6.8E-05 36.5 6.7 57 292-355 13-69 (153)
28 TIGR01889 Staph_reg_Sar staphy 84.9 2.7 5.8E-05 34.5 5.9 52 286-339 22-77 (109)
29 PF03965 Penicillinase_R: Peni 84.2 1.1 2.3E-05 37.3 3.2 59 390-453 6-64 (115)
30 PRK10857 DNA-binding transcrip 84.2 3.6 7.8E-05 36.5 6.8 45 291-337 12-57 (164)
31 smart00347 HTH_MARR helix_turn 84.1 2.3 5E-05 33.6 5.1 53 284-338 5-57 (101)
32 smart00346 HTH_ICLR helix_turn 83.8 2.7 5.8E-05 32.8 5.3 45 292-338 8-53 (91)
33 PRK15090 DNA-binding transcrip 83.3 2.9 6.4E-05 39.9 6.3 47 291-339 16-62 (257)
34 COG3355 Predicted transcriptio 81.9 4.1 8.8E-05 34.4 5.7 37 300-338 39-75 (126)
35 TIGR02010 IscR iron-sulfur clu 81.1 5 0.00011 34.3 6.3 44 292-337 13-57 (135)
36 PF01978 TrmB: Sugar-specific 81.1 1.5 3.3E-05 32.5 2.7 49 288-338 7-55 (68)
37 smart00420 HTH_DEOR helix_turn 80.9 3.7 8E-05 28.1 4.6 43 293-337 4-46 (53)
38 PRK13777 transcriptional regul 80.7 3.6 7.9E-05 37.3 5.5 53 285-339 41-93 (185)
39 PRK03573 transcriptional regul 79.8 4.1 9E-05 35.0 5.5 53 285-339 27-80 (144)
40 PF04703 FaeA: FaeA-like prote 79.4 4.6 0.0001 29.6 4.7 56 294-353 5-61 (62)
41 PF05732 RepL: Firmicute plasm 78.6 4.1 8.8E-05 36.3 5.1 51 303-362 75-125 (165)
42 COG1959 Predicted transcriptio 78.5 5.8 0.00013 34.7 6.0 59 290-355 11-70 (150)
43 PF13404 HTH_AsnC-type: AsnC-t 78.0 3.5 7.6E-05 27.6 3.4 35 293-327 7-41 (42)
44 PF08784 RPA_C: Replication pr 77.1 4.3 9.4E-05 32.7 4.5 44 286-329 44-91 (102)
45 PF04492 Phage_rep_O: Bacterio 76.3 10 0.00022 30.7 6.3 62 286-357 29-98 (100)
46 PRK10870 transcriptional repre 76.1 7.3 0.00016 35.0 6.1 52 286-339 52-105 (176)
47 PRK10163 DNA-binding transcrip 75.9 6.9 0.00015 37.7 6.3 47 291-339 27-74 (271)
48 PF08280 HTH_Mga: M protein tr 74.9 4.1 8.8E-05 29.4 3.3 38 291-328 7-44 (59)
49 PRK11569 transcriptional repre 74.7 7.1 0.00015 37.7 6.0 47 291-339 30-77 (274)
50 TIGR00738 rrf2_super rrf2 fami 74.6 9.1 0.0002 32.3 6.0 46 290-337 11-57 (132)
51 COG1414 IclR Transcriptional r 74.4 7.6 0.00016 36.9 6.0 46 292-339 7-53 (246)
52 PHA00738 putative HTH transcri 73.9 9.9 0.00022 31.0 5.6 67 284-356 7-73 (108)
53 smart00345 HTH_GNTR helix_turn 73.7 7.6 0.00017 27.2 4.6 39 298-338 14-53 (60)
54 TIGR02431 pcaR_pcaU beta-ketoa 73.7 8.6 0.00019 36.4 6.3 44 292-337 12-56 (248)
55 PF05584 Sulfolobus_pRN: Sulfo 73.5 8.9 0.00019 28.9 4.8 45 289-337 6-50 (72)
56 smart00419 HTH_CRP helix_turn_ 73.3 9 0.0002 25.6 4.7 33 303-337 8-40 (48)
57 TIGR01884 cas_HTH CRISPR locus 72.3 6.9 0.00015 35.9 5.1 51 286-338 140-190 (203)
58 PF11994 DUF3489: Protein of u 72.3 9.2 0.0002 28.8 4.7 47 288-334 9-55 (72)
59 PRK09834 DNA-binding transcrip 70.7 9.4 0.0002 36.6 5.8 46 292-339 14-60 (263)
60 PF13463 HTH_27: Winged helix 70.4 4.9 0.00011 29.4 3.0 53 390-450 6-61 (68)
61 TIGR02944 suf_reg_Xantho FeS a 69.9 13 0.00027 31.4 5.8 44 292-337 12-57 (130)
62 PF01978 TrmB: Sugar-specific 69.7 5.3 0.00011 29.5 3.0 47 398-452 19-65 (68)
63 PF09756 DDRGK: DDRGK domain; 68.3 2.7 5.9E-05 38.1 1.4 56 390-453 102-157 (188)
64 PF13601 HTH_34: Winged helix 68.1 5 0.00011 31.0 2.7 43 292-336 3-45 (80)
65 COG1846 MarR Transcriptional r 67.8 12 0.00026 30.5 5.2 51 287-339 20-70 (126)
66 PF08220 HTH_DeoR: DeoR-like h 67.7 3.7 8.1E-05 29.4 1.8 45 391-443 4-48 (57)
67 TIGR03879 near_KaiC_dom probab 67.5 8.3 0.00018 29.2 3.6 30 299-328 28-57 (73)
68 COG2345 Predicted transcriptio 67.4 7.9 0.00017 36.0 4.2 43 292-336 14-56 (218)
69 PF04545 Sigma70_r4: Sigma-70, 67.3 14 0.00031 25.3 4.7 33 292-326 11-43 (50)
70 smart00550 Zalpha Z-DNA-bindin 66.9 7.1 0.00015 29.1 3.2 53 389-449 8-62 (68)
71 cd00090 HTH_ARSR Arsenical Res 66.6 12 0.00027 27.2 4.6 47 288-337 6-52 (78)
72 PF13730 HTH_36: Helix-turn-he 65.6 16 0.00036 25.4 4.8 25 305-329 27-51 (55)
73 smart00418 HTH_ARSR helix_turn 63.8 10 0.00023 26.7 3.6 45 393-446 3-47 (66)
74 COG1318 Predicted transcriptio 63.6 9.1 0.0002 33.9 3.6 50 257-327 36-85 (182)
75 smart00344 HTH_ASNC helix_turn 63.5 13 0.00028 30.0 4.5 45 290-336 4-48 (108)
76 PRK11014 transcriptional repre 63.4 25 0.00053 30.2 6.4 40 298-339 20-59 (141)
77 PF10771 DUF2582: Protein of u 63.3 13 0.00028 27.5 3.9 38 292-329 11-48 (65)
78 PF02796 HTH_7: Helix-turn-hel 63.2 10 0.00022 25.6 3.2 30 294-325 14-43 (45)
79 PRK10141 DNA-binding transcrip 63.1 16 0.00035 30.4 5.0 60 290-355 17-76 (117)
80 PF01325 Fe_dep_repress: Iron 62.6 17 0.00037 26.3 4.5 44 294-339 13-56 (60)
81 PRK10434 srlR DNA-bindng trans 61.2 11 0.00023 36.1 4.1 47 290-338 6-52 (256)
82 cd00092 HTH_CRP helix_turn_hel 61.1 24 0.00052 25.4 5.2 35 302-338 24-58 (67)
83 PF08281 Sigma70_r4_2: Sigma-7 60.3 18 0.00038 25.1 4.1 23 303-325 26-48 (54)
84 PF02002 TFIIE_alpha: TFIIE al 59.7 7.9 0.00017 31.4 2.5 44 291-336 15-58 (105)
85 PF09012 FeoC: FeoC like trans 59.6 11 0.00025 27.9 3.2 33 297-329 8-40 (69)
86 COG1349 GlpR Transcriptional r 59.2 13 0.00028 35.5 4.2 47 290-338 6-52 (253)
87 COG4190 Predicted transcriptio 58.1 30 0.00065 29.3 5.6 64 292-357 67-133 (144)
88 smart00421 HTH_LUXR helix_turn 58.0 23 0.00051 24.2 4.5 39 288-328 5-43 (58)
89 PF12324 HTH_15: Helix-turn-he 57.5 28 0.00061 26.6 4.9 39 290-328 25-63 (77)
90 smart00418 HTH_ARSR helix_turn 56.5 20 0.00044 25.1 4.1 35 301-337 8-42 (66)
91 cd06170 LuxR_C_like C-terminal 56.5 26 0.00056 24.0 4.5 38 289-328 3-40 (57)
92 cd07153 Fur_like Ferric uptake 56.3 16 0.00035 29.9 3.9 57 392-451 6-63 (116)
93 PF14394 DUF4423: Domain of un 56.0 33 0.00073 30.6 6.1 55 283-339 18-75 (171)
94 PF06784 UPF0240: Uncharacteri 55.7 21 0.00046 32.1 4.8 64 260-328 96-161 (179)
95 PF01726 LexA_DNA_bind: LexA D 54.2 23 0.0005 26.1 4.0 24 422-445 39-62 (65)
96 PF07106 TBPIP: Tat binding pr 54.1 1.1E+02 0.0025 27.0 9.3 59 291-355 3-64 (169)
97 TIGR02844 spore_III_D sporulat 54.1 22 0.00049 27.4 4.0 35 290-325 7-41 (80)
98 PF01853 MOZ_SAS: MOZ/SAS fami 53.5 13 0.00029 33.6 3.1 25 303-327 150-174 (188)
99 PRK13509 transcriptional repre 53.4 22 0.00047 33.9 4.8 47 290-338 6-52 (251)
100 TIGR02702 SufR_cyano iron-sulf 53.2 35 0.00076 31.2 6.0 44 293-338 5-48 (203)
101 TIGR00373 conserved hypothetic 53.0 27 0.00058 30.8 4.9 43 292-336 17-59 (158)
102 PRK06266 transcription initiat 53.0 19 0.00042 32.4 4.0 44 291-336 24-67 (178)
103 COG4189 Predicted transcriptio 52.6 23 0.00051 33.0 4.5 49 288-338 22-70 (308)
104 PF08221 HTH_9: RNA polymerase 51.7 20 0.00044 26.1 3.3 35 300-336 24-58 (62)
105 PF02186 TFIIE_beta: TFIIE bet 50.9 9.2 0.0002 28.3 1.4 54 389-453 7-61 (65)
106 PF01726 LexA_DNA_bind: LexA D 50.3 23 0.0005 26.1 3.4 51 287-339 4-60 (65)
107 PRK00215 LexA repressor; Valid 50.3 39 0.00083 30.9 5.8 51 287-339 2-58 (205)
108 PF05158 RNA_pol_Rpc34: RNA po 50.2 21 0.00045 35.5 4.2 143 286-445 81-260 (327)
109 cd07377 WHTH_GntR Winged helix 49.9 40 0.00086 23.9 4.8 38 299-338 20-58 (66)
110 PRK10681 DNA-binding transcrip 49.1 25 0.00055 33.4 4.5 39 290-328 8-46 (252)
111 PF00196 GerE: Bacterial regul 49.0 30 0.00066 24.5 3.9 39 288-328 5-43 (58)
112 PRK10906 DNA-binding transcrip 48.2 26 0.00056 33.4 4.4 47 290-338 6-52 (252)
113 PF13412 HTH_24: Winged helix- 48.0 14 0.0003 25.1 1.8 44 389-440 5-48 (48)
114 PF04967 HTH_10: HTH DNA bindi 47.9 29 0.00062 24.5 3.4 30 298-327 18-47 (53)
115 PRK09802 DNA-binding transcrip 47.1 26 0.00057 33.7 4.3 48 289-338 17-64 (269)
116 TIGR02404 trehalos_R_Bsub treh 46.4 14 0.0003 34.6 2.2 33 417-450 32-64 (233)
117 PF00165 HTH_AraC: Bacterial r 46.3 32 0.0007 22.5 3.4 28 301-328 6-33 (42)
118 PRK11179 DNA-binding transcrip 45.8 35 0.00076 29.7 4.5 48 287-336 7-54 (153)
119 KOG3054 Uncharacterized conser 45.3 21 0.00046 33.4 3.1 54 392-453 205-258 (299)
120 PF13384 HTH_23: Homeodomain-l 45.0 25 0.00054 23.9 2.8 32 294-327 10-41 (50)
121 PRK11169 leucine-responsive tr 44.7 34 0.00073 30.2 4.3 48 287-336 12-59 (164)
122 PF00325 Crp: Bacterial regula 44.7 31 0.00067 21.6 2.8 26 303-328 2-27 (32)
123 smart00344 HTH_ASNC helix_turn 44.5 16 0.00035 29.5 2.1 46 388-441 4-49 (108)
124 PRK04424 fatty acid biosynthes 44.0 31 0.00067 31.2 4.0 40 290-329 8-47 (185)
125 TIGR00498 lexA SOS regulatory 43.6 28 0.0006 31.7 3.7 50 287-338 4-59 (199)
126 PF09860 DUF2087: Uncharacteri 43.5 33 0.00072 25.8 3.4 25 421-449 44-68 (71)
127 COG1654 BirA Biotin operon rep 43.4 79 0.0017 24.4 5.5 41 296-336 12-52 (79)
128 PRK11402 DNA-binding transcrip 43.4 16 0.00035 34.3 2.2 32 418-450 42-73 (241)
129 PLN03238 probable histone acet 43.3 40 0.00088 32.6 4.7 38 290-327 209-247 (290)
130 cd06171 Sigma70_r4 Sigma70, re 43.0 63 0.0014 21.3 4.7 39 288-327 12-50 (55)
131 KOG2747 Histone acetyltransfer 42.9 32 0.00069 34.8 4.1 64 263-328 282-354 (396)
132 PRK04172 pheS phenylalanyl-tRN 42.8 38 0.00083 35.7 5.0 50 286-337 3-52 (489)
133 PF00392 GntR: Bacterial regul 42.8 15 0.00032 26.7 1.4 32 417-449 32-63 (64)
134 PRK13239 alkylmercury lyase; P 42.5 48 0.001 30.6 4.9 39 290-328 23-61 (206)
135 PF12802 MarR_2: MarR family; 42.4 13 0.00028 26.5 1.0 26 419-444 31-56 (62)
136 PHA02591 hypothetical protein; 41.8 33 0.0007 26.2 3.0 24 303-326 59-82 (83)
137 PRK10079 phosphonate metabolis 41.7 18 0.00039 34.0 2.2 33 417-450 43-75 (241)
138 TIGR02325 C_P_lyase_phnF phosp 41.2 18 0.00039 33.8 2.1 32 418-450 41-72 (238)
139 TIGR03433 padR_acidobact trans 40.7 46 0.001 26.7 4.1 53 388-441 5-57 (100)
140 smart00531 TFIIE Transcription 40.6 34 0.00075 29.6 3.6 31 300-330 12-42 (147)
141 PRK09334 30S ribosomal protein 40.1 23 0.00049 27.8 2.1 37 417-453 49-85 (86)
142 PRK10411 DNA-binding transcrip 39.9 43 0.00092 31.7 4.4 40 290-329 5-44 (240)
143 PF01047 MarR: MarR family; I 39.8 11 0.00024 26.7 0.3 41 395-443 11-51 (59)
144 PF09904 HTH_43: Winged helix- 39.5 54 0.0012 25.9 4.1 33 297-330 16-48 (90)
145 smart00345 HTH_GNTR helix_turn 39.4 22 0.00048 24.7 1.9 28 417-444 28-55 (60)
146 PF13542 HTH_Tnp_ISL3: Helix-t 38.7 78 0.0017 21.5 4.6 35 290-326 16-50 (52)
147 PF09107 SelB-wing_3: Elongati 37.9 70 0.0015 22.2 4.1 41 296-338 3-43 (50)
148 TIGR00122 birA_repr_reg BirA b 36.7 1.4E+02 0.0031 21.7 6.0 32 297-329 8-39 (69)
149 PRK14999 histidine utilization 36.6 23 0.00049 33.4 2.0 47 395-450 29-76 (241)
150 PF09681 Phage_rep_org_N: N-te 36.1 62 0.0013 27.1 4.3 37 299-337 49-85 (121)
151 PF04760 IF2_N: Translation in 35.4 26 0.00056 24.5 1.7 22 303-324 3-24 (54)
152 PRK06474 hypothetical protein; 35.2 1.2E+02 0.0025 27.3 6.3 52 285-338 7-60 (178)
153 COG2188 PhnF Transcriptional r 35.0 25 0.00054 33.1 2.0 35 415-450 37-71 (236)
154 COG1522 Lrp Transcriptional re 34.8 78 0.0017 27.1 5.0 47 288-336 7-53 (154)
155 TIGR00721 tfx DNA-binding prot 34.6 76 0.0016 27.3 4.7 40 286-327 6-45 (137)
156 PLN03239 histone acetyltransfe 34.5 60 0.0013 32.4 4.5 38 290-327 267-308 (351)
157 PF06163 DUF977: Bacterial pro 34.2 80 0.0017 26.6 4.5 41 289-329 12-52 (127)
158 PF00356 LacI: Bacterial regul 33.8 51 0.0011 22.4 2.9 21 305-325 1-21 (46)
159 PF00392 GntR: Bacterial regul 33.7 61 0.0013 23.4 3.5 39 299-339 19-58 (64)
160 cd07977 TFIIE_beta_winged_heli 33.3 31 0.00067 26.3 1.9 57 387-453 9-70 (75)
161 PF02270 TFIIF_beta: Transcrip 33.0 62 0.0013 31.3 4.4 57 290-356 217-273 (275)
162 PF03444 HrcA_DNA-bdg: Winged 32.7 1.6E+02 0.0034 22.7 5.6 48 290-339 10-57 (78)
163 TIGR02989 Sig-70_gvs1 RNA poly 32.5 79 0.0017 27.1 4.7 38 287-326 112-150 (159)
164 PF04182 B-block_TFIIIC: B-blo 32.1 79 0.0017 23.8 4.0 48 289-338 2-51 (75)
165 PF04539 Sigma70_r3: Sigma-70 32.0 48 0.001 24.8 2.8 26 302-327 19-44 (78)
166 PRK09764 DNA-binding transcrip 32.0 32 0.00069 32.3 2.2 32 418-450 38-69 (240)
167 TIGR02018 his_ut_repres histid 31.9 30 0.00066 32.2 2.0 32 418-450 34-65 (230)
168 PRK00135 scpB segregation and 31.6 2E+02 0.0043 26.2 7.1 111 240-357 34-153 (188)
169 PF01399 PCI: PCI domain; Int 31.3 89 0.0019 24.4 4.5 40 290-329 47-86 (105)
170 KOG2905 Transcription initiati 31.1 68 0.0015 30.1 4.0 58 290-357 187-244 (254)
171 PF01638 HxlR: HxlR-like helix 31.1 97 0.0021 24.1 4.5 45 291-338 7-52 (90)
172 TIGR01889 Staph_reg_Sar staphy 31.0 39 0.00084 27.5 2.3 41 398-446 40-82 (109)
173 COG1522 Lrp Transcriptional re 31.0 31 0.00068 29.7 1.8 50 386-443 7-56 (154)
174 smart00347 HTH_MARR helix_turn 30.8 59 0.0013 25.2 3.3 47 389-443 12-58 (101)
175 COG2771 CsgD DNA-binding HTH d 30.8 1.4E+02 0.0029 21.0 5.0 41 286-328 4-44 (65)
176 smart00346 HTH_ICLR helix_turn 30.6 76 0.0016 24.4 3.9 44 393-444 11-55 (91)
177 PF08318 COG4: COG4 transport 30.6 5.4E+02 0.012 25.4 15.7 147 1-161 34-214 (331)
178 PHA02943 hypothetical protein; 30.1 96 0.0021 27.1 4.5 54 294-354 16-69 (165)
179 PF08820 DUF1803: Domain of un 30.0 34 0.00073 27.3 1.6 27 415-442 34-60 (93)
180 cd07377 WHTH_GntR Winged helix 29.9 40 0.00086 23.9 2.0 27 417-443 33-59 (66)
181 PRK09647 RNA polymerase sigma 29.9 78 0.0017 28.9 4.3 35 290-326 143-177 (203)
182 PRK03975 tfx putative transcri 29.8 1E+02 0.0022 26.7 4.7 39 286-326 6-44 (141)
183 TIGR01714 phage_rep_org_N phag 29.8 86 0.0019 26.2 4.1 47 289-337 29-83 (119)
184 PLN00104 MYST -like histone ac 29.7 81 0.0018 32.7 4.7 38 290-327 360-398 (450)
185 PF12395 DUF3658: Protein of u 29.5 67 0.0015 26.4 3.4 48 402-451 62-109 (111)
186 PF14947 HTH_45: Winged helix- 29.4 1.3E+02 0.0028 22.7 4.8 42 292-336 9-50 (77)
187 PRK13719 conjugal transfer tra 29.3 1E+02 0.0022 28.6 4.9 41 286-328 143-183 (217)
188 PF02847 MA3: MA3 domain; Int 28.9 82 0.0018 25.4 3.9 51 64-114 56-110 (113)
189 COG5090 TFG2 Transcription ini 28.8 80 0.0017 29.5 4.0 55 293-357 199-253 (297)
190 TIGR02983 SigE-fam_strep RNA p 28.5 83 0.0018 27.1 4.1 39 288-327 112-150 (162)
191 COG3413 Predicted DNA binding 28.5 96 0.0021 28.6 4.7 42 286-327 155-202 (215)
192 PRK10430 DNA-binding transcrip 28.4 1E+02 0.0022 28.6 5.0 47 287-335 159-208 (239)
193 PF13936 HTH_38: Helix-turn-he 28.4 1E+02 0.0023 20.5 3.7 24 302-325 19-42 (44)
194 PF13545 HTH_Crp_2: Crp-like h 28.0 1.2E+02 0.0027 22.2 4.5 33 303-337 28-60 (76)
195 smart00753 PAM PCI/PINT associ 28.0 85 0.0018 24.1 3.7 31 299-329 20-50 (88)
196 smart00088 PINT motif in prote 28.0 85 0.0018 24.1 3.7 31 299-329 20-50 (88)
197 PRK03573 transcriptional regul 27.9 44 0.00095 28.5 2.2 26 418-443 55-80 (144)
198 PRK12525 RNA polymerase sigma 27.9 95 0.0021 27.1 4.4 34 290-325 123-156 (168)
199 COG1349 GlpR Transcriptional r 27.8 30 0.00066 33.0 1.2 45 390-442 8-52 (253)
200 COG2197 CitB Response regulato 27.7 1.1E+02 0.0023 28.3 4.8 42 286-329 148-189 (211)
201 PRK09642 RNA polymerase sigma 27.6 99 0.0022 26.6 4.5 23 303-325 122-144 (160)
202 PF13551 HTH_29: Winged helix- 27.6 1.1E+02 0.0024 24.3 4.5 35 293-328 3-37 (112)
203 PRK08301 sporulation sigma fac 27.5 1.1E+02 0.0023 28.5 5.0 37 289-325 181-220 (234)
204 PRK04214 rbn ribonuclease BN/u 27.3 1.7E+02 0.0038 30.0 6.8 38 298-337 305-342 (412)
205 PF01418 HTH_6: Helix-turn-hel 27.3 61 0.0013 24.5 2.6 33 295-327 26-58 (77)
206 PF10007 DUF2250: Uncharacteri 27.1 1.3E+02 0.0029 23.9 4.5 52 285-338 3-54 (92)
207 PRK12522 RNA polymerase sigma 27.0 97 0.0021 27.1 4.3 32 292-325 126-157 (173)
208 PRK00135 scpB segregation and 26.7 90 0.002 28.4 4.0 34 295-328 11-45 (188)
209 PRK12529 RNA polymerase sigma 26.6 82 0.0018 27.9 3.8 37 287-325 128-165 (178)
210 PRK12514 RNA polymerase sigma 26.6 83 0.0018 27.7 3.8 36 288-325 131-167 (179)
211 PF14394 DUF4423: Domain of un 26.5 59 0.0013 29.0 2.8 60 380-450 21-80 (171)
212 COG1321 TroR Mn-dependent tran 26.5 1.2E+02 0.0027 26.5 4.8 44 293-338 14-57 (154)
213 PRK15411 rcsA colanic acid cap 26.5 1.1E+02 0.0024 28.0 4.7 41 286-328 137-177 (207)
214 PF07638 Sigma70_ECF: ECF sigm 26.4 73 0.0016 28.6 3.5 26 302-327 150-175 (185)
215 smart00544 MA3 Domain in DAP-5 26.4 1.8E+02 0.0038 23.5 5.5 51 64-114 56-110 (113)
216 PRK10434 srlR DNA-bindng trans 26.2 35 0.00076 32.6 1.4 46 389-442 7-52 (256)
217 PRK00118 putative DNA-binding 26.2 1.1E+02 0.0024 24.9 4.0 25 303-327 33-57 (104)
218 PF08672 APC2: Anaphase promot 26.1 65 0.0014 23.4 2.4 52 392-443 2-55 (60)
219 PRK03902 manganese transport t 26.1 1.1E+02 0.0024 26.1 4.4 43 293-337 12-54 (142)
220 PF08784 RPA_C: Replication pr 26.1 44 0.00096 26.7 1.8 43 389-439 49-95 (102)
221 PRK09462 fur ferric uptake reg 25.8 1E+02 0.0022 26.6 4.1 58 391-451 21-80 (148)
222 PRK11050 manganese transport r 25.7 1.3E+02 0.0029 26.1 4.8 43 293-337 41-83 (152)
223 PRK10840 transcriptional regul 25.6 1.3E+02 0.0027 27.3 5.0 41 286-328 150-190 (216)
224 COG1510 Predicted transcriptio 25.5 93 0.002 27.8 3.7 36 300-337 38-73 (177)
225 TIGR02835 spore_sigmaE RNA pol 25.4 1.2E+02 0.0027 28.2 4.9 35 291-325 184-220 (234)
226 PF04079 DUF387: Putative tran 25.4 82 0.0018 27.8 3.4 32 296-328 6-37 (159)
227 PF13314 DUF4083: Domain of un 25.3 1.7E+02 0.0036 21.1 4.2 32 104-135 24-55 (58)
228 PRK09639 RNA polymerase sigma 25.2 1.2E+02 0.0027 26.1 4.7 32 291-325 118-149 (166)
229 COG4742 Predicted transcriptio 25.1 1.2E+02 0.0026 29.0 4.7 42 294-338 18-59 (260)
230 TIGR01764 excise DNA binding d 25.0 94 0.002 20.3 3.1 21 304-324 2-22 (49)
231 PF12728 HTH_17: Helix-turn-he 24.9 92 0.002 21.1 3.0 21 304-324 2-22 (51)
232 PRK09047 RNA polymerase factor 24.6 1.2E+02 0.0026 25.9 4.4 24 302-325 121-144 (161)
233 PRK04217 hypothetical protein; 24.5 81 0.0018 26.0 3.0 40 287-327 43-82 (110)
234 PRK12547 RNA polymerase sigma 24.5 1.2E+02 0.0026 26.3 4.5 39 288-327 114-152 (164)
235 PRK08295 RNA polymerase factor 24.3 98 0.0021 27.9 4.0 38 288-327 157-194 (208)
236 TIGR02392 rpoH_proteo alternat 24.3 1.3E+02 0.0028 28.9 4.9 36 289-324 221-257 (270)
237 PF10668 Phage_terminase: Phag 24.3 1.1E+02 0.0023 22.3 3.2 23 300-322 19-41 (60)
238 PRK15201 fimbriae regulatory p 24.2 1.6E+02 0.0035 26.6 4.9 40 287-328 134-173 (198)
239 PF14493 HTH_40: Helix-turn-he 24.2 1.2E+02 0.0027 23.6 4.0 33 294-328 6-38 (91)
240 PF06163 DUF977: Bacterial pro 24.1 76 0.0016 26.8 2.7 51 386-444 11-61 (127)
241 PRK15431 ferrous iron transpor 24.0 66 0.0014 24.7 2.2 31 414-444 21-51 (78)
242 TIGR02999 Sig-70_X6 RNA polyme 23.9 1.2E+02 0.0026 26.7 4.4 23 303-325 150-172 (183)
243 TIGR02698 CopY_TcrY copper tra 23.8 2.3E+02 0.0049 23.9 5.8 49 287-337 2-54 (130)
244 PRK11475 DNA-binding transcrip 23.3 1.5E+02 0.0033 27.2 5.0 41 286-328 134-174 (207)
245 PRK11169 leucine-responsive tr 23.3 77 0.0017 27.9 2.9 47 387-441 14-60 (164)
246 PRK12537 RNA polymerase sigma 23.2 1.2E+02 0.0026 26.8 4.3 32 293-326 141-172 (182)
247 PRK10906 DNA-binding transcrip 22.9 46 0.001 31.7 1.5 46 389-442 7-52 (252)
248 PF01475 FUR: Ferric uptake re 22.9 96 0.0021 25.5 3.3 57 392-451 13-70 (120)
249 PF10007 DUF2250: Uncharacteri 22.8 57 0.0012 26.0 1.7 27 418-444 30-56 (92)
250 PRK12536 RNA polymerase sigma 22.8 1.3E+02 0.0028 26.6 4.3 39 288-327 131-169 (181)
251 TIGR02337 HpaR homoprotocatech 22.7 86 0.0019 25.7 2.9 44 392-443 33-76 (118)
252 PRK09416 lstR lineage-specific 22.6 1.2E+02 0.0027 25.9 3.8 58 383-442 39-96 (135)
253 PRK14165 winged helix-turn-hel 22.6 1.6E+02 0.0035 27.4 5.0 44 293-338 11-54 (217)
254 PRK02363 DNA-directed RNA poly 22.5 1.2E+02 0.0025 25.8 3.7 35 395-433 12-47 (129)
255 PRK12530 RNA polymerase sigma 22.4 1.3E+02 0.0028 26.9 4.3 23 303-325 150-172 (189)
256 PRK06759 RNA polymerase factor 22.1 1.5E+02 0.0032 25.2 4.5 24 303-326 122-145 (154)
257 PRK11512 DNA-binding transcrip 22.0 66 0.0014 27.5 2.2 38 398-443 51-88 (144)
258 PF10078 DUF2316: Uncharacteri 21.8 1E+02 0.0022 24.3 3.0 24 302-325 22-45 (89)
259 PRK13919 putative RNA polymera 21.8 1.3E+02 0.0029 26.5 4.2 38 287-325 136-173 (186)
260 TIGR03209 P21_Cbot clostridium 21.7 89 0.0019 26.3 2.9 29 291-321 113-141 (142)
261 PRK12527 RNA polymerase sigma 21.7 1.3E+02 0.0028 25.8 4.1 38 287-325 106-143 (159)
262 TIGR02985 Sig70_bacteroi1 RNA 21.6 1.6E+02 0.0035 24.8 4.7 38 288-327 115-153 (161)
263 PRK11179 DNA-binding transcrip 21.5 76 0.0016 27.5 2.5 46 388-441 10-55 (153)
264 cd04762 HTH_MerR-trunc Helix-T 21.3 1.2E+02 0.0026 19.6 3.1 21 304-324 1-21 (49)
265 PF13518 HTH_28: Helix-turn-he 21.1 2.2E+02 0.0049 18.9 4.4 24 305-328 14-37 (52)
266 COG4367 Uncharacterized protei 21.0 1.2E+02 0.0026 23.8 3.0 23 303-325 23-45 (97)
267 COG1846 MarR Transcriptional r 20.9 64 0.0014 25.9 1.8 27 418-444 45-71 (126)
268 PRK09645 RNA polymerase sigma 20.9 1.6E+02 0.0035 25.6 4.5 23 303-325 134-156 (173)
269 PF06971 Put_DNA-bind_N: Putat 20.7 2.1E+02 0.0046 19.9 4.1 25 300-324 25-49 (50)
270 PRK06704 RNA polymerase factor 20.6 1.3E+02 0.0029 28.1 4.1 39 287-326 117-155 (228)
271 PRK14165 winged helix-turn-hel 20.5 77 0.0017 29.5 2.4 49 396-452 16-64 (217)
272 PRK09483 response regulator; P 20.5 1.9E+02 0.0041 25.7 5.1 41 286-328 148-188 (217)
273 PRK10100 DNA-binding transcrip 20.3 1.7E+02 0.0037 27.0 4.7 40 287-328 156-195 (216)
274 PRK09651 RNA polymerase sigma 20.3 1.2E+02 0.0026 26.5 3.6 24 302-325 134-157 (172)
275 TIGR02394 rpoS_proteo RNA poly 20.3 1.6E+02 0.0034 28.5 4.7 35 291-325 228-264 (285)
276 PRK10046 dpiA two-component re 20.3 1.4E+02 0.003 27.4 4.2 42 293-336 166-208 (225)
277 cd07153 Fur_like Ferric uptake 20.3 2.4E+02 0.0052 22.7 5.2 44 293-338 5-54 (116)
278 COG2865 Predicted transcriptio 20.2 73 0.0016 33.3 2.4 56 389-452 404-459 (467)
279 TIGR02716 C20_methyl_CrtF C-20 20.2 1.5E+02 0.0032 28.9 4.5 35 302-338 22-56 (306)
280 PRK12520 RNA polymerase sigma 20.1 1.7E+02 0.0036 26.1 4.5 24 303-326 147-170 (191)
281 smart00342 HTH_ARAC helix_turn 20.1 1.3E+02 0.0029 21.9 3.4 26 303-328 1-26 (84)
282 PRK12533 RNA polymerase sigma 20.1 1.4E+02 0.003 27.7 4.0 26 302-327 149-174 (216)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.8e-89 Score=720.44 Aligned_cols=435 Identities=70% Similarity=1.104 Sum_probs=409.7
Q ss_pred CccccccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHH
Q 012914 1 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHK 80 (453)
Q Consensus 1 ly~L~~r~~~~l~~l~~~~~~~i~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~ 80 (453)
||+|++|++.||+.+++.++.|++.+|.+++.+..... ..+|..+++.+++++++|..++..||+++..|..
T Consensus 291 my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~--------~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~ 362 (725)
T KOG2166|consen 291 MYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETA--------ATNPVEYVQGLLELHDKYKVLVKECFANDTLFKK 362 (725)
T ss_pred HHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhc--------ccchHHHHhccHHHHHHHHHHHHHHhhccHHHHH
Confidence 79999999999999999999999999999998876542 1578999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCChHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHhhccChhHHHHHHHHHHHHHHcCCC
Q 012914 81 ALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDR 160 (453)
Q Consensus 81 ~l~~af~~~~N~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~ 160 (453)
+++.||..|+|.+.. ..+|+||+|||.+||++ ..+.++++++..|++++.+|+|+.+||+|+.+|+++||+|||+++
T Consensus 363 ~ld~a~~~fin~n~~--~~~E~la~y~D~~lkk~-~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~ 439 (725)
T KOG2166|consen 363 ALDAAFEEFINKNVA--TSAELLATYCDDILKKG-SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDR 439 (725)
T ss_pred HHHHHHHHHHcccCC--CcHHHHHHHhHHHhccc-ccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcC
Confidence 999999999999863 23699999999999994 467789999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHHHHHHHhhCChhhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCCcCC
Q 012914 161 SANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLP 240 (453)
Q Consensus 161 s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLs~~~WP~~~~~~~~lP 240 (453)
|.|++.|+.||++|+++||.+||.+|++|++|+..|+++...|.++ .+.....+++|.|.|||+|+||.+++.++.||
T Consensus 440 S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~--~~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP 517 (725)
T KOG2166|consen 440 SASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADY--ANYSANLGIDFTVTVLTTGFWPSYKSTDINLP 517 (725)
T ss_pred ccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhh--hchhccCCCceeEEEeecCCcCCccCCCCCCC
Confidence 9999999999999999999999999999999999999999999987 12223457999999999999999888889999
Q ss_pred HHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHH
Q 012914 241 SEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDL 320 (453)
Q Consensus 241 ~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l 320 (453)
++|..+++.|..||.++|+||+|.|+|++|+|+|.++|.+++++++||++||+||++||+.+.+|+++|.+.|+++.+++
T Consensus 518 ~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l 597 (725)
T KOG2166|consen 518 SEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDL 597 (725)
T ss_pred hhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCcceeeccCCCchhhhhhHHhHHHhhhhhhcceeeehhccCC
Q 012914 321 VRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPVDERKKIVEDVDKDRRYAIDAALVRIMKSRK 400 (453)
Q Consensus 321 ~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~~~~~~i~i~~~~~~e~~~~~~~v~~~R~~~i~A~IVRimK~~k 400 (453)
.++|+||++.|.+++.. |.+.. .+++.|.+|.+|+++.+|++++.++..|.+++.+.+++||+.+|+||||||||+||
T Consensus 598 ~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK 675 (725)
T KOG2166|consen 598 ARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRK 675 (725)
T ss_pred HHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhc
Confidence 99999998888666666 66666 78999999999999999999998888888889999999999999999999999999
Q ss_pred CCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEe
Q 012914 401 VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 451 (453)
Q Consensus 401 ~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Y 451 (453)
.+.|++|+.||++|+++||.|++.+||+|||.|||||||+|| +|+++|+|
T Consensus 676 ~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 676 VLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred cccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 999999999999999999999999999999999999999999 89999998
No 2
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=5.4e-90 Score=683.20 Aligned_cols=431 Identities=39% Similarity=0.685 Sum_probs=407.5
Q ss_pred CccccccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCC--HHH
Q 012914 1 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINH--TLF 78 (453)
Q Consensus 1 ly~L~~r~~~~l~~l~~~~~~~i~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~--~~f 78 (453)
||.|++++.+|...++..|+.|+++-|..++.+.+ .+..+|+++++++++.+-++..||..+ ..|
T Consensus 225 ly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~-------------kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f 291 (661)
T KOG2167|consen 225 LYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEE-------------KDKDMVQELLDFKKKVDIIVDESFLKYVAEKF 291 (661)
T ss_pred HHHHHHHHhcchHHHHHHHHHHHhcccceeccCch-------------hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHH
Confidence 68999999999999999999999999999997653 367899999999999999999999988 999
Q ss_pred HHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHhhccChhHHHHHHHHHHHHHHcC
Q 012914 79 HKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLF 158 (453)
Q Consensus 79 ~~~l~~af~~~~N~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~ 158 (453)
..++++||+.|+|... +++||+||+|.|..|+.|. +..++++++..++.++.||||+..||+|+.+|++.||+|||.
T Consensus 292 ~~~~~~afe~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl 368 (661)
T KOG2167|consen 292 LNSMSKAFETFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLL 368 (661)
T ss_pred HHHHHHHHHHHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHh
Confidence 9999999999999765 5799999999999999865 456788899999999999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCCc
Q 012914 159 DRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLN 238 (453)
Q Consensus 159 ~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLs~~~WP~~~~~~~~ 238 (453)
++|+|.|+|..|+.+||.+||..||++|++|++|+..|++++..|+++...+.....++ +.+.|+|.++||.+++.++.
T Consensus 369 ~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~ 447 (661)
T KOG2167|consen 369 GKSASVDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVL 447 (661)
T ss_pred ccchhhcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhcc
Confidence 99999999999999999999999999999999999999999999999865544334445 99999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChH
Q 012914 239 LPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHD 318 (453)
Q Consensus 239 lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~ 318 (453)
||++|..+++-|..||..+|.||+|.|.+++|+|.+++.|..|++++.+|++|++||++||+++++|++||.++|++.+.
T Consensus 448 Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~ 527 (661)
T KOG2167|consen 448 LPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDI 527 (661)
T ss_pred CCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCcceeeccCCCc----hhhhhhHHhHHHhhhhhhcceeee
Q 012914 319 DLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV----DERKKIVEDVDKDRRYAIDAALVR 394 (453)
Q Consensus 319 ~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~v~~~R~~~i~A~IVR 394 (453)
+|.++|+||.|+|.++|.+.|.|+.+.+++.|.+|..|+.+..||+|+.+.. +|..++.++|.+||.+.|||||||
T Consensus 528 el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivr 607 (661)
T KOG2167|consen 528 ELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVR 607 (661)
T ss_pred HHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999998754 566778899999999999999999
Q ss_pred hhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 395 IMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 395 imK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
|||+||+|+|+.|+.++.++++ ||..+ ++|+|||+||+|||++||+ | +.|+|||
T Consensus 608 imk~rk~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd~-n-~~y~yva 661 (661)
T KOG2167|consen 608 IMKMRKTLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERDD-N-NIYNYVA 661 (661)
T ss_pred HHHHHHhhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhcccc-c-ccccccC
Confidence 9999999999999999999997 99888 9999999999999999994 4 8999998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.9e-84 Score=656.36 Aligned_cols=444 Identities=35% Similarity=0.613 Sum_probs=392.4
Q ss_pred CccccccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCC------CCcchHHHHHHHHHHHHHHHHHHHHhcCC
Q 012914 1 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSS------GAVQEQVLIRKIIELHDKYMEYVTNCFIN 74 (453)
Q Consensus 1 ly~L~~r~~~~l~~l~~~~~~~i~~~G~~~~~~~~~~~~~~~~~~------~~~~~~~~i~~l~~l~~~~~~l~~~~F~~ 74 (453)
||+|+||++.|+.+|++.|..||...|.-+ ........ ..+.+ ....|..+++.++++++.+..++.+.|.+
T Consensus 315 lY~l~se~~~~v~pl~~~f~~yV~~~g~~~-~i~~~~~~-~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~ 392 (773)
T COG5647 315 LYRLLSETKYGVQPLQEVFERYVKDEGVLI-NIETNYIF-HCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEG 392 (773)
T ss_pred HHHHhhhhhhhhhhHHHHHHHHHHhhchhh-hhHHhhhh-ccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCC
Confidence 699999999999999999999999999222 22221111 11110 13678899999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHhcCC-CCCChHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHhhccChhHHHHHHHHHHH
Q 012914 75 HTLFHKALKEAFEIFCNKAV-GGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLA 153 (453)
Q Consensus 75 ~~~f~~~l~~af~~~~N~~~-~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La 153 (453)
|..+..++++||..|+|.+. +...+||+||+|+|.+||++++. .....++..+.+++.||+|+.+||+|+++|+++||
T Consensus 393 D~~~~~~l~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~k~-s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~la 471 (773)
T COG5647 393 DGSIVKALGNAFKTFINGNESADSGPSEYLAKYIDGLLKKDGKQ-SFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLA 471 (773)
T ss_pred cchHHHHHHHHHHHHhccccccccccHHHHHHHhHHHhhccccc-cccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 99999999999999999854 23578999999999999996532 22345777889999999999999999999999999
Q ss_pred HHHcCCCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCC
Q 012914 154 RRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYK 233 (453)
Q Consensus 154 ~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLs~~~WP~~~ 233 (453)
||||+++|++.+.|..||++||+.||.+||+|+++||+||..|+++...|++... + ..+.+++.|.||++.+||..+
T Consensus 472 KRLL~g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~-s--~~~~~Dl~v~VLt~a~WP~sp 548 (773)
T COG5647 472 KRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQ-S--YNKYLDLFVWVLTQAYWPLSP 548 (773)
T ss_pred HHHhcCCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCch-h--hccccchhHHHHHHhcCCCCc
Confidence 9999999999999999999999999999999999999999999999999986441 1 235789999999999999654
Q ss_pred -CCCCcCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEE---EcHHHHHHHHhhcCCCCcCHHHH
Q 012914 234 -SSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELI---VSTYQAATLLLFNTSDRLSYSEI 309 (453)
Q Consensus 234 -~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~---vs~~Qa~ILllFn~~~~~t~~ei 309 (453)
...+.||++|.+.++.|++||.++|+||+|.|.|+||+|+|+++|+.+++.+. ++++|+.|+++||+++++|+++|
T Consensus 549 ~~~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei 628 (773)
T COG5647 549 EEVSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEI 628 (773)
T ss_pred cccccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHH
Confidence 56899999999999999999999999999999999999999999998765554 55789999999999999999999
Q ss_pred HHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCcceeeccCCCc----hhhhhhHHhHHHhhh
Q 012914 310 MTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV----DERKKIVEDVDKDRR 385 (453)
Q Consensus 310 ~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~v~~~R~ 385 (453)
.+.|+++..+++++|+||+++|..++.+ +++..+|++.|.+|.+|+++..+|+++.+.. ++..++++.+++||+
T Consensus 629 ~e~T~l~~~dl~~~L~sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~ 706 (773)
T COG5647 629 LELTKLSTDDLKRVLQSLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQ 706 (773)
T ss_pred HhhcCCChhhHHHHHHHHHhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHH
Confidence 9999999999999999999876555554 3677889999999999999999999998653 445567788999999
Q ss_pred hhhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 386 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 386 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
..+|||||||||+||.|.|++|+++|+.+++.||.|++.+||++|+.|||||||+|.++| ..|+|+|
T Consensus 707 ~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 707 AELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred HHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999999999999999999999999999999999999999999999999999988 8999997
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4e-76 Score=561.56 Aligned_cols=408 Identities=30% Similarity=0.539 Sum_probs=380.6
Q ss_pred CccccccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHH
Q 012914 1 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHK 80 (453)
Q Consensus 1 ly~L~~r~~~~l~~l~~~~~~~i~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~ 80 (453)
||+|++.+..||..+.+.|++||.++|...+.+..++ ..|..||+.++.+|.+|.+++...|.+|..|..
T Consensus 313 my~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~e----------n~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s 382 (728)
T KOG2284|consen 313 MYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGE----------NVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSS 382 (728)
T ss_pred HHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhccc----------cchHHHHHHHHHHHHHHHHHHHHHhcCchhhhH
Confidence 7999999999999999999999999999999887553 478999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCC---CCChHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHhhccChhHHHHHHHHHHHHHHc
Q 012914 81 ALKEAFEIFCNKAVG---GSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLL 157 (453)
Q Consensus 81 ~l~~af~~~~N~~~~---~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL 157 (453)
+++.|+..++|...+ -.+.||.||+|||.+|+++. +++++.+++.+|+..+.+|+|++|||+|.++|.++||+||+
T Consensus 383 ~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~-kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli 461 (728)
T KOG2284|consen 383 GLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKST-KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLI 461 (728)
T ss_pred HHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhh-cCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHH
Confidence 999999999998764 25789999999999999975 67899999999999999999999999999999999999999
Q ss_pred CCCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCC
Q 012914 158 FDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDL 237 (453)
Q Consensus 158 ~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLs~~~WP~~~~~~~ 237 (453)
.+.|.|.|.|..||++||+.||++||+++- +.|+..|.+++.+|.+.+. ++
T Consensus 462 ~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~---------------------------nf 512 (728)
T KOG2284|consen 462 ASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIA---------------------------NF 512 (728)
T ss_pred hhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHH---------------------------hc
Confidence 999999999999999999999999999998 9999999999999987654 27
Q ss_pred cCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCh
Q 012914 238 NLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTH 317 (453)
Q Consensus 238 ~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~ 317 (453)
.+|.+|+...+.|+.||..+|+||+|+|++.+++++++.++-++.|.-.+.+|||++||+||..+.+++.||.+.+|++.
T Consensus 513 ~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~ 592 (728)
T KOG2284|consen 513 HLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSG 592 (728)
T ss_pred cchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCcceeeccCCCc-----hhhhhhHHhHHHhhhhhhccee
Q 012914 318 DDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV-----DERKKIVEDVDKDRRYAIDAAL 392 (453)
Q Consensus 318 ~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~~~~~~i~i~~~~~-----~e~~~~~~~v~~~R~~~i~A~I 392 (453)
+.|.+.+.++.+. ++|.. ++.++..+..|++|.+|+++..++++..|.+ +|.+.+...+.+||++.++|||
T Consensus 593 ~~l~kti~tildv--~~~~~--d~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~ai 668 (728)
T KOG2284|consen 593 DYLLKTIRTILDV--TLLTC--DDQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAI 668 (728)
T ss_pred HHHHHHHHHHHhc--eeecc--cccccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHH
Confidence 9999999999763 56754 3446777889999999999999999987653 4455677789999999999999
Q ss_pred eehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 393 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 393 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
|||||+||.+.|+.|+.||+.|.++||.|++++||+|||.||++.||+|.+.+ +.|.|+|
T Consensus 669 vrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 669 VRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 99999999999999999999999999999999999999999999999999876 8999998
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-68 Score=513.78 Aligned_cols=444 Identities=30% Similarity=0.506 Sum_probs=393.8
Q ss_pred CccccccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHH
Q 012914 1 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHK 80 (453)
Q Consensus 1 ly~L~~r~~~~l~~l~~~~~~~i~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~ 80 (453)
||+|+.||+.|++++.+.+..||...|.+-+....+.+ ++++..||+.|+.++++|..++.++|++||.|..
T Consensus 292 mfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~aaE~i--------ttDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLT 363 (777)
T KOG2285|consen 292 MFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNAAENI--------TTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLT 363 (777)
T ss_pred HHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhhhhhc--------cCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhh
Confidence 79999999999999999999999999999888766554 4688999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCC------------------CCCChHHHHHHHHHHHhhcC-CCCCCChHHHHHHHHHHHHHHhhccCh
Q 012914 81 ALKEAFEIFCNKAV------------------GGSSSSELLATFCDNILKKG-GNEKLSDEAIEETLEKVVKLLAYISDK 141 (453)
Q Consensus 81 ~l~~af~~~~N~~~------------------~~~~~~e~La~y~d~~l~~~-~~~~~~~~~~~~~l~~i~~lf~~l~~K 141 (453)
|.+.||..++|... +..++||+||.|||.+||+. .+++++.++++.+|++++.+++|+.+|
T Consensus 364 ARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NK 443 (777)
T KOG2285|consen 364 ARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENK 443 (777)
T ss_pred hhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhccc
Confidence 99999999999764 23578999999999999984 246788999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHhhC--ChhhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCcce
Q 012914 142 DLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCG--GQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDL 219 (453)
Q Consensus 142 D~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G--~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~ 219 (453)
|+|..|++.||++||+...|++.+.|..|++.|+ +|| .+|++++.+|++|++.|++++..|++.+.........-.+
T Consensus 444 DVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsi 522 (777)
T KOG2285|consen 444 DVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSI 522 (777)
T ss_pred HHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccce
Confidence 9999999999999999999999999999999998 577 6799999999999999999999999988766544455678
Q ss_pred EEEEeecCCCCCCCC-CCCcCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhh
Q 012914 220 SVTVLTTGFWPSYKS-SDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLF 298 (453)
Q Consensus 220 ~~~VLs~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Qa~ILllF 298 (453)
++.||+.|.|...+. ..+.||.+|+..+-.-++||+++|+||+|.|.|+++.++|++.-+-|.|.+.|+++||+||.+|
T Consensus 523 NiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFaw 602 (777)
T KOG2285|consen 523 NIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAW 602 (777)
T ss_pred eeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHh
Confidence 999999999997643 4689999999999999999999999999999999998888876555899999999999999999
Q ss_pred cCC--CCcCHHHHHHHhCCChHHHHHHHhHhhh---cccceeecCCCC----CCCCCCCeEEEccCCCC-----Ccceee
Q 012914 299 NTS--DRLSYSEIMTQLNLTHDDLVRLLHSLSC---AKYKILLKEPNT----KTISQSDHFEFNSKFTD-----RMRRIK 364 (453)
Q Consensus 299 n~~--~~~t~~ei~~~t~i~~~~l~~~L~sL~~---~k~~iL~~~~~~----~~i~~~~~f~~N~~f~~-----~~~~i~ 364 (453)
|+. +.+|++.+.-+|.+|+.+|.+.|-||+. .|+.||..+|+. +++.++..|.+|.+|.- ..+|-+
T Consensus 603 NqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGK 682 (777)
T KOG2285|consen 603 NQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGK 682 (777)
T ss_pred ccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhccc
Confidence 975 6899999999999999999999999974 357888877642 45678889999999963 122444
Q ss_pred ccCCCc----hh--hhhhHHhHHHhhhhhhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhcc
Q 012914 365 IPLPPV----DE--RKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDY 438 (453)
Q Consensus 365 i~~~~~----~e--~~~~~~~v~~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIerey 438 (453)
++...- .| .++..+.+.+-|....+-+|++|||.||+++..+|-.|.++.|+..|.|+..+||+.||.|||..|
T Consensus 683 vNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKY 762 (777)
T KOG2285|consen 683 VNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKY 762 (777)
T ss_pred ceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhh
Confidence 443321 11 223356678899999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCceEecC
Q 012914 439 LERDKENPNMFRYLA 453 (453)
Q Consensus 439 i~R~~~d~~~y~Yia 453 (453)
++||++|-++|+|+|
T Consensus 763 mrRd~dDINtFiYia 777 (777)
T KOG2285|consen 763 MRRDADDINTFIYIA 777 (777)
T ss_pred hccchhhccceeeeC
Confidence 999999999999997
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=3.8e-61 Score=515.04 Aligned_cols=344 Identities=43% Similarity=0.755 Sum_probs=300.6
Q ss_pred CccccccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHH
Q 012914 1 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHK 80 (453)
Q Consensus 1 ly~L~~r~~~~l~~l~~~~~~~i~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~ 80 (453)
||+|++++++|++.++..|++||.+.|..+++.... ...+..||+.++++|++|+.++..||++++.|..
T Consensus 243 ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~----------~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~ 312 (588)
T PF00888_consen 243 LYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK----------SSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKK 312 (588)
T ss_dssp HHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC----------GGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHH
T ss_pred HHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc----------ccchHHHHHHHHHHHHHHHHHHHHhccccHHHHH
Confidence 689999999999999999999999999999998641 2467899999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCChHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHhhccChhHHHHHHHHHHHHHHcCCC
Q 012914 81 ALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDR 160 (453)
Q Consensus 81 ~l~~af~~~~N~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~ 160 (453)
++++||+.++|.. ...+|++||+|||.+|++++ .+.++++++..++.++.+|+|+++||+|+.+|+++||+|||.++
T Consensus 313 ~l~~af~~~~n~~--~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~ 389 (588)
T PF00888_consen 313 ALDEAFEEFLNKN--NNKIPELLAKYCDSLLRKSN-KKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNK 389 (588)
T ss_dssp HHHHHHHHHHHCS--TSHHHHHHHHHHHHHHBSSC-CCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-
T ss_pred HHHHhHHHHHHcC--CcchHHHHHHHhhHhhhhcc-cccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhccc
Confidence 9999999999998 35899999999999999965 55677889999999999999999999999999999999999999
Q ss_pred CCChHHHHHHHHHHHHhhCChhhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCC-CCcceEEEEeecCCCCCCCCCC-Cc
Q 012914 161 SANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAH-PGIDLSVTVLTTGFWPSYKSSD-LN 238 (453)
Q Consensus 161 s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~-~~~~~~~~VLs~~~WP~~~~~~-~~ 238 (453)
+.+.+.|+.+|++|+.+||.+++++|++|++|+..|++++..|++....++... .+++|+|.||++++||..+... +.
T Consensus 390 ~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~ 469 (588)
T PF00888_consen 390 SFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIK 469 (588)
T ss_dssp BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-S-S-SS---
T ss_pred ccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCCCCCCCcccc
Confidence 999999999999999999999999999999999999999999999987655322 2789999999999999988766 99
Q ss_pred CCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChH
Q 012914 239 LPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHD 318 (453)
Q Consensus 239 lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~ 318 (453)
+|++|+.+++.|++||+.+|+||+|+|.|.+|+|+|++++++++++++||++||+||++||+.+++|++||++.||++++
T Consensus 470 lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~ 549 (588)
T PF00888_consen 470 LPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEE 549 (588)
T ss_dssp --HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HH
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCC
Q 012914 319 DLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 357 (453)
Q Consensus 319 ~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~ 357 (453)
+++++|.+|+..+..++.+.++++++++++.|++|.+|+
T Consensus 550 ~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 550 ELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp HHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 999999999865433333678888899999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=3.2e-35 Score=256.59 Aligned_cols=141 Identities=48% Similarity=0.896 Sum_probs=132.5
Q ss_pred hccChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 012914 137 YISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPG 216 (453)
Q Consensus 137 ~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 216 (453)
|+++||+|+.+|+++||+|||..++++.+.|..||++|+.+||.+++++|++|++|++.|+++++.|++++..++ ...+
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 789999999999999999999999999999999999999999999999999999999999999999999876542 2346
Q ss_pred cceEEEEeecCCCCCCCC-CCCcCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEe
Q 012914 217 IDLSVTVLTTGFWPSYKS-SDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKF 278 (453)
Q Consensus 217 ~~~~~~VLs~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~ 278 (453)
++|+|.|||+++||..+. .++.||++|+.+++.|++||..+|++|+|+|.|++|+|+|+++|
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 78999999999999999999999999999999999999999865
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=8.4e-30 Score=258.43 Aligned_cols=301 Identities=24% Similarity=0.326 Sum_probs=241.8
Q ss_pred HHHHHhhccChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHHHHHHHHHHHHHHHH--Hh
Q 012914 131 VVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY--LS 208 (453)
Q Consensus 131 i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~--~~ 208 (453)
+-.|+..+.+|+.|++.||.+||.||+....++.+.|..-++.||-++|....+.|++|++|+..|+++++.++.. ..
T Consensus 442 ~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~ 521 (765)
T KOG2165|consen 442 FGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELS 521 (765)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhh
Confidence 4578888999999999999999999999999999999999999999999999999999999999999999999874 22
Q ss_pred cCCCCCCCcceEEEEeecCCCCCCCCCCCcCCHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEc
Q 012914 209 NNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVS 288 (453)
Q Consensus 209 ~~~~~~~~~~~~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs 288 (453)
......+.+.+++.+||+.+||......+.+|.+++..++.|.+-|.+..++|+|.|.+++|+|+|+++|.+++.+++||
T Consensus 522 r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVs 601 (765)
T KOG2165|consen 522 RGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVS 601 (765)
T ss_pred cccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeC
Confidence 21112346789999999999999888889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCcceeeccCC
Q 012914 289 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLP 368 (453)
Q Consensus 289 ~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~~~~~~i~i~~~ 368 (453)
+.||+|+.+|.+.++||++++++.+|+|...+.+.|..|.. .++|..+|. ++++.+|+++++=.+..+- -.++
T Consensus 602 p~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~--~GvL~e~~~---~s~tgt~T~iEse~d~~q~--~~~~ 674 (765)
T KOG2165|consen 602 PEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQ--KGVLREEPI---ISDTGTLTVIESEMDFDQA--EGTV 674 (765)
T ss_pred HHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHH--cCeeecCCC---CCCCceeeecccccccccc--CCCc
Confidence 99999999999999999999999999999999999999974 578887653 2677899999854432211 1111
Q ss_pred Cc---hhh--hhhHHhHHHhhh--hhhcceeeehhccCCCCChhHHHHHHHHHhccCCCC-------ChhHHHHHHHhhh
Q 012914 369 PV---DER--KKIVEDVDKDRR--YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKP-------DIKAIKKRMEDLI 434 (453)
Q Consensus 369 ~~---~e~--~~~~~~v~~~R~--~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~-------~~~~ik~~Ie~LI 434 (453)
.. ++. ......+.+-+. ..-...||-.+-.-+.|..+.+.+... .|.| +-++++.-+..++
T Consensus 675 ~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLk-----mF~~~~~~~~~TlqeL~~fLq~kV 749 (765)
T KOG2165|consen 675 LLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLK-----MFVPPDGSAEITLQELQGFLQRKV 749 (765)
T ss_pred ccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHe-----eeecCCCCCcccHHHHHHHHHHHh
Confidence 11 111 111122222111 233457888888889999888877543 4544 4466777777777
Q ss_pred hhccccccC
Q 012914 435 TRDYLERDK 443 (453)
Q Consensus 435 ereyi~R~~ 443 (453)
..|-++-.+
T Consensus 750 ~e~kL~f~~ 758 (765)
T KOG2165|consen 750 REGKLEFIA 758 (765)
T ss_pred hccceEEec
Confidence 766665543
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=99.83 E-value=1.4e-21 Score=147.51 Aligned_cols=68 Identities=50% Similarity=0.963 Sum_probs=62.5
Q ss_pred HHHhhhhhhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCC
Q 012914 380 VDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPN 447 (453)
Q Consensus 380 v~~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~ 447 (453)
++++|.+.|+|+||||||++|+++|++|+.+|.++++++|.|+..+||++||+||++|||+||++|+|
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 36799999999999999999999999999999999999999999999999999999999999999875
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=94.54 E-value=0.12 Score=41.41 Aligned_cols=66 Identities=17% Similarity=0.229 Sum_probs=52.3
Q ss_pred EEEEcHHHHHHHHhhc--------CCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 012914 284 ELIVSTYQAATLLLFN--------TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 355 (453)
Q Consensus 284 ~l~vs~~Qa~ILllFn--------~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~ 355 (453)
...++.-|+.+|+... ....+|-.||++.+|++.+.+.++|..|. +.++|.+.. ....|.+|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~ 91 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTP 91 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCC
Confidence 3467788898888655 46689999999999999999999999996 357776532 2368999988
Q ss_pred CC
Q 012914 356 FT 357 (453)
Q Consensus 356 f~ 357 (453)
++
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 64
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=94.05 E-value=0.1 Score=36.76 Aligned_cols=45 Identities=27% Similarity=0.294 Sum_probs=36.7
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 292 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 292 a~ILllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
+.||..|.+.. .+|+.||++.+|+|...+.+.|..|.. .+++.++
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~--~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE--EGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CcCeecC
Confidence 46788888776 589999999999999999999999974 4677654
No 12
>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=93.65 E-value=0.24 Score=38.63 Aligned_cols=59 Identities=15% Similarity=0.233 Sum_probs=41.4
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 012914 290 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 355 (453)
Q Consensus 290 ~Qa~ILllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~ 355 (453)
+++.+.+..+..+ .+|.++|++.+++++..+.+.|+.|. +.+++..... +++.|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~G-----~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSRG-----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEETS-----TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecCC-----CCCceeecCC
Confidence 4455555544444 49999999999999999999999996 4578765421 3567887765
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=92.87 E-value=0.16 Score=36.81 Aligned_cols=51 Identities=18% Similarity=0.298 Sum_probs=41.9
Q ss_pred EcHHHHHHHHhhcCCCC--cCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 287 VSTYQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+|+.|+.||......+. +|..||++.++++...+.+.+..|.. .+++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~--~Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK--KGLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEeC
Confidence 46789999988777666 99999999999999999999999974 46777653
No 14
>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=92.63 E-value=0.28 Score=33.72 Aligned_cols=42 Identities=19% Similarity=0.299 Sum_probs=34.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
+..+..||....+++.+|..||++.+|++...+.+.|..|..
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 456777888888888999999999999999999999999964
No 15
>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=91.24 E-value=0.34 Score=34.84 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=38.5
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 291 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 291 Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
|..|+...++.+.+|++||++.+|+++..+.+-|..|.. .+++.+.
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 456777888889999999999999999999999999974 3556553
No 16
>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=90.88 E-value=0.2 Score=35.99 Aligned_cols=50 Identities=16% Similarity=0.317 Sum_probs=42.3
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
+|..|+.+|....+.+.+|..+|++.++++...+.+.+..|.. .+++.+.
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~--~g~I~r~ 50 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEK--KGLIERE 50 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHH--CCCEEec
Confidence 3678999998888888899999999999999999999999974 4677654
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=90.23 E-value=0.55 Score=34.61 Aligned_cols=50 Identities=16% Similarity=0.279 Sum_probs=38.2
Q ss_pred EcHHHHHHHHhhc-CCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 287 VSTYQAATLLLFN-TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 287 vs~~Qa~ILllFn-~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
+|..|..||.... ....+|..+|++.++++...+-+.|..|.. .+++.+.
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~--~glv~~~ 51 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEE--KGLVEKE 51 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHH--TTSEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEec
Confidence 4678889998888 778999999999999999999999999974 4677654
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=89.88 E-value=0.72 Score=38.36 Aligned_cols=52 Identities=12% Similarity=0.201 Sum_probs=44.9
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
.++..|..||.....++.+|..+|++.++++...+-+.+..|. +.+++.+.+
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 4578999999988888899999999999999999999999996 347777653
No 19
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=88.67 E-value=1 Score=38.97 Aligned_cols=53 Identities=19% Similarity=0.183 Sum_probs=45.1
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 285 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 285 l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
..+|..|+.||......+.+|..+|++.++++...+-+.+..|. +.+++.+.+
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 45778999999877667789999999999999999999999996 457887654
No 20
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=88.63 E-value=0.71 Score=33.54 Aligned_cols=48 Identities=15% Similarity=0.216 Sum_probs=39.3
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
++.-..||.++...+++|+.||++.+|++...+..+|..|.. .+++..
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~--aGli~~ 56 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE--AGLIEV 56 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEE
Confidence 456677888887778999999999999999999999999964 567754
No 21
>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=88.59 E-value=1.3 Score=30.35 Aligned_cols=44 Identities=20% Similarity=0.260 Sum_probs=34.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
...-||.+.-+ +..++.||++.+|++...+.++|..|.. .+++.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~--~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLRE--AGLVE 46 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHH--CcCee
Confidence 34566766666 6799999999999999999999999963 45553
No 22
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=87.27 E-value=0.31 Score=36.51 Aligned_cols=44 Identities=18% Similarity=0.321 Sum_probs=34.1
Q ss_pred eehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCC
Q 012914 393 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 444 (453)
Q Consensus 393 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~ 444 (453)
-.+|+.++.++..+|-. +|..+++.+...|+.|+.+|||++.+.
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 34677788888877765 589999999999999999999998753
No 23
>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=86.69 E-value=1.4 Score=31.03 Aligned_cols=37 Identities=16% Similarity=0.315 Sum_probs=29.2
Q ss_pred HHHHhh-cCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 293 ATLLLF-NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 293 ~ILllF-n~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
.||..+ +..+.+|.++|++.+|++...+.+.|..|..
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344434 6666699999999999999999999999854
No 24
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=86.49 E-value=0.68 Score=38.74 Aligned_cols=62 Identities=21% Similarity=0.302 Sum_probs=52.5
Q ss_pred hhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 387 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 387 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
..++-|++||=.++..+.+|++.++.. .+.++..-|+--|..|..||.|.|.-+ ...|.|-|
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 478899999999999999999999874 46788754
No 25
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=85.53 E-value=1.3 Score=32.98 Aligned_cols=47 Identities=19% Similarity=0.234 Sum_probs=37.8
Q ss_pred HHHHHHHhhcCCCC--cCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 290 YQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 290 ~Qa~ILllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
..-.||.++.+... +|..||++.+|++...+.++|..|.. .+++.+.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~--~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK--KGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 44567777777665 99999999999999999999999963 4666654
No 26
>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=85.15 E-value=1.1 Score=38.14 Aligned_cols=60 Identities=18% Similarity=0.232 Sum_probs=44.7
Q ss_pred cceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 389 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 389 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
+..|++++-..+.++..+++.. +.....++..-|...|..|.++|||+|..+ ...|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~----l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRI----LAEKKDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHH----HhhccCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 3446677766777777666655 433466788999999999999999999864 45788864
No 27
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=84.93 E-value=3.1 Score=36.46 Aligned_cols=57 Identities=11% Similarity=0.080 Sum_probs=41.3
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 355 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~ 355 (453)
+.+.|..+....+|..+|++..++|...|.+.|..|. +.+++..... .++.|.++..
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 4444555666678999999999999999999999996 5678765421 2455666543
No 28
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=84.91 E-value=2.7 Score=34.46 Aligned_cols=52 Identities=25% Similarity=0.367 Sum_probs=42.8
Q ss_pred EEcHHHHHHHHhhc----CCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 286 IVSTYQAATLLLFN----TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 286 ~vs~~Qa~ILllFn----~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
.+|..|..||.... ..+.+|..+|++.++++...+-+.+..|. +.+++.+.+
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 45788888887655 55689999999999999999999999996 357787654
No 29
>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=84.20 E-value=1.1 Score=37.28 Aligned_cols=59 Identities=12% Similarity=0.216 Sum_probs=41.7
Q ss_pred ceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 390 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 390 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
..|++++=..+.++..|++.. +.....+....|...+..|.+||||.|... ...|.|-|
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 345555555566666665554 444567889999999999999999999875 45788864
No 30
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=84.17 E-value=3.6 Score=36.54 Aligned_cols=45 Identities=16% Similarity=0.216 Sum_probs=36.2
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 291 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 291 Qa~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.+++.+.|+.. ..+|.++|++.+++|...+.+.|..|. +.+|+..
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 34455566654 589999999999999999999999996 4678874
No 31
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=84.08 E-value=2.3 Score=33.56 Aligned_cols=53 Identities=21% Similarity=0.253 Sum_probs=44.8
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 284 ELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 284 ~l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
++.++..+..||........+|..+|++.++++...+.+.|..|.. .+++.+.
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~--~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEK--KGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHH--CCCeEec
Confidence 3567788999998888777899999999999999999999999974 4677643
No 32
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=83.81 E-value=2.7 Score=32.84 Aligned_cols=45 Identities=22% Similarity=0.314 Sum_probs=37.0
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 292 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 292 a~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
..||..+... ..+|..||++.+|++...+.+.|..|.. .+++.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeec
Confidence 4566667666 6899999999999999999999999964 4777654
No 33
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=83.29 E-value=2.9 Score=39.90 Aligned_cols=47 Identities=11% Similarity=0.244 Sum_probs=39.9
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 291 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 291 Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
-+.||.+|.....+|+.||++.+|+|...+.+.|.+|.. .+.|.+.+
T Consensus 16 ~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~ 62 (257)
T PRK15090 16 VFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG 62 (257)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 346788898877899999999999999999999999974 46777643
No 34
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=81.88 E-value=4.1 Score=34.37 Aligned_cols=37 Identities=22% Similarity=0.271 Sum_probs=33.1
Q ss_pred CCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 300 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 300 ~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
.++.+|+++|++.++.+...+.++|+.|.. .+++.+.
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Re 75 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVERE 75 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeee
Confidence 677999999999999999999999999975 5788765
No 35
>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=81.08 E-value=5 Score=34.25 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=34.7
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 292 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 292 a~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
+.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
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 4444555544 479999999999999999999999996 4577764
No 36
>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=81.05 E-value=1.5 Score=32.46 Aligned_cols=49 Identities=22% Similarity=0.274 Sum_probs=39.1
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
|-.++-|+...-..+..|..||++.+|++...+.+.|..|.. .+++.+.
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 445666666555677899999999999999999999999974 4666654
No 37
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=80.90 E-value=3.7 Score=28.06 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=34.0
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.|+..+.+...+|..+|++.++++...+.+.|..|.. .+++.+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~ 46 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTR 46 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 4555556667899999999999999999999999964 345543
No 38
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=80.73 E-value=3.6 Score=37.29 Aligned_cols=53 Identities=13% Similarity=-0.011 Sum_probs=45.4
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 285 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 285 l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+.+|..|..||......+++|..+|++.++++...+.+.+..|. +-+++.+.+
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 46778999999998888899999999999999999999999996 347777653
No 39
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=79.79 E-value=4.1 Score=35.00 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=43.7
Q ss_pred EEEcHHHHHHHHhhcCC-CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 285 LIVSTYQAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 285 l~vs~~Qa~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+.+|..|..+|...... +.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 45778898888877654 568999999999999999999999996 457777654
No 40
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=79.40 E-value=4.6 Score=29.58 Aligned_cols=56 Identities=20% Similarity=0.192 Sum_probs=36.9
Q ss_pred HHHhhcC-CCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEc
Q 012914 294 TLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFN 353 (453)
Q Consensus 294 ILllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N 353 (453)
||-.++. +..+|..||++.+|++.......|..|.. .+.+.+.|.+.. ....|.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~--eG~V~~~~~~rG--~~~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEK--EGKVERSPVRRG--KSTYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHH--CTSEEEES-SSS--SS-EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH--CCCEEEecCCCC--cceeeeec
Confidence 4445555 67899999999999999999999999964 455555443221 12356665
No 41
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=78.59 E-value=4.1 Score=36.26 Aligned_cols=51 Identities=20% Similarity=0.272 Sum_probs=41.4
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCcce
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRR 362 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~~~~~~ 362 (453)
.+|..+|++.+|++...+.+++..|.. .++|.+. ..+.|.+|++|-.+..+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e--~~iI~k~-------~~G~Y~iNP~~~~kG~~ 125 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEE--KNIIKKI-------RNGAYMINPNFFFKGDR 125 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHh--CCcEEEc-------cCCeEEECcHHheeCcH
Confidence 578899999999999999999999974 4688764 34689999998654443
No 42
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=78.55 E-value=5.8 Score=34.67 Aligned_cols=59 Identities=15% Similarity=0.208 Sum_probs=42.2
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 012914 290 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 355 (453)
Q Consensus 290 ~Qa~ILllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~ 355 (453)
+.+.+.|.-+..+ ..|.++|++..|+|+..|.+.|..|. |.+++..... +++.|.++.+
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 4445555555554 68899999999999999999999996 5678865421 2455666553
No 43
>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=78.01 E-value=3.5 Score=27.59 Aligned_cols=35 Identities=29% Similarity=0.469 Sum_probs=26.5
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
.||-...+....++.+|++.+|++...+.+-+..|
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 46666666688999999999999999998877654
No 44
>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=77.12 E-value=4.3 Score=32.75 Aligned_cols=44 Identities=23% Similarity=0.306 Sum_probs=37.3
Q ss_pred EEcHHHHHHHHhhcC----CCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 286 IVSTYQAATLLLFNT----SDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~----~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
.++..|-.||-.+.. .+.+++++|++.++++..+++.+|..|+.
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 35899999999999999999999999975
No 45
>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=76.26 E-value=10 Score=30.66 Aligned_cols=62 Identities=24% Similarity=0.393 Sum_probs=44.9
Q ss_pred EEcHHHHHHHHh-------hcC-CCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCC
Q 012914 286 IVSTYQAATLLL-------FNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 357 (453)
Q Consensus 286 ~vs~~Qa~ILll-------Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~ 357 (453)
.++.-|.-|++. ||. .+.+|..++++.||++...+.+++..|. +.++|... +..+-+|.+++
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 344555555544 454 3589999999999999999999999996 46788653 35566666553
No 46
>PRK10870 transcriptional repressor MprA; Provisional
Probab=76.10 E-value=7.3 Score=34.95 Aligned_cols=52 Identities=13% Similarity=0.185 Sum_probs=42.2
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 286 IVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
.+|..|..||..... ..++|..||++.++++...+.+.+..|. +.+++.+.+
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 456778888877654 4579999999999999999999999996 457887654
No 47
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=75.91 E-value=6.9 Score=37.74 Aligned_cols=47 Identities=26% Similarity=0.312 Sum_probs=39.1
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 291 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 291 Qa~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
-..||.+|... ..+|+.||++.+|+|...+.+.|.+|.. .+.|.+.+
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~~ 74 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQDS 74 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 34678889865 4799999999999999999999999975 46776643
No 48
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=74.93 E-value=4.1 Score=29.40 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=29.7
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 291 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 291 Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
|.-+|-++-+.+.+|+.+|++.+|++...++..+.-|-
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 45555444447799999999999999999999888774
No 49
>PRK11569 transcriptional repressor IclR; Provisional
Probab=74.72 E-value=7.1 Score=37.69 Aligned_cols=47 Identities=17% Similarity=0.173 Sum_probs=38.9
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 291 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 291 Qa~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
-..||.+|.+. ..+|+.||++.+|++...+.+.|.+|.. .+.|.+.+
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG 77 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 34677789875 4799999999999999999999999975 46776643
No 50
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=74.57 E-value=9.1 Score=32.26 Aligned_cols=46 Identities=20% Similarity=0.237 Sum_probs=34.8
Q ss_pred HHHHHHHhhcCC-CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 290 YQAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 290 ~Qa~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
+++.+.+.-++. ..+|.++|++.+++|...+.+.|..|.. .+++..
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~--~gli~~ 57 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR--AGLVES 57 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH--CCcEEe
Confidence 344444443433 3899999999999999999999999974 467754
No 51
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=74.42 E-value=7.6 Score=36.93 Aligned_cols=46 Identities=28% Similarity=0.386 Sum_probs=38.9
Q ss_pred HHHHHhhcCCCC-cCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 292 AATLLLFNTSDR-LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 292 a~ILllFn~~~~-~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+.||.+|..... +++.||++.+|+|...+.+.|..|.. .+.+.+.+
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~--~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVE--LGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 467888887654 78999999999999999999999974 57888764
No 52
>PHA00738 putative HTH transcription regulator
Probab=73.88 E-value=9.9 Score=31.05 Aligned_cols=67 Identities=18% Similarity=0.069 Sum_probs=49.8
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCC
Q 012914 284 ELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 356 (453)
Q Consensus 284 ~l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f 356 (453)
++...+.=-.||.+..+++.+++.+|++.++++...+-++|.-|.. .+|+.....|. .-.|++|.+.
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLre--AGLV~srK~Gr----~vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNE--QGYIELYKEGR----TLYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHH--CCceEEEEECC----EEEEEECCCc
Confidence 4555566666777667777899999999999999999999999964 57887554332 2357777764
No 53
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=73.66 E-value=7.6 Score=27.23 Aligned_cols=39 Identities=21% Similarity=0.347 Sum_probs=31.8
Q ss_pred hcCCCCc-CHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 298 FNTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 298 Fn~~~~~-t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
+.....+ |..+|++.+|++...+.++|..|.. .+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~--~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEA--EGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 4455567 8999999999999999999999974 4677654
No 54
>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=73.66 E-value=8.6 Score=36.44 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=37.1
Q ss_pred HHHHHhhcC-CCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 292 AATLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 292 a~ILllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
..||.+|.. ...+|+.||++.+|+|...+.+.|.+|.. .+.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 467888986 45899999999999999999999999975 466764
No 55
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=73.50 E-value=8.9 Score=28.93 Aligned_cols=45 Identities=18% Similarity=0.310 Sum_probs=34.0
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 289 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 289 ~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
..|. ||+..... ..|++||.+.||++.+.+...|..|. +-+++.+
T Consensus 6 ~~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 6 VTQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred HHHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 3443 34444444 89999999999999999999999996 3466654
No 56
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=73.27 E-value=9 Score=25.59 Aligned_cols=33 Identities=27% Similarity=0.353 Sum_probs=28.4
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.+|..+|++.+|++...+.+.|..|.. .+++..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~--~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK--EGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 578999999999999999999999964 467764
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=72.31 E-value=6.9 Score=35.94 Aligned_cols=51 Identities=16% Similarity=0.154 Sum_probs=44.3
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
.++..|..||..+.+++.++..+|++.+|++...+.+.|..|.. .+++.+.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~--~GlI~r~ 190 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEK--KGLVEQK 190 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 56788999999988878899999999999999999999999963 4777765
No 58
>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=72.26 E-value=9.2 Score=28.83 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=39.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccce
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKI 334 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~i 334 (453)
++=|+.++-++...+..|+++|++.||.....+.-+|..+...|.++
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 45689999899888899999999999999999999998886434444
No 59
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=70.69 E-value=9.4 Score=36.60 Aligned_cols=46 Identities=17% Similarity=0.150 Sum_probs=38.2
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 292 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 292 a~ILllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+.||.+|.+.. .+|..||++.+|++...+.+.|..|.. .++|.+.+
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~--~g~v~~~~ 60 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE--EGYVRRSA 60 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEec
Confidence 45777887655 599999999999999999999999974 57787654
No 60
>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=70.36 E-value=4.9 Score=29.39 Aligned_cols=53 Identities=11% Similarity=0.211 Sum_probs=32.8
Q ss_pred ceeeehhc-cCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhcccccc--CCCCCceE
Q 012914 390 AALVRIMK-SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD--KENPNMFR 450 (453)
Q Consensus 390 A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~--~~d~~~y~ 450 (453)
..|.+.+. ....++..+|.. .+..+...+-+.|+.|+++|||++. +.|+....
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~--------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~ 61 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAE--------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKR 61 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHH--------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEE
T ss_pred HHHHHHHHccCCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeE
Confidence 34455555 555666655554 3556788899999999999999664 44555333
No 61
>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=69.88 E-value=13 Score=31.42 Aligned_cols=44 Identities=25% Similarity=0.263 Sum_probs=34.2
Q ss_pred HHHHHhhc--CCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 292 AATLLLFN--TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 292 a~ILllFn--~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
..+|..+. ..+.+|+.||++.+|++...+.+.|..|.. .+++..
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~--~Gli~~ 57 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSL--AGIVTS 57 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHH--CCcEEe
Confidence 34444443 335799999999999999999999999964 577764
No 62
>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=69.72 E-value=5.3 Score=29.49 Aligned_cols=47 Identities=13% Similarity=0.328 Sum_probs=33.4
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEec
Q 012914 398 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYL 452 (453)
Q Consensus 398 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yi 452 (453)
.++.++..+|... ...+...+-+.++.|.++|+++|.+.++..|..+
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 4445555554443 3367888999999999999999998765555443
No 63
>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=68.32 E-value=2.7 Score=38.11 Aligned_cols=56 Identities=18% Similarity=0.351 Sum_probs=39.0
Q ss_pred ceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 390 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 390 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
...|...|.+|.+..+||-. .|..+.+++-.+|..|...|-|.=--+|++.|+||.
T Consensus 102 ~~Fi~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 102 QEFINYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 34457888999988888765 488999999999999999999888778899999984
No 64
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=68.08 E-value=5 Score=30.97 Aligned_cols=43 Identities=26% Similarity=0.351 Sum_probs=32.6
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
..||...+..+.+++.+|.+.+|+++..+-++|..|.. .+.+.
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~--~GyV~ 45 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEE--AGYVE 45 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEE
Confidence 45565566677899999999999999999999999974 34444
No 65
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=67.78 E-value=12 Score=30.46 Aligned_cols=51 Identities=20% Similarity=0.303 Sum_probs=42.7
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+++.|..+|.........+..+|++.++++...+.+.+..|. +.+++.+.+
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 788999999888777766669999999999999999999996 356777653
No 66
>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=67.71 E-value=3.7 Score=29.36 Aligned_cols=45 Identities=13% Similarity=0.343 Sum_probs=39.1
Q ss_pred eeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccC
Q 012914 391 ALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 391 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
.|+..++.++.++..+|.+ .|..|...|.+=+..|-++|+|.|.-
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 4677788889999888877 38899999999999999999999864
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=67.53 E-value=8.3 Score=29.24 Aligned_cols=30 Identities=20% Similarity=0.168 Sum_probs=25.3
Q ss_pred cCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 299 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 299 n~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
.....+|+.||++.+|++...++..+..+.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 333578999999999999999999888764
No 68
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=67.40 E-value=7.9 Score=35.99 Aligned_cols=43 Identities=21% Similarity=0.253 Sum_probs=35.8
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
..||.+.+....+|.+||++.+|++...++++|..|.. -+++.
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 35667778888999999999999999999999999974 24444
No 69
>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=67.26 E-value=14 Score=25.25 Aligned_cols=33 Identities=21% Similarity=0.391 Sum_probs=24.5
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhH
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
.+|-+.| ...+|+.||++.+|++...+.+.+..
T Consensus 11 ~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 11 EVIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 3444556 45789999999999999988776543
No 70
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=66.95 E-value=7.1 Score=29.06 Aligned_cols=53 Identities=9% Similarity=0.201 Sum_probs=39.9
Q ss_pred cceeeehhccCCC--CChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCce
Q 012914 389 DAALVRIMKSRKV--LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 449 (453)
Q Consensus 389 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y 449 (453)
+..|...|+.++. ++..+|-.+ .-.+...+.+.+..|.++|||.+++..+..|
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 3456677888766 887776654 3356778999999999999999987654554
No 71
>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=66.55 E-value=12 Score=27.17 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=37.8
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
+..+..|+..+.... ++..||++.+|++...+.+.|..|.. .+++..
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 356777887766666 99999999999999999999999964 356654
No 72
>PF13730 HTH_36: Helix-turn-helix domain
Probab=65.60 E-value=16 Score=25.41 Aligned_cols=25 Identities=16% Similarity=0.272 Sum_probs=23.4
Q ss_pred CHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 305 SYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 305 t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
|.+.|++.+|++...+.+++..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999963
No 73
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=63.81 E-value=10 Score=26.68 Aligned_cols=45 Identities=11% Similarity=0.200 Sum_probs=31.9
Q ss_pred eehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCC
Q 012914 393 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENP 446 (453)
Q Consensus 393 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~ 446 (453)
++.+. .+.++..++... +..+...+.+.|+.|.++|++.+....+
T Consensus 3 l~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 3 LKLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 34444 556666665443 3467788999999999999999876443
No 74
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=63.64 E-value=9.1 Score=33.89 Aligned_cols=50 Identities=28% Similarity=0.357 Sum_probs=37.6
Q ss_pred cCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 257 KTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 257 ~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+++.++|+|.++|- .-|..+-. +...+|+++|++.+|.++.+++++|..=
T Consensus 36 ~~~~~~lTWvdSLa-------------------vAAga~ar--ekag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 36 KDPYERLTWVDSLA-------------------VAAGALAR--EKAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred hCcccccchhhHHH-------------------HHHHHHHH--HHccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 46899999998662 22222322 4458999999999999999999998754
No 75
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=63.46 E-value=13 Score=30.03 Aligned_cols=45 Identities=13% Similarity=0.198 Sum_probs=37.3
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
..-.||..+......|+.+|++.+|++...+.+.+..|.. .+++.
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 3456777777778899999999999999999999999964 35664
No 76
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=63.36 E-value=25 Score=30.18 Aligned_cols=40 Identities=15% Similarity=0.262 Sum_probs=32.9
Q ss_pred hcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 298 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 298 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+.....++..+|++.+|+|...+.++|..|. +.+++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEec
Confidence 4444578999999999999999999999996 457886543
No 77
>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=63.27 E-value=13 Score=27.52 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=32.4
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
..|-.+.++...+|+.+|++.+++++.++..+|-.|..
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 45666778888999999999999999999999999964
No 78
>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=63.17 E-value=10 Score=25.58 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=21.5
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 294 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 294 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
|+-++.+. +|+.+|++.+|++...+.+.|.
T Consensus 14 i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 44455554 8999999999999999988775
No 79
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=63.10 E-value=16 Score=30.44 Aligned_cols=60 Identities=22% Similarity=0.316 Sum_probs=42.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 355 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~ 355 (453)
.-..||.+.-+.+++++.||++.+|++...+-++|.-|.. .+++.....|. .-.|++|.+
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~--AGLV~~~r~Gr----~~~Y~l~~~ 76 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE--SGLLLDRKQGK----WVHYRLSPH 76 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCceEEEEEcC----EEEEEECch
Confidence 3345555444455799999999999999999999999964 57887554321 234777653
No 80
>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=62.62 E-value=17 Score=26.27 Aligned_cols=44 Identities=16% Similarity=0.233 Sum_probs=34.1
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 294 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 294 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
|..+-.+...++..+|++.+|+++..+...+..|.. .+++...+
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~--~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE--KGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH--CCCEEecC
Confidence 444445778999999999999999999999999963 46776543
No 81
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=61.19 E-value=11 Score=36.09 Aligned_cols=47 Identities=19% Similarity=0.186 Sum_probs=40.3
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
-|..||-+.++++.+++.||++.+|++...++|-|..|.. .++|.+.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~--~g~l~r~ 52 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEH--AGTVIRT 52 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEE
Confidence 4678888899999999999999999999999999999963 4666554
No 82
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=61.12 E-value=24 Score=25.41 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=30.1
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
..+|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~--~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE--EGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 4799999999999999999999999974 4677654
No 83
>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=60.34 E-value=18 Score=25.14 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=17.2
Q ss_pred CcCHHHHHHHhCCChHHHHHHHh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
++|+.||++.+|++...+...+.
T Consensus 26 g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 26 GMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 67999999999999999888764
No 84
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=59.65 E-value=7.9 Score=31.39 Aligned_cols=44 Identities=14% Similarity=0.185 Sum_probs=30.1
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 291 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 291 Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
.+.|+..+..++.++-++|++.+|++..++.+.|..|... +++.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~--~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYED--GLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHH--SS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHC--CCeE
Confidence 3456666666678999999999999999999999999753 4553
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=59.61 E-value=11 Score=27.91 Aligned_cols=33 Identities=15% Similarity=0.343 Sum_probs=26.4
Q ss_pred hhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 297 LFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 297 lFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
...++..+|++||+..++++++.+...|..|..
T Consensus 8 ~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 8 YLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345677899999999999999999999999974
No 86
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=59.21 E-value=13 Score=35.54 Aligned_cols=47 Identities=19% Similarity=0.258 Sum_probs=40.1
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
-|-.||-+.++++.++++||++.+|+++.+++|=|..|.. .++|.+.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~--~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEE--QGLLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHH--CCcEEEE
Confidence 3567888889999999999999999999999999999963 4566654
No 87
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=58.07 E-value=30 Score=29.32 Aligned_cols=64 Identities=16% Similarity=0.210 Sum_probs=47.6
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCC---CeEEEccCCC
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQS---DHFEFNSKFT 357 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~---~~f~~N~~f~ 357 (453)
..+|-+..+.+..|+.|+++.+|-+...+.+.|..|.+ ++++..+.+++.-.+. +.+.++-.|.
T Consensus 67 leLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~--~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 67 LELLELIAQEEPASINELAELVGRDVKNVHRTLSTLAD--LGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHh--cCeEEEecCCcccCceeeccccEEeeecC
Confidence 34566777888999999999999999999999999964 6888766555443322 4455665554
No 88
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=57.97 E-value=23 Score=24.16 Aligned_cols=39 Identities=18% Similarity=0.312 Sum_probs=29.5
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
+.-+.-++.++. .+++..+|++.+|++...+.+.+..+.
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 444555555553 357999999999999999999887664
No 89
>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=57.46 E-value=28 Score=26.62 Aligned_cols=39 Identities=10% Similarity=0.208 Sum_probs=28.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
+.-.+|-+.-....+|..+|+..+|.+.+++...|..+.
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 344566677888999999999999999999999998874
No 90
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=56.53 E-value=20 Score=25.10 Aligned_cols=35 Identities=17% Similarity=0.218 Sum_probs=29.7
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 301 SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 301 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.+..|..+|++.+|++...+.+.|..|.. .+++..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeee
Confidence 56789999999999999999999999974 456654
No 91
>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=56.53 E-value=26 Score=24.04 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=28.1
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 289 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 289 ~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
..|.-++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 3 ~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 3 PREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34444454442 467999999999999999988887653
No 92
>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=56.35 E-value=16 Score=29.92 Aligned_cols=57 Identities=9% Similarity=0.113 Sum_probs=42.7
Q ss_pred eeehhcc-CCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEe
Q 012914 392 LVRIMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 451 (453)
Q Consensus 392 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Y 451 (453)
|..+|.. .+.++.++|...+.++ ...++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~---~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKK---GPSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhc---CCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4445554 5579999999988764 2457889999999999999999997644344444
No 93
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=56.00 E-value=33 Score=30.60 Aligned_cols=55 Identities=20% Similarity=0.184 Sum_probs=40.7
Q ss_pred EEEEEcHHHHHHHHhhcCCCCc-CHHHHHHHh--CCChHHHHHHHhHhhhcccceeecCC
Q 012914 283 IELIVSTYQAATLLLFNTSDRL-SYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 283 ~~l~vs~~Qa~ILllFn~~~~~-t~~ei~~~t--~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+++--+.+..+|+-+..-.+.- +.++|++.+ +++.++++.+|..|. +.++|.+..
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 3333445556666665544433 899999999 999999999999996 578998753
No 94
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=55.73 E-value=21 Score=32.15 Aligned_cols=64 Identities=16% Similarity=0.164 Sum_probs=48.8
Q ss_pred CceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 260 HRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTS--DRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 260 ~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Qa~ILllFn~~--~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
.|.-.|.+.+|..+++- .+.| .||+.||.-|+.-... ..||.+.|++..+++.+++...|..+.
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 3333 5778999888764433 489999999999999999999888774
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=54.17 E-value=23 Score=26.10 Aligned_cols=24 Identities=17% Similarity=0.499 Sum_probs=20.5
Q ss_pred ChhHHHHHHHhhhhhccccccCCC
Q 012914 422 DIKAIKKRMEDLITRDYLERDKEN 445 (453)
Q Consensus 422 ~~~~ik~~Ie~LIereyi~R~~~d 445 (453)
|..-+...++.|.++|||+|+++-
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 466778899999999999999853
No 96
>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=54.08 E-value=1.1e+02 Score=26.95 Aligned_cols=59 Identities=22% Similarity=0.255 Sum_probs=43.3
Q ss_pred HHHHHHhhcCCC-CcCHHHHHHHh--CCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 012914 291 QAATLLLFNTSD-RLSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 355 (453)
Q Consensus 291 Qa~ILllFn~~~-~~t~~ei~~~t--~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~ 355 (453)
...|+-.+..++ ++|..+|...+ +++...+.++|..|+. +.+|..+. +...-+|..|.+
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 356777776655 99999999998 5899999999999985 34566553 223456777755
No 97
>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=54.07 E-value=22 Score=27.44 Aligned_cols=35 Identities=3% Similarity=-0.031 Sum_probs=30.3
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
-++.|+-.... ..+|+.+|++..|++...+.+.|.
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 46678877888 899999999999999999988774
No 98
>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=53.48 E-value=13 Score=33.59 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=22.4
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
.+|+++|++.||+..+++..+|+.|
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 99
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=53.42 E-value=22 Score=33.89 Aligned_cols=47 Identities=15% Similarity=0.129 Sum_probs=39.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
-|..|+..++++..+++.||++.+|++...+++-|..|.. .+++.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~--~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDE--SGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEe
Confidence 4667888899999999999999999999999999999963 3566554
No 100
>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=53.25 E-value=35 Score=31.24 Aligned_cols=44 Identities=14% Similarity=0.171 Sum_probs=34.9
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
.||......+.+|..+|++.+|++...+.++|..|.. .+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~--~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLET--EGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEe
Confidence 3454444456799999999999999999999999974 4677654
No 101
>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=52.99 E-value=27 Score=30.80 Aligned_cols=43 Identities=14% Similarity=0.163 Sum_probs=34.1
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
..|+...-.+..+|-+||++.+|++..++.+.|..|.. .+++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e--~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYD--AGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCce
Confidence 44555444556899999999999999999999999975 35663
No 102
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.98 E-value=19 Score=32.41 Aligned_cols=44 Identities=14% Similarity=0.108 Sum_probs=35.6
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 291 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 291 Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
...||.+.-.+..+|-++|++.+|++...++++|..|.. .+++.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e--~gLv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYD--ARLAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeE
Confidence 345666555667899999999999999999999999974 35655
No 103
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=52.62 E-value=23 Score=33.02 Aligned_cols=49 Identities=24% Similarity=0.318 Sum_probs=41.4
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
|..-..||-+......+.+.||++.+|+|...+..+++.|. +.+++..+
T Consensus 22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le--~aGlirT~ 70 (308)
T COG4189 22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLE--KAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHH--hcCceeee
Confidence 44556788888888899999999999999999999999996 56777644
No 104
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=51.75 E-value=20 Score=26.09 Aligned_cols=35 Identities=20% Similarity=0.295 Sum_probs=26.5
Q ss_pred CCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 300 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 300 ~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
.++..|+.+|...|++|...++.+|-.|.. .+++.
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 445889999999999999999999999964 45543
No 105
>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=50.92 E-value=9.2 Score=28.30 Aligned_cols=54 Identities=26% Similarity=0.253 Sum_probs=31.3
Q ss_pred cceeeehhccCC-CCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 389 DAALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 389 ~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
=|.||..||++. .++.+||..++ + +..+ ...++.|-+.+=|+-|++ .++|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l----~--~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYL----S--LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHH----T--SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHH----c--CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 366888899874 47777776654 3 3333 245566668889999874 47999975
No 106
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=50.35 E-value=23 Score=26.14 Aligned_cols=51 Identities=20% Similarity=0.253 Sum_probs=34.3
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-hHHHHHHHhHhhhcccceeecCC
Q 012914 287 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 287 vs~~Qa~ILllFn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+|.-|.-||...-+ +-.-|+.||++.+|+. ...+..+|..|.. .+.|.+.+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~--kG~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALER--KGYIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH--TTSEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH--CcCccCCC
Confidence 35567767654332 2356999999999997 8999999999963 46777654
No 107
>PRK00215 LexA repressor; Validated
Probab=50.33 E-value=39 Score=30.90 Aligned_cols=51 Identities=22% Similarity=0.244 Sum_probs=39.5
Q ss_pred EcHHHHHHHHhhc-----CCCCcCHHHHHHHhCC-ChHHHHHHHhHhhhcccceeecCC
Q 012914 287 VSTYQAATLLLFN-----TSDRLSYSEIMTQLNL-THDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 287 vs~~Qa~ILllFn-----~~~~~t~~ei~~~t~i-~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
++.-|..+|.... .....|+.||++.+|+ +...+.+.|..|.. .+.+.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~--~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALER--KGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHH--CCCEEeCC
Confidence 3567888886554 2346899999999999 99999999999974 46676554
No 108
>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=50.20 E-value=21 Score=35.53 Aligned_cols=143 Identities=13% Similarity=0.173 Sum_probs=38.4
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCccee
Q 012914 286 IVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRI 363 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~~~~~~i 363 (453)
.++..+..|+-+..+ ..++-..+|...||++...+.++|.+|.. | +++.... +.+.+++|+
T Consensus 81 ~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~-k-~lIK~vk---------------sv~~~~rK~ 143 (327)
T PF05158_consen 81 GLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLES-K-KLIKSVK---------------SVKNPNRKV 143 (327)
T ss_dssp SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHH-T-TSEEEE-----------------SS-SS--E
T ss_pred CCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHh-C-CCEEEec---------------CcCCCCeEE
Confidence 456677777766654 45888999999999999999999999975 2 4544211 112233333
Q ss_pred eccCC--Cchhh-h---hhHHhHHHhhhhhhcceeeehhccCCC-----------------------------CChhHHH
Q 012914 364 KIPLP--PVDER-K---KIVEDVDKDRRYAIDAALVRIMKSRKV-----------------------------LGHQQLV 408 (453)
Q Consensus 364 ~i~~~--~~~e~-~---~~~~~v~~~R~~~i~A~IVRimK~~k~-----------------------------l~~~~L~ 408 (453)
-+... |..|- . =+..+.+.+=...+...|.+.+.++.. .+.+++.
T Consensus 144 Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~ 223 (327)
T PF05158_consen 144 YMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIA 223 (327)
T ss_dssp EEESSS--------------------------------------------------------------------------
T ss_pred EEEccCCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHH
Confidence 22211 00000 0 001122222233344444444444433 3444444
Q ss_pred HHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCC
Q 012914 409 SECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 445 (453)
Q Consensus 409 ~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d 445 (453)
..+.+.=-..-..+.++|...|+-|+=.|-|++-...
T Consensus 224 ~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~ 260 (327)
T PF05158_consen 224 EFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSG 260 (327)
T ss_dssp -------------------------------------
T ss_pred HHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEecc
Confidence 4444331112456889999999999999988886543
No 109
>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=49.95 E-value=40 Score=23.92 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=29.5
Q ss_pred cCCCCc-CHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 299 NTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 299 n~~~~~-t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
.....+ |..+|++.+|++...+.++|..|.. .++|...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELEA--EGLVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 333334 5999999999999999999999974 4677643
No 110
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=49.13 E-value=25 Score=33.43 Aligned_cols=39 Identities=21% Similarity=0.224 Sum_probs=36.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
-|..|+.+.+.+..+++.||++.+|+++..++|-|..|.
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 577899999999999999999999999999999999885
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=48.96 E-value=30 Score=24.45 Aligned_cols=39 Identities=15% Similarity=0.224 Sum_probs=31.2
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
|.-+..||.++.. +.+..||++.+|+++..+..++..+.
T Consensus 5 T~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 5 TERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp -HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 5566777777766 45899999999999999999998886
No 112
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=48.20 E-value=26 Score=33.43 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=39.5
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
-+..|+...++.+.+++.||++.++++...++|-|..|.. .++|.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~--~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAE--QNKILRH 52 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 4567787888889999999999999999999999999964 3566654
No 113
>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=47.96 E-value=14 Score=25.06 Aligned_cols=44 Identities=7% Similarity=0.274 Sum_probs=32.5
Q ss_pred cceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhcccc
Q 012914 389 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLE 440 (453)
Q Consensus 389 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~ 440 (453)
+-.|+..+.....++..+|-.. +..+.+-+...|..|.+.|||+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~--------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEK--------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHH--------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH--------hCCCHHHHHHHHHHHHHCcCcC
Confidence 3345667777777888777664 3468889999999999999985
No 114
>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=47.92 E-value=29 Score=24.55 Aligned_cols=30 Identities=17% Similarity=0.424 Sum_probs=25.1
Q ss_pred hcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 298 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 298 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
|+.-...|.+||++.+|++...+..+|..-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 555568999999999999999888888653
No 115
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=47.09 E-value=26 Score=33.73 Aligned_cols=48 Identities=6% Similarity=0.065 Sum_probs=40.3
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 289 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 289 ~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
--|..|+.+.+....+++.||++.+|++...++|-|..|.. .+++.+.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~--~G~l~r~ 64 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEK--QGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHh--CCCeEEE
Confidence 35778888899998999999999999999999999999953 3555543
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=46.37 E-value=14 Score=34.59 Aligned_cols=33 Identities=9% Similarity=0.235 Sum_probs=28.9
Q ss_pred cCCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 417 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 417 ~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
.+|..+...+.++|+.|++.|+|.|..+ +++|+
T Consensus 32 ~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 32 DQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 3599999999999999999999999874 56765
No 117
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=46.30 E-value=32 Score=22.47 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=20.5
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 301 SDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 301 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
...+|+++|++..|++...+.+..+...
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 4579999999999999999988876553
No 118
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=45.80 E-value=35 Score=29.66 Aligned_cols=48 Identities=13% Similarity=0.225 Sum_probs=39.8
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
++..--.||..+......|+.+|++.+|+++..+.+-++.|.. .+++.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~--~GvI~ 54 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ--AGIIT 54 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 4556667888888888999999999999999999999999975 34554
No 119
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=45.31 E-value=21 Score=33.40 Aligned_cols=54 Identities=22% Similarity=0.379 Sum_probs=43.6
Q ss_pred eeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 392 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 392 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
-|-..|+.|.+..+||-. .|....++.-.+|..|+..|.|.-.-+|++.|+||.
T Consensus 205 Fv~YIk~nKvV~ledLas--------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLAS--------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHH--------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 345567777777777655 477777888889999999999998888999999984
No 120
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=45.01 E-value=25 Score=23.87 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=21.4
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 294 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 294 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
++.++.+ ++|..+|++.+|++...+.+-+..+
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4444444 7899999999999999998877655
No 121
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=44.72 E-value=34 Score=30.20 Aligned_cols=48 Identities=13% Similarity=0.171 Sum_probs=40.1
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
+.-.-.-||....+....|+.+|++.+|++...+.+-++.|.. .+++.
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 3446667888888889999999999999999999999999964 35554
No 122
>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=44.69 E-value=31 Score=21.64 Aligned_cols=26 Identities=27% Similarity=0.482 Sum_probs=20.8
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
.+|-+||++.+|+..+.+-|.|..|.
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 123
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=44.45 E-value=16 Score=29.45 Aligned_cols=46 Identities=11% Similarity=0.223 Sum_probs=38.0
Q ss_pred hcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccc
Q 012914 388 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 441 (453)
Q Consensus 388 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R 441 (453)
+|-.|++.+.....++..+|-.. +..+...+.++|..|.++|+|+|
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~--------l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK--------VGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeec
Confidence 35567788888888888877765 45788999999999999999995
No 124
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=43.99 E-value=31 Score=31.23 Aligned_cols=40 Identities=13% Similarity=0.067 Sum_probs=36.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
-+..|+.+.+.+..+++.+|++.+|++...++|-|..|..
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~ 47 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI 47 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc
Confidence 5677888889999999999999999999999999999963
No 125
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=43.57 E-value=28 Score=31.70 Aligned_cols=50 Identities=18% Similarity=0.151 Sum_probs=39.5
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-hHHHHHHHhHhhhcccceeecC
Q 012914 287 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 287 vs~~Qa~ILllFn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
++..|..||....+ .-..|+.||++.+|++ ...+.++|..|.. .++|.+.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~--~g~i~~~ 59 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALER--KGYIERD 59 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHH--CCCEecC
Confidence 46788888876553 2258899999999999 9999999999963 4677664
No 126
>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=43.51 E-value=33 Score=25.82 Aligned_cols=25 Identities=20% Similarity=0.433 Sum_probs=17.4
Q ss_pred CChhHHHHHHHhhhhhccccccCCCCCce
Q 012914 421 PDIKAIKKRMEDLITRDYLERDKENPNMF 449 (453)
Q Consensus 421 ~~~~~ik~~Ie~LIereyi~R~~~d~~~y 449 (453)
.+...+. ..||+-|||+|+++ .+.|
T Consensus 44 ~D~a~LR---R~LVd~g~L~R~~d-g~~Y 68 (71)
T PF09860_consen 44 DDYATLR---RYLVDYGLLERTRD-GSRY 68 (71)
T ss_pred ccHHHHH---HHHHHcCCeeecCC-CCee
Confidence 3444444 46999999999984 4556
No 127
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=43.45 E-value=79 Score=24.38 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=32.5
Q ss_pred HhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 296 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 296 llFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
+.-++.+-+|-++|++.+|++...+-++++.|-...+.|..
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 34556668999999999999999999999999644444443
No 128
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=43.40 E-value=16 Score=34.34 Aligned_cols=32 Identities=22% Similarity=0.298 Sum_probs=27.8
Q ss_pred CCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 418 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 418 ~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
.|..+...++++|+.|++.|+|.|... +++|+
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 578899999999999999999999874 56765
No 129
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=43.29 E-value=40 Score=32.58 Aligned_cols=38 Identities=18% Similarity=0.299 Sum_probs=30.8
Q ss_pred HHHHHHHhhc-CCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 290 YQAATLLLFN-TSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 290 ~Qa~ILllFn-~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+...|+-.+. ....+|+++|++.|||..+++..+|++|
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 4455555443 3568999999999999999999999988
No 130
>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=43.02 E-value=63 Score=21.35 Aligned_cols=39 Identities=26% Similarity=0.367 Sum_probs=27.8
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+..+..++.++- ..++|..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444444554432 246799999999999999998877654
No 131
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=42.95 E-value=32 Score=34.84 Aligned_cols=64 Identities=22% Similarity=0.286 Sum_probs=42.0
Q ss_pred EEeccCCceEEEEeEecCeeEEEEE-------cHHHHHHHHhhcC-CC-CcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 263 LTWIYSLGQCNINGKFEQKNIELIV-------STYQAATLLLFNT-SD-RLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 263 L~w~~~lg~~~i~~~~~~~~~~l~v-------s~~Qa~ILllFn~-~~-~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
+.+.|.||..|-++--+ .+-|.= +-+-..||-++-+ ++ .+|+.+|++.|||..+++...|++|-
T Consensus 282 IdFSYeLSr~E~~~GsP--EKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 282 IDFSYELSRREGKIGSP--EKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhcccCcCCCC--CCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 56778888877654322 222321 2233344433333 22 39999999999999999999999983
No 132
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=42.78 E-value=38 Score=35.68 Aligned_cols=50 Identities=14% Similarity=0.169 Sum_probs=43.5
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.+|..|..||......+.+|..+|++.+|++...+.+.+.+|.. | +++..
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~-k-GlV~~ 52 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEE-K-GLVKV 52 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHh-C-CCEEE
Confidence 46889999999998888999999999999999999999999974 2 56654
No 133
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=42.77 E-value=15 Score=26.70 Aligned_cols=32 Identities=13% Similarity=0.280 Sum_probs=26.0
Q ss_pred cCCCCChhHHHHHHHhhhhhccccccCCCCCce
Q 012914 417 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 449 (453)
Q Consensus 417 ~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y 449 (453)
++|..+..-+.+++..|.+.|+|.+.+. ++++
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 3588999999999999999999999874 4444
No 134
>PRK13239 alkylmercury lyase; Provisional
Probab=42.46 E-value=48 Score=30.59 Aligned_cols=39 Identities=13% Similarity=0.242 Sum_probs=34.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
+...||.++-++..+|+.+|++.+|.+.+.+.+.|+.|.
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 555677778888999999999999999999999999884
No 135
>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=42.42 E-value=13 Score=26.50 Aligned_cols=26 Identities=12% Similarity=0.332 Sum_probs=21.0
Q ss_pred CCCChhHHHHHHHhhhhhccccccCC
Q 012914 419 FKPDIKAIKKRMEDLITRDYLERDKE 444 (453)
Q Consensus 419 F~~~~~~ik~~Ie~LIereyi~R~~~ 444 (453)
+..+.+-+.+.|..|+++|||+|..+
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 34678889999999999999999754
No 136
>PHA02591 hypothetical protein; Provisional
Probab=41.77 E-value=33 Score=26.25 Aligned_cols=24 Identities=21% Similarity=0.321 Sum_probs=21.9
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhH
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
++|.++|++.+|++.+.+.+.|.+
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHhc
Confidence 789999999999999999988865
No 137
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=41.75 E-value=18 Score=34.04 Aligned_cols=33 Identities=6% Similarity=0.401 Sum_probs=28.7
Q ss_pred cCCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 417 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 417 ~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
..|..+...++++|+.|++.|+|.|..+ +++|+
T Consensus 43 ~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 43 ARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 3688999999999999999999999875 56665
No 138
>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=41.23 E-value=18 Score=33.79 Aligned_cols=32 Identities=16% Similarity=0.380 Sum_probs=28.3
Q ss_pred CCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 418 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 418 ~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
+|..+...+.++|+.|.+.|||.|... +++|+
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 589999999999999999999999874 56665
No 139
>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=40.65 E-value=46 Score=26.66 Aligned_cols=53 Identities=8% Similarity=0.156 Sum_probs=43.3
Q ss_pred hcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccc
Q 012914 388 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 441 (453)
Q Consensus 388 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R 441 (453)
++-+|..++. .+.++=-+|.+++.+...+.+.++...+=..+..|-++|+|++
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 4445566665 4678888999998887665678899999999999999999998
No 140
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=40.65 E-value=34 Score=29.63 Aligned_cols=31 Identities=13% Similarity=0.201 Sum_probs=27.5
Q ss_pred CCCCcCHHHHHHHhCCChHHHHHHHhHhhhc
Q 012914 300 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCA 330 (453)
Q Consensus 300 ~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 330 (453)
.+..+|-++|++.+|++...+++.|..|...
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed 42 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDE 42 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhh
Confidence 4457999999999999999999999999753
No 141
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=40.11 E-value=23 Score=27.80 Aligned_cols=37 Identities=22% Similarity=0.216 Sum_probs=33.0
Q ss_pred cCCCCChhHHHHHHHhhhhhccccccCCCCCceEecC
Q 012914 417 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 453 (453)
Q Consensus 417 ~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 453 (453)
.++....+.-++.|..|.++|.|..-..++..-+|.|
T Consensus 49 erlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 49 SKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 3677899999999999999999998888888999975
No 142
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=39.92 E-value=43 Score=31.67 Aligned_cols=40 Identities=25% Similarity=0.309 Sum_probs=35.3
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
-|..|+..+++++.++++||++.+|++...+++-|..|..
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3566788888888999999999999999999999999964
No 143
>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=39.75 E-value=11 Score=26.70 Aligned_cols=41 Identities=12% Similarity=0.272 Sum_probs=28.3
Q ss_pred hhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccC
Q 012914 395 IMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 395 imK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
++-....++..+|-. .+..+..-+-+.+..|.++|||+|..
T Consensus 11 ~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 11 ILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 333444455554443 34568899999999999999999864
No 144
>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=39.50 E-value=54 Score=25.88 Aligned_cols=33 Identities=12% Similarity=0.307 Sum_probs=22.9
Q ss_pred hhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhc
Q 012914 297 LFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCA 330 (453)
Q Consensus 297 lFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 330 (453)
+..+... ++..|.+.||||...++.+|.+|...
T Consensus 16 li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~ 48 (90)
T PF09904_consen 16 LIDSGER-NVPALMEATGMPRRTIQDTIKALPEL 48 (90)
T ss_dssp HHHHS-B--HHHHHHHH---HHHHHHHHHGGGGG
T ss_pred HHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcC
Confidence 3444445 99999999999999999999999643
No 145
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=39.37 E-value=22 Score=24.74 Aligned_cols=28 Identities=7% Similarity=0.172 Sum_probs=24.4
Q ss_pred cCCCCChhHHHHHHHhhhhhccccccCC
Q 012914 417 RMFKPDIKAIKKRMEDLITRDYLERDKE 444 (453)
Q Consensus 417 ~~F~~~~~~ik~~Ie~LIereyi~R~~~ 444 (453)
.+|..+..-+.+.+..|.+.|+|.+.++
T Consensus 28 ~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 28 AQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3577899999999999999999998764
No 146
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=38.67 E-value=78 Score=21.55 Aligned_cols=35 Identities=17% Similarity=0.360 Sum_probs=25.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhH
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
+.+.|+.+.-+. .|+.+++..+|++...+.+.+..
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 444454443332 69999999999999999988764
No 147
>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=37.88 E-value=70 Score=22.24 Aligned_cols=41 Identities=20% Similarity=0.257 Sum_probs=32.4
Q ss_pred HhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 296 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 296 llFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
-+|.+++.+|+.++.+.+|++-+.....|.-|= +.++..+.
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 467788899999999999999999988888883 45666553
No 148
>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=36.68 E-value=1.4e+02 Score=21.71 Aligned_cols=32 Identities=13% Similarity=0.231 Sum_probs=26.6
Q ss_pred hhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 297 LFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 297 lFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
...+. ..+..+|++.+|++...+.+.+..|..
T Consensus 8 ~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 8 LLADN-PFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34443 478999999999999999999999964
No 149
>PRK14999 histidine utilization repressor; Provisional
Probab=36.56 E-value=23 Score=33.36 Aligned_cols=47 Identities=15% Similarity=0.289 Sum_probs=35.2
Q ss_pred hhccCCCC-ChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 395 IMKSRKVL-GHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 395 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
.++....+ +-.+|.. .|..+...|+++|+.|.+.|+|.|..+ +++|+
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 4445544 488999999999999999999999874 57765
No 150
>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=36.13 E-value=62 Score=27.14 Aligned_cols=37 Identities=8% Similarity=0.042 Sum_probs=31.3
Q ss_pred cCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 299 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 299 n~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
+..-.+|.++||..++-+.+.++.+|..|. +.+++..
T Consensus 49 ~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~ 85 (121)
T PF09681_consen 49 SGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEI 85 (121)
T ss_pred CCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 344589999999999999999999999996 5677764
No 151
>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=35.43 E-value=26 Score=24.54 Aligned_cols=22 Identities=18% Similarity=0.511 Sum_probs=19.3
Q ss_pred CcCHHHHHHHhCCChHHHHHHH
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLL 324 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L 324 (453)
.+++.||++.+|++..++.+.|
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 152
>PRK06474 hypothetical protein; Provisional
Probab=35.20 E-value=1.2e+02 Score=27.29 Aligned_cols=52 Identities=15% Similarity=0.197 Sum_probs=39.8
Q ss_pred EEEcHHHHHHHHhhcCCC-CcCHHHHHHHh-CCChHHHHHHHhHhhhcccceeecC
Q 012914 285 LIVSTYQAATLLLFNTSD-RLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 285 l~vs~~Qa~ILllFn~~~-~~t~~ei~~~t-~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
+-.++.-..||..+...+ .+|..+|++.+ +++...+-++|..|.. .+++...
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e--~GLI~~~ 60 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVD--SGILHVV 60 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 344566677776665544 49999999999 7999999999999974 5777654
No 153
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=34.96 E-value=25 Score=33.07 Aligned_cols=35 Identities=17% Similarity=0.384 Sum_probs=29.6
Q ss_pred hccCCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 415 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 415 l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
|..+|.+|...++++|..|.+.|+|.|-.+ +++|+
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 334699999999999999999999999874 56665
No 154
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=34.76 E-value=78 Score=27.11 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=38.8
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
.-.-.-||.........++.+|++.+|++...+.+.+..|.. .+++.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~--~GiI~ 53 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEE--EGVIK 53 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCcee
Confidence 445567787888888899999999999999999999999964 45665
No 155
>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=34.61 E-value=76 Score=27.27 Aligned_cols=40 Identities=23% Similarity=0.225 Sum_probs=31.8
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
.+|.-|..|+.++ ..++|.+||++.+|++...+...+...
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 468899999999999998887665544
No 156
>PLN03239 histone acetyltransferase; Provisional
Probab=34.55 E-value=60 Score=32.38 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=29.9
Q ss_pred HHHHHHHhhcCC----CCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 290 YQAATLLLFNTS----DRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 290 ~Qa~ILllFn~~----~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+...|+-.+-+. ..+|+++|+..|||..+++..+|+.|
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 455566544222 46999999999999999999999988
No 157
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=34.15 E-value=80 Score=26.60 Aligned_cols=41 Identities=15% Similarity=0.308 Sum_probs=36.4
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 289 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 289 ~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
.+.+-|+-+--++..+|+.++...||++-..+.+++.-|+.
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa 52 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA 52 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35677788888889999999999999999999999999974
No 158
>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=33.84 E-value=51 Score=22.44 Aligned_cols=21 Identities=14% Similarity=0.390 Sum_probs=18.9
Q ss_pred CHHHHHHHhCCChHHHHHHHh
Q 012914 305 SYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 305 t~~ei~~~t~i~~~~l~~~L~ 325 (453)
|+.||++..|++...+-+.|+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 688999999999999988875
No 159
>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=33.68 E-value=61 Score=23.39 Aligned_cols=39 Identities=21% Similarity=0.356 Sum_probs=29.9
Q ss_pred cCCCCc-CHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 299 NTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 299 n~~~~~-t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
..++.+ |..+|++..|++...+.++|..|.. .+++...+
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~--~g~i~~~~ 58 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEA--EGLIERRP 58 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEET
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHH--CCcEEEEC
Confidence 345678 9999999999999999999999974 46776543
No 160
>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=33.33 E-value=31 Score=26.27 Aligned_cols=57 Identities=19% Similarity=0.211 Sum_probs=33.2
Q ss_pred hhcceeeehhccCC--CCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccc---cccCCCCCceEecC
Q 012914 387 AIDAALVRIMKSRK--VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYL---ERDKENPNMFRYLA 453 (453)
Q Consensus 387 ~i~A~IVRimK~~k--~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi---~R~~~d~~~y~Yia 453 (453)
..=|.||..||++. .++.+|+..++.. +... ..++ +.|-+-.-+ +-+.. .++|.|.|
T Consensus 9 t~l~~aV~ymK~r~~~Plt~~EIl~~ls~-----~d~~-~~~~---~~L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 9 TQLAKIVDYMKKRHQHPLTLDEILDYLSL-----LDIG-PKLK---EWLKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhHHHHHHHHHhcCCCCccHHHHHHHHhc-----cCcc-HHHH---HHHHhhhhccCceeccC-CCEEEecc
Confidence 34578899999987 5888888777642 2222 2222 333332333 44443 46899875
No 161
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=33.03 E-value=62 Score=31.29 Aligned_cols=57 Identities=14% Similarity=0.274 Sum_probs=32.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCC
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 356 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f 356 (453)
+--.|.-+|.++..|++.+|.+.|+=|+..|+.+|..++ ++.+.++ -...|.+=.+|
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 445677789999999999999999999999999999875 5555432 12456665554
No 162
>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=32.67 E-value=1.6e+02 Score=22.67 Aligned_cols=48 Identities=15% Similarity=0.240 Sum_probs=37.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCC
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 339 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~ 339 (453)
+++.|=+.-.....+.-.+|++.++++...++..+..|- ..++|.+.|
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 444444555566789999999999999999999999995 357886543
No 163
>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=32.49 E-value=79 Score=27.07 Aligned_cols=38 Identities=21% Similarity=0.288 Sum_probs=28.2
Q ss_pred EcHHHHHHHHh-hcCCCCcCHHHHHHHhCCChHHHHHHHhH
Q 012914 287 VSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 287 vs~~Qa~ILll-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
+|+-|..|+.+ +- .+++++||++.+|++...+...+.-
T Consensus 112 L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 112 LPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 44555555554 43 4689999999999999988877654
No 164
>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=32.11 E-value=79 Score=23.83 Aligned_cols=48 Identities=15% Similarity=0.180 Sum_probs=38.4
Q ss_pred HHHHHHHHhhcC--CCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 289 TYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 289 ~~Qa~ILllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
..|.++|...-. .++++-.+|...+|++...+-..+..|.. .+++.+.
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~--~gLI~k~ 51 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEK--KGLIVKQ 51 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHH--CCCEEEE
Confidence 467778877654 45889999999999999999999999964 4676654
No 165
>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=32.02 E-value=48 Score=24.85 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=20.3
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
..-|.+||++.+|++.+.+...+...
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 166
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=32.01 E-value=32 Score=32.32 Aligned_cols=32 Identities=13% Similarity=0.275 Sum_probs=28.1
Q ss_pred CCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 418 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 418 ~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
.|..+...|+++|+.|...|+|.|... +++|+
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 56664
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=31.93 E-value=30 Score=32.20 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=28.3
Q ss_pred CCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 418 MFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 418 ~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
.|..+...|.++|..|.+.|+|.|..+ +++|+
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 589999999999999999999999874 56664
No 168
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=31.64 E-value=2e+02 Score=26.17 Aligned_cols=111 Identities=15% Similarity=0.154 Sum_probs=57.1
Q ss_pred CHHHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeE--e-------cCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHH
Q 012914 240 PSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGK--F-------EQKNIELIVSTYQAATLLLFNTSDRLSYSEIM 310 (453)
Q Consensus 240 P~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~--~-------~~~~~~l~vs~~Qa~ILllFn~~~~~t~~ei~ 310 (453)
|.++..+++....-|.....+ +.-...-|...+..+ + ......-..|...+-+|-..--+..+|-.||.
T Consensus 34 ~~~v~~~l~~L~~~y~~~~~g--i~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~ 111 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGDDRG--LKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEID 111 (188)
T ss_pred HHHHHHHHHHHHHHHhhCCCC--EEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHH
Confidence 357888999999999765333 322221222222111 0 01111223444444445444444589999999
Q ss_pred HHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCC
Q 012914 311 TQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 357 (453)
Q Consensus 311 ~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~ 357 (453)
+..|++...+ +..|.. .+++...+..........|.++..|-
T Consensus 112 ~irGv~~~~i---i~~L~~--~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNSDGA---LQTLLA--KGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCHHHH---HHHHHH--CCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999997554 444432 35655322111111234566666664
No 169
>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=31.32 E-value=89 Score=24.44 Aligned_cols=40 Identities=23% Similarity=0.257 Sum_probs=31.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
....+.-++.....+++++|++.++++.+++...+..+..
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 4444555566788999999999999999999999988864
No 170
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=31.13 E-value=68 Score=30.14 Aligned_cols=58 Identities=10% Similarity=0.212 Sum_probs=43.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCC
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 357 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~ 357 (453)
+-..+.-+|.++..||+.+|.+.|+=|...|+.+|..++ ++.+.++ -..+|.+-.+|.
T Consensus 187 vld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-----v~NkKg~-----~k~tyeLKPEYK 244 (254)
T KOG2905|consen 187 VLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-----VLNKKGP-----YKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-----HHhccCc-----ccCceecCHHHh
Confidence 334556689999999999999999999999999999886 4443221 135677766664
No 171
>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=31.10 E-value=97 Score=24.15 Aligned_cols=45 Identities=16% Similarity=0.205 Sum_probs=35.3
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHh-CCChHHHHHHHhHhhhcccceeecC
Q 012914 291 QAATLLLFNTSDRLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 291 Qa~ILllFn~~~~~t~~ei~~~t-~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
-+.||..... +...+.||.+.+ |++...|.+.|..|.. .+++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~--~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEE--AGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHH--cchhhcc
Confidence 3566666555 688999999999 9999999999999974 5777653
No 172
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=31.05 E-value=39 Score=27.48 Aligned_cols=41 Identities=17% Similarity=0.340 Sum_probs=30.0
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccc--cCCCC
Q 012914 398 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER--DKENP 446 (453)
Q Consensus 398 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R--~~~d~ 446 (453)
....++..+|... ...+..-+-+.|..|.++|||.| ++.|+
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 3355666666553 44677889999999999999997 55554
No 173
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=30.98 E-value=31 Score=29.65 Aligned_cols=50 Identities=12% Similarity=0.247 Sum_probs=41.5
Q ss_pred hhhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccC
Q 012914 386 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 386 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
..+|..|.+++.....++..+|-..+ ..++..+..||+.|.+.|.|++-.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l--------glS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV--------GLSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCceeeEE
Confidence 34677788889998888988887765 268889999999999999999854
No 174
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=30.78 E-value=59 Score=25.16 Aligned_cols=47 Identities=13% Similarity=0.224 Sum_probs=34.5
Q ss_pred cceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccC
Q 012914 389 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 389 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
+..|...+...+.++..+|... +.++...+.+.|..|.++|+|++..
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~--------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKR--------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH--------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 4455566666667777776554 3467778999999999999998764
No 175
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=30.78 E-value=1.4e+02 Score=21.02 Aligned_cols=41 Identities=17% Similarity=0.198 Sum_probs=35.3
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
.+|.-+..++.++..+ .+..||+...+++...+..++....
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 4577888888888876 7999999999999999999988775
No 176
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=30.63 E-value=76 Score=24.37 Aligned_cols=44 Identities=16% Similarity=0.226 Sum_probs=33.4
Q ss_pred eehhccC-CCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCC
Q 012914 393 VRIMKSR-KVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 444 (453)
Q Consensus 393 VRimK~~-k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~ 444 (453)
+..+... ..++..+|..++ ..+...+.+.+..|.+.|||.+++.
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 3344444 578888877764 4577889999999999999999853
No 177
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=30.57 E-value=5.4e+02 Score=25.45 Aligned_cols=147 Identities=11% Similarity=0.197 Sum_probs=81.8
Q ss_pred CccccccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCcchHHHHHHHHHHHHH-------HHHHHHHhcC
Q 012914 1 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDK-------YMEYVTNCFI 73 (453)
Q Consensus 1 ly~L~~r~~~~l~~l~~~~~~~i~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~-------~~~l~~~~F~ 73 (453)
||-|+++-..||+...+.+.+.|..+..+.++.......+ +..+.-|+..|..|++. ...++..+|+
T Consensus 34 LFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~------~~~~~~~~~~lt~LFe~ia~ii~~h~~lI~~~yG 107 (331)
T PF08318_consen 34 LFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSD------SRSPVFYADALTKLFEHIATIIEQHQPLIEKYYG 107 (331)
T ss_pred HhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc------ccccccHHHHHHHHHHHHHHHHHHccHHHHHHcC
Confidence 4556677789999999999999999999988876432211 12333455555555544 4566778888
Q ss_pred CCHHH--HHHHHHH--------HHHHHhcCCCCCChHHHHHHHHHHHhhc-----------------CCCCCCChHHHHH
Q 012914 74 NHTLF--HKALKEA--------FEIFCNKAVGGSSSSELLATFCDNILKK-----------------GGNEKLSDEAIEE 126 (453)
Q Consensus 74 ~~~~f--~~~l~~a--------f~~~~N~~~~~~~~~e~La~y~d~~l~~-----------------~~~~~~~~~~~~~ 126 (453)
..... ...+..- +..|..... -.+....+..|-...+.+ +.....+.-+++.
T Consensus 108 ~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~-l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~reld~ 186 (331)
T PF08318_consen 108 PGYMVYVIEKLQKECDLQAGIILDTFMDERR-LDRKLQDIQSYNFSFLVKNSGRSSSSSSRAASSSQSEDEGIDPRELDA 186 (331)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-HHHHHHHHHhhhhhhhccccccccccccccccccccccCCCCHHHHHH
Confidence 65321 1112111 111211110 001122233333333322 0012234457788
Q ss_pred HHHHHHHHHhhccChhHHHHHHHHHHHHHHcCCCC
Q 012914 127 TLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRS 161 (453)
Q Consensus 127 ~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s 161 (453)
.|+.+..++.. ...|.++++.|.-....
T Consensus 187 lL~Eis~i~~~-------w~lY~rFi~~k~~~~~~ 214 (331)
T PF08318_consen 187 LLNEISLILQR-------WSLYCRFISRKWNEFSD 214 (331)
T ss_pred HHHHHHHHHHH-------HHHHHHHHHHHHhcccc
Confidence 88888877764 45799999999887543
No 178
>PHA02943 hypothetical protein; Provisional
Probab=30.12 E-value=96 Score=27.10 Aligned_cols=54 Identities=22% Similarity=0.249 Sum_probs=35.7
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEcc
Q 012914 294 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 354 (453)
Q Consensus 294 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~ 354 (453)
||-.+ ..+..|..||++.+|++-..++-+|.-|- |-+.+.+..- .....|.+|+
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 44444 55678899999999999999998888774 3334433221 1234566655
No 179
>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=30.01 E-value=34 Score=27.27 Aligned_cols=27 Identities=33% Similarity=0.615 Sum_probs=19.9
Q ss_pred hccCCCCChhHHHHHHHhhhhhcccccc
Q 012914 415 LSRMFKPDIKAIKKRMEDLITRDYLERD 442 (453)
Q Consensus 415 l~~~F~~~~~~ik~~Ie~LIereyi~R~ 442 (453)
+++.| |...-+..-||.||.-|||.|+
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 33344 3445577899999999999994
No 180
>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=29.93 E-value=40 Score=23.93 Aligned_cols=27 Identities=11% Similarity=0.251 Sum_probs=23.6
Q ss_pred cCCCCChhHHHHHHHhhhhhccccccC
Q 012914 417 RMFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 417 ~~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
.+|..+..-+.+.+..|.++|||.+.+
T Consensus 33 ~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 33 EELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 356788999999999999999999875
No 181
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=29.88 E-value=78 Score=28.89 Aligned_cols=35 Identities=29% Similarity=0.413 Sum_probs=25.1
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhH
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
.+.+++|.+ ..+++++||++.+|++...++..|.-
T Consensus 143 ~r~v~~L~~--~~g~s~~EIA~~Lgis~~tV~~~l~R 177 (203)
T PRK09647 143 FRAAVVLCD--IEGLSYEEIAATLGVKLGTVRSRIHR 177 (203)
T ss_pred HHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 334444544 34679999999999999887776643
No 182
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=29.80 E-value=1e+02 Score=26.65 Aligned_cols=39 Identities=18% Similarity=0.198 Sum_probs=30.4
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhH
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
.+|.-|..||.++ ..++|.+||++.+|++...+...+..
T Consensus 6 ~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 6 FLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4577888888776 36799999999999999776665543
No 183
>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=29.77 E-value=86 Score=26.24 Aligned_cols=47 Identities=19% Similarity=0.217 Sum_probs=36.5
Q ss_pred HHHHHHHHhhcCC--------CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 289 TYQAATLLLFNTS--------DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 289 ~~Qa~ILllFn~~--------~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.+.-..|+..|.. -+.|.++|+..++-+.+.++.+|..|. +++++..
T Consensus 29 I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~ 83 (119)
T TIGR01714 29 IWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEK 83 (119)
T ss_pred HHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 4555555555543 478999999999999999999999996 5677764
No 184
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=29.69 E-value=81 Score=32.67 Aligned_cols=38 Identities=21% Similarity=0.321 Sum_probs=30.1
Q ss_pred HHHHHHHh-hcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 290 YQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 290 ~Qa~ILll-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+-..||-. .+....+|+++|++.|||..+++..+|+.|
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 33445533 344468999999999999999999999988
No 185
>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=29.49 E-value=67 Score=26.36 Aligned_cols=48 Identities=17% Similarity=0.201 Sum_probs=36.6
Q ss_pred CChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEe
Q 012914 402 LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 451 (453)
Q Consensus 402 l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Y 451 (453)
.....++.+|+..+. .+ ++...+--||+.||+.|.++-.++-.++-.|
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 445678888988864 23 6778899999999999999988755444443
No 186
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=29.38 E-value=1.3e+02 Score=22.73 Aligned_cols=42 Identities=21% Similarity=0.241 Sum_probs=29.8
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
+-||.... .++.+..+|+..++++...+.+.|..|.. .+++.
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~--~gLI~ 50 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEE--KGLIK 50 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CcCee
Confidence 45666665 56788999999999999999999999974 46664
No 187
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=29.34 E-value=1e+02 Score=28.63 Aligned_cols=41 Identities=22% Similarity=0.288 Sum_probs=36.3
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
.+|+-+..||.+.-+ ++|..||++.+++++.+++.++..+.
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 568899999988877 57999999999999999999998875
No 188
>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=28.88 E-value=82 Score=25.40 Aligned_cols=51 Identities=18% Similarity=0.310 Sum_probs=33.8
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC----CCCChHHHHHHHHHHHhhcC
Q 012914 64 YMEYVTNCFINHTLFHKALKEAFEIFCNKAV----GGSSSSELLATFCDNILKKG 114 (453)
Q Consensus 64 ~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~----~~~~~~e~La~y~d~~l~~~ 114 (453)
+..++..+...+......+..||+.+++.-+ +.+..++++|+++..++..+
T Consensus 56 ~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~ 110 (113)
T PF02847_consen 56 YSKLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADG 110 (113)
T ss_dssp HHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcC
Confidence 3445555555555666777788888776543 23578899999998888753
No 189
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=28.79 E-value=80 Score=29.47 Aligned_cols=55 Identities=11% Similarity=0.202 Sum_probs=40.9
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecCCCCCCCCCCCeEEEccCCC
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 357 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~f~ 357 (453)
.+.-+|.+.+.||+..|++.+|-|+..|+.+|.+.+ +|.+.++ -...|++-++|.
T Consensus 199 ~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~ia-----vLnKkgp-----ya~kY~LrPEYK 253 (297)
T COG5090 199 MLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIA-----VLNKKGP-----YANKYELRPEYK 253 (297)
T ss_pred HHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHH-----hhhccCc-----ccceeecCHHHH
Confidence 445689999999999999999999999999998875 4544321 123566666554
No 190
>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=28.52 E-value=83 Score=27.10 Aligned_cols=39 Identities=18% Similarity=0.194 Sum_probs=27.4
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+.-|-.++.+.- -.++|.+||++.+|++...++..+..-
T Consensus 112 ~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra 150 (162)
T TIGR02983 112 PARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRA 150 (162)
T ss_pred CHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 344444553322 347899999999999999888776544
No 191
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=28.46 E-value=96 Score=28.61 Aligned_cols=42 Identities=21% Similarity=0.337 Sum_probs=34.1
Q ss_pred EEcHHHHHHHHh------hcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 286 IVSTYQAATLLL------FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 286 ~vs~~Qa~ILll------Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
..|.-|..+|.. |+.-..++..||++.+||++..+..+|..=
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 788999998853 444458999999999999998888877653
No 192
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=28.43 E-value=1e+02 Score=28.56 Aligned_cols=47 Identities=19% Similarity=0.173 Sum_probs=35.1
Q ss_pred EcHHHHHHHHh---hcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhccccee
Q 012914 287 VSTYQAATLLL---FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKIL 335 (453)
Q Consensus 287 vs~~Qa~ILll---Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL 335 (453)
.+.-+.-+++. -+...++|.++|++.+++++..++.++..|+. +.++
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 23356899999999999999999999999975 4566
No 193
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.42 E-value=1e+02 Score=20.49 Aligned_cols=24 Identities=25% Similarity=0.343 Sum_probs=16.2
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHh
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
.++|..+|++.+|.+...+.+.|.
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 194
>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=28.04 E-value=1.2e+02 Score=22.25 Aligned_cols=33 Identities=24% Similarity=0.326 Sum_probs=28.1
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.+|-++|++.+|++...+.+.|..|.. -+++..
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~--~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKD--EGIIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHH--TTSEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 578999999999999999999999964 466654
No 195
>smart00753 PAM PCI/PINT associated module.
Probab=28.00 E-value=85 Score=24.05 Aligned_cols=31 Identities=16% Similarity=0.248 Sum_probs=26.8
Q ss_pred cCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 299 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 299 n~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
.....+++++|++.++++.+++...+..++.
T Consensus 20 ~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~ 50 (88)
T smart00753 20 EPYSSISLSDLAKLLGLSVPEVEKLVSKAIR 50 (88)
T ss_pred HHhceeeHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 3467899999999999999999998888864
No 196
>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=28.00 E-value=85 Score=24.05 Aligned_cols=31 Identities=16% Similarity=0.248 Sum_probs=26.8
Q ss_pred cCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 299 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 299 n~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
.....+++++|++.++++.+++...+..++.
T Consensus 20 ~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~ 50 (88)
T smart00088 20 EPYSSISLSDLAKLLGLSVPEVEKLVSKAIR 50 (88)
T ss_pred HHhceeeHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 3467899999999999999999998888864
No 197
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=27.90 E-value=44 Score=28.50 Aligned_cols=26 Identities=8% Similarity=0.266 Sum_probs=22.1
Q ss_pred CCCCChhHHHHHHHhhhhhccccccC
Q 012914 418 MFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 418 ~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 35567788999999999999999964
No 198
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=27.87 E-value=95 Score=27.08 Aligned_cols=34 Identities=24% Similarity=0.292 Sum_probs=24.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 290 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 290 ~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
.+.++.|.+- +++|++||++.+|++...++..|.
T Consensus 123 ~r~v~~L~~~--eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 123 ARAAFLMSQL--EGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred HHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3444444443 467999999999999988776653
No 199
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=27.76 E-value=30 Score=32.97 Aligned_cols=45 Identities=16% Similarity=0.345 Sum_probs=39.8
Q ss_pred ceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhcccccc
Q 012914 390 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 442 (453)
Q Consensus 390 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~ 442 (453)
-.|+.+++.++.++.+||.+ +|..|...|.+=|..|-++|+|.|.
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~--------~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKEKGKVSVEELAE--------LFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHH--------HhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 35778888999999888877 5899999999999999999999994
No 200
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=27.72 E-value=1.1e+02 Score=28.26 Aligned_cols=42 Identities=21% Similarity=0.302 Sum_probs=37.1
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhh
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 329 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 329 (453)
..|.-|..||.++-+ ++|..||++.+++++.+++.+...+..
T Consensus 148 ~LT~RE~eVL~lla~--G~snkeIA~~L~iS~~TVk~h~~~i~~ 189 (211)
T COG2197 148 LLTPRELEVLRLLAE--GLSNKEIAEELNLSEKTVKTHVSNILR 189 (211)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHhHHHHHHHHHHH
Confidence 578899999998877 579999999999999999999988763
No 201
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.63 E-value=99 Score=26.57 Aligned_cols=23 Identities=26% Similarity=0.203 Sum_probs=20.0
Q ss_pred CcCHHHHHHHhCCChHHHHHHHh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
++|++||++.+|++...++..|.
T Consensus 122 g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 122 EKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 67999999999999998876654
No 202
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.59 E-value=1.1e+02 Score=24.26 Aligned_cols=35 Identities=23% Similarity=0.364 Sum_probs=27.8
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
.+++++.+... |..+++..+|++...+.+.+..+.
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 35555665443 799999999999999999888775
No 203
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=27.54 E-value=1.1e+02 Score=28.51 Aligned_cols=37 Identities=19% Similarity=0.319 Sum_probs=26.3
Q ss_pred HHHHHHH-Hhh--cCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 289 TYQAATL-LLF--NTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 289 ~~Qa~IL-llF--n~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
.-|-.|+ +.| +..+++|++||++.+|++...++..+.
T Consensus 181 ~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~ 220 (234)
T PRK08301 181 DREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3333444 444 345689999999999999998876653
No 204
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=27.31 E-value=1.7e+02 Score=29.99 Aligned_cols=38 Identities=24% Similarity=0.223 Sum_probs=33.0
Q ss_pred hcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 298 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 298 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
+.....+|.++|++.+++|...+.+.|..|.. .+++.+
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~--agLI~~ 342 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELAR--IGLLRR 342 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHh--CCCeEe
Confidence 56677999999999999999999999999964 577764
No 205
>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=27.26 E-value=61 Score=24.53 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=23.3
Q ss_pred HHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 295 LLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 295 LllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+....+-..+|+.||++.+|+++..+.|..+.|
T Consensus 26 l~~~~~~~~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 26 LENPDEIAFMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp HH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHh
Confidence 333444458999999999999999999988766
No 206
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=27.08 E-value=1.3e+02 Score=23.90 Aligned_cols=52 Identities=15% Similarity=0.188 Sum_probs=42.5
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 285 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 285 l~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
+..+....-||..+...+.=...-|+..+++|.+++...|..|.. .++|.+.
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~--~GLler~ 54 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEE--MGLLERV 54 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEEe
Confidence 445667788888888777667788999999999999999999964 5788765
No 207
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=26.97 E-value=97 Score=27.11 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=23.5
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 292 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 292 a~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
.++++.+-+ +++++||++.+|++...++..|.
T Consensus 126 ~i~~l~~~~--~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 126 TVLVLYYYE--QYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHH
Confidence 344444433 56999999999999988877664
No 208
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=26.69 E-value=90 Score=28.36 Aligned_cols=34 Identities=29% Similarity=0.489 Sum_probs=29.8
Q ss_pred HHhhcCCCC-cCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 295 LLLFNTSDR-LSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 295 LllFn~~~~-~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
-++|-..+. +|+++|++.++++..++..+|..|.
T Consensus 11 A~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~ 45 (188)
T PRK00135 11 ALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQ 45 (188)
T ss_pred HHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356778775 9999999999999999999999885
No 209
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.63 E-value=82 Score=27.88 Aligned_cols=37 Identities=14% Similarity=0.284 Sum_probs=26.6
Q ss_pred EcHHHHHHHHh-hcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 287 VSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 287 vs~~Qa~ILll-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
++.-|-.|+.+ +- +++|++||++.+|++...++..|.
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 44444444443 33 468999999999999998887665
No 210
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.59 E-value=83 Score=27.72 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=25.6
Q ss_pred cHHHHH-HHHhhcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 288 STYQAA-TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 288 s~~Qa~-ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
+.-+-. +++.|- +++|++||++.+|++...++..|.
T Consensus 131 ~~~~r~i~~l~~~--~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 131 EKDRAAAVRRAYL--EGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CHHHHHHHHHHHH--cCCCHHHHHHHHCCChHHHHHHHH
Confidence 444443 444443 468999999999999988877664
No 211
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=26.54 E-value=59 Score=29.04 Aligned_cols=60 Identities=15% Similarity=0.135 Sum_probs=37.8
Q ss_pred HHHhhhhhhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceE
Q 012914 380 VDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 450 (453)
Q Consensus 380 v~~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 450 (453)
...+.-.+|-+ ++.+|.... +. ..+.+.+. =..+.++++++|+.|.+-|+|+++++ +.|.
T Consensus 21 ~~~W~~~~ir~-l~~l~~~~~--d~----~~iak~l~--p~is~~ev~~sL~~L~~~gli~k~~~--g~y~ 80 (171)
T PF14394_consen 21 YSSWYHPAIRE-LLPLMPFAP--DP----EWIAKRLR--PKISAEEVRDSLEFLEKLGLIKKDGD--GKYV 80 (171)
T ss_pred HhhhHHHHHHH-HhhcCCCCC--CH----HHHHHHhc--CCCCHHHHHHHHHHHHHCCCeEECCC--CcEE
Confidence 44555555555 445555443 22 22333221 14688999999999999999999985 4453
No 212
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=26.51 E-value=1.2e+02 Score=26.47 Aligned_cols=44 Identities=14% Similarity=0.196 Sum_probs=34.8
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
+|..+..+.......+|++.+++++..+...++-|.. .+++...
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~--~GlV~~~ 57 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLER--LGLVEYE 57 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHH--CCCeEEe
Confidence 3444555677899999999999999999999999963 4677654
No 213
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=26.47 E-value=1.1e+02 Score=28.01 Aligned_cols=41 Identities=12% Similarity=0.159 Sum_probs=36.7
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
..|.-+.-||.+.-+ ++|..||++.+++++..++.++..+.
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 488999999988877 56899999999999999999998886
No 214
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=26.42 E-value=73 Score=28.55 Aligned_cols=26 Identities=27% Similarity=0.381 Sum_probs=23.1
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
.++|.+||++.+|+++..+.+.|...
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999988754
No 215
>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=26.40 E-value=1.8e+02 Score=23.47 Aligned_cols=51 Identities=14% Similarity=0.199 Sum_probs=36.7
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC----CCCChHHHHHHHHHHHhhcC
Q 012914 64 YMEYVTNCFINHTLFHKALKEAFEIFCNKAV----GGSSSSELLATFCDNILKKG 114 (453)
Q Consensus 64 ~~~l~~~~F~~~~~f~~~l~~af~~~~N~~~----~~~~~~e~La~y~d~~l~~~ 114 (453)
|..++......+......+..||..+++.-+ ..+..++++|.++..++..+
T Consensus 56 ~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~ 110 (113)
T smart00544 56 YSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLISDG 110 (113)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHHcC
Confidence 4455555565666777888888888887644 23467899999998888753
No 216
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=26.22 E-value=35 Score=32.57 Aligned_cols=46 Identities=17% Similarity=0.224 Sum_probs=39.6
Q ss_pred cceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhcccccc
Q 012914 389 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 442 (453)
Q Consensus 389 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~ 442 (453)
...|+..++.++.++..||-+ .|.++...|.+-|+.|-++|.|.|.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~--------~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQ--------YFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 345777889999999988877 4889999999999999999999884
No 217
>PRK00118 putative DNA-binding protein; Validated
Probab=26.16 E-value=1.1e+02 Score=24.92 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=21.6
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+.|+.||++.+|++...+.+.+..-
T Consensus 33 g~S~~EIAe~lGIS~~TV~r~L~RA 57 (104)
T PRK00118 33 DYSLGEIAEEFNVSRQAVYDNIKRT 57 (104)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 6799999999999999888877643
No 218
>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=26.13 E-value=65 Score=23.38 Aligned_cols=52 Identities=12% Similarity=0.133 Sum_probs=32.7
Q ss_pred eeehhccCCCCChhHHHHHHHHH--hccCCCCChhHHHHHHHhhhhhccccccC
Q 012914 392 LVRIMKSRKVLGHQQLVSECVEQ--LSRMFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 392 IVRimK~~k~l~~~~L~~~v~~~--l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
|+..+..-..++.+.+.....-. ....+.++.++++.-++.+++.|-|+-+.
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 34444555566777766655444 23568899999999999999999998873
No 219
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=26.12 E-value=1.1e+02 Score=26.06 Aligned_cols=43 Identities=16% Similarity=0.262 Sum_probs=33.9
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.|..+.+..+..++.+|++.++++...+.+.|..|.. .+++.+
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~--~Gli~~ 54 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDK--DEYLIY 54 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHH--CCCEEE
Confidence 3444556667889999999999999999999999964 356653
No 220
>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=26.08 E-value=44 Score=26.74 Aligned_cols=43 Identities=7% Similarity=0.172 Sum_probs=28.8
Q ss_pred cceeeehhcc----CCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccc
Q 012914 389 DAALVRIMKS----RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYL 439 (453)
Q Consensus 389 ~A~IVRimK~----~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi 439 (453)
+..|..++|. .-.++.++|.+.+ ..+..+|+++|+.|++.|+|
T Consensus 49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--------~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 49 QDKVLNFIKQQPNSEEGVHVDEIAQQL--------GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHC----TTTEEHHHHHHHS--------TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHhcCCCCCcccHHHHHHHh--------CcCHHHHHHHHHHHHhCCeE
Confidence 3344445555 4456666666543 35789999999999999976
No 221
>PRK09462 fur ferric uptake regulator; Provisional
Probab=25.75 E-value=1e+02 Score=26.56 Aligned_cols=58 Identities=3% Similarity=0.122 Sum_probs=41.9
Q ss_pred eeeehhcc--CCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEe
Q 012914 391 ALVRIMKS--RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 451 (453)
Q Consensus 391 ~IVRimK~--~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Y 451 (453)
+|.+++.. .+-++.++|...+.+.- ..++..-|=+.|+.|.+.|.|.+-..+.+...|
T Consensus 21 ~Il~~l~~~~~~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y 80 (148)
T PRK09462 21 KILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80 (148)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEE
Confidence 34455554 35899999999887643 456888999999999999999886432233444
No 222
>PRK11050 manganese transport regulator MntR; Provisional
Probab=25.67 E-value=1.3e+02 Score=26.06 Aligned_cols=43 Identities=12% Similarity=0.161 Sum_probs=34.8
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
.|+.++...+.++..+|++.++++...+.+.|..|.. .+++.+
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 4555667777899999999999999999999999964 356654
No 223
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=25.62 E-value=1.3e+02 Score=27.31 Aligned_cols=41 Identities=22% Similarity=0.214 Sum_probs=36.0
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
..|.-+.-||.+.-+ ++|..||++.++++...++.++..+.
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 378888889988765 57999999999999999999998886
No 224
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=25.51 E-value=93 Score=27.76 Aligned_cols=36 Identities=19% Similarity=0.339 Sum_probs=28.4
Q ss_pred CCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeec
Q 012914 300 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 300 ~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
..+++|++||+++||++...+-..+.-|.. .+|+.+
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~--~~lV~~ 73 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVSMGLKKLQD--WNLVKK 73 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHHHHHHHHHh--cchHHh
Confidence 456899999999999999888888877754 355543
No 225
>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=25.43 E-value=1.2e+02 Score=28.21 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=26.0
Q ss_pred HHHHHHhh--cCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 291 QAATLLLF--NTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 291 Qa~ILllF--n~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
+-++.+.+ ++.+++|++||++.+|++...+...+.
T Consensus 184 R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 184 KKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred HHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34444444 334689999999999999998877664
No 226
>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=25.40 E-value=82 Score=27.78 Aligned_cols=32 Identities=28% Similarity=0.493 Sum_probs=25.3
Q ss_pred HhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 296 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 296 llFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
++|-..+.+|+++|++.++ +...+...|..|.
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 5677888899999999999 9999999999886
No 227
>PF13314 DUF4083: Domain of unknown function (DUF4083)
Probab=25.32 E-value=1.7e+02 Score=21.09 Aligned_cols=32 Identities=25% Similarity=0.514 Sum_probs=20.6
Q ss_pred HHHHHHHhhcCCCCCCChHHHHHHHHHHHHHH
Q 012914 104 ATFCDNILKKGGNEKLSDEAIEETLEKVVKLL 135 (453)
Q Consensus 104 a~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf 135 (453)
..++-.++.++.-++-+..+++++||.|+.|+
T Consensus 24 tl~IRri~~~s~~kkq~~~~~eqKLDrIIeLL 55 (58)
T PF13314_consen 24 TLFIRRILINSNAKKQDVDSMEQKLDRIIELL 55 (58)
T ss_pred HHHHHHHHHhccccccchhHHHHHHHHHHHHH
Confidence 34455555554323334568999999999885
No 228
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=25.24 E-value=1.2e+02 Score=26.07 Aligned_cols=32 Identities=28% Similarity=0.405 Sum_probs=24.5
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 291 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 291 Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
+.++.+.+ .++++.||++.+|++...+...+.
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 44444555 478999999999999988777664
No 229
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=25.11 E-value=1.2e+02 Score=29.05 Aligned_cols=42 Identities=21% Similarity=0.365 Sum_probs=33.1
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 294 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 294 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
||++.-+ ++.|++||...++++...+..+|.-|.. .+++.+.
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~~--~~LV~~~ 59 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLKD--KGLVVQE 59 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHhh--CCCEEec
Confidence 4444444 6789999999999999999999999964 4677654
No 230
>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=25.03 E-value=94 Score=20.34 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=17.9
Q ss_pred cCHHHHHHHhCCChHHHHHHH
Q 012914 304 LSYSEIMTQLNLTHDDLVRLL 324 (453)
Q Consensus 304 ~t~~ei~~~t~i~~~~l~~~L 324 (453)
+|+.|+++.+|++...+.+-+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 689999999999998876644
No 231
>PF12728 HTH_17: Helix-turn-helix domain
Probab=24.88 E-value=92 Score=21.12 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=17.8
Q ss_pred cCHHHHHHHhCCChHHHHHHH
Q 012914 304 LSYSEIMTQLNLTHDDLVRLL 324 (453)
Q Consensus 304 ~t~~ei~~~t~i~~~~l~~~L 324 (453)
+|++|+++.+|++...+.+.+
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 232
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.56 E-value=1.2e+02 Score=25.94 Aligned_cols=24 Identities=4% Similarity=0.126 Sum_probs=20.3
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHh
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
.++|++||++.+|++...++..+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHH
Confidence 367999999999999988876654
No 233
>PRK04217 hypothetical protein; Provisional
Probab=24.51 E-value=81 Score=25.97 Aligned_cols=40 Identities=18% Similarity=0.199 Sum_probs=27.6
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
++.-|..++.+. ..+.+|++||++.+|++...+.+.|...
T Consensus 43 Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 43 MTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 344444444332 2246799999999999999888877654
No 234
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=24.46 E-value=1.2e+02 Score=26.26 Aligned_cols=39 Identities=13% Similarity=0.181 Sum_probs=26.9
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+.-|-.|+.+.-- +++|++||++.+|++...++..|..-
T Consensus 114 ~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra 152 (164)
T PRK12547 114 SADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRA 152 (164)
T ss_pred CHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4444444444221 46799999999999998888776543
No 235
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.35 E-value=98 Score=27.92 Aligned_cols=38 Identities=29% Similarity=0.362 Sum_probs=27.2
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+.-+..|+.++- .++|++||++.+|++...++..|.-.
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 344444554443 46899999999999999887766543
No 236
>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=24.29 E-value=1.3e+02 Score=28.88 Aligned_cols=36 Identities=8% Similarity=0.246 Sum_probs=25.5
Q ss_pred HHHHHHH-HhhcCCCCcCHHHHHHHhCCChHHHHHHH
Q 012914 289 TYQAATL-LLFNTSDRLSYSEIMTQLNLTHDDLVRLL 324 (453)
Q Consensus 289 ~~Qa~IL-llFn~~~~~t~~ei~~~t~i~~~~l~~~L 324 (453)
.-|-.|| +.|-..+++|..||++.+|++...+.+..
T Consensus 221 ~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~ 257 (270)
T TIGR02392 221 ARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIE 257 (270)
T ss_pred HHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 3344444 44544458999999999999998887543
No 237
>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=24.25 E-value=1.1e+02 Score=22.30 Aligned_cols=23 Identities=9% Similarity=0.403 Sum_probs=19.2
Q ss_pred CCCCcCHHHHHHHhCCChHHHHH
Q 012914 300 TSDRLSYSEIMTQLNLTHDDLVR 322 (453)
Q Consensus 300 ~~~~~t~~ei~~~t~i~~~~l~~ 322 (453)
..+.++..+|++.+|+++..+..
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHHH
Confidence 44589999999999999987643
No 238
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=24.24 E-value=1.6e+02 Score=26.61 Aligned_cols=40 Identities=23% Similarity=0.227 Sum_probs=35.6
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
+|+-+.-||.+..+ +.|..||++.+++++..++..+..+.
T Consensus 134 LSpRErEVLrLLAq--GkTnKEIAe~L~IS~rTVkth~srIm 173 (198)
T PRK15201 134 FSVTERHLLKLIAS--GYHLSETAALLSLSEEQTKSLRRSIM 173 (198)
T ss_pred CCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 78889999988877 56899999999999999999988876
No 239
>PF14493 HTH_40: Helix-turn-helix domain
Probab=24.15 E-value=1.2e+02 Score=23.63 Aligned_cols=33 Identities=30% Similarity=0.293 Sum_probs=28.2
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 294 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 294 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
-+-+|++ ++|++||++.-|+....+..+|..++
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 3556775 68999999999999999999998775
No 240
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.08 E-value=76 Score=26.75 Aligned_cols=51 Identities=20% Similarity=0.343 Sum_probs=44.3
Q ss_pred hhhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCC
Q 012914 386 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 444 (453)
Q Consensus 386 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~ 444 (453)
..|.+-||-..+.++.++..++... +-.+...++..+..|+++|.|-+.+.
T Consensus 11 ~eLk~rIvElVRe~GRiTi~ql~~~--------TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 11 EELKARIVELVREHGRITIKQLVAK--------TGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHcCCccHHHHHHH--------HCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 6788999999999999999999885 44688889999999999999888753
No 241
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=24.03 E-value=66 Score=24.74 Aligned_cols=31 Identities=19% Similarity=0.192 Sum_probs=26.7
Q ss_pred HhccCCCCChhHHHHHHHhhhhhccccccCC
Q 012914 414 QLSRMFKPDIKAIKKRMEDLITRDYLERDKE 444 (453)
Q Consensus 414 ~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~ 444 (453)
+|+.+|..+++.|..-+|.|+.+|-|+|-+.
T Consensus 21 ~Ls~~~~~p~~~VeaMLe~l~~kGkverv~~ 51 (78)
T PRK15431 21 QISQTLNTPQPMINAMLQQLESMGKAVRIQE 51 (78)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCeEeecc
Confidence 3445788999999999999999999999863
No 242
>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=23.89 E-value=1.2e+02 Score=26.69 Aligned_cols=23 Identities=22% Similarity=0.215 Sum_probs=20.4
Q ss_pred CcCHHHHHHHhCCChHHHHHHHh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
++|++||++.+|++...++..|.
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 150 GLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 67999999999999998887765
No 243
>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=23.79 E-value=2.3e+02 Score=23.94 Aligned_cols=49 Identities=16% Similarity=0.136 Sum_probs=37.4
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHh----CCChHHHHHHHhHhhhcccceeec
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQL----NLTHDDLVRLLHSLSCAKYKILLK 337 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t----~i~~~~l~~~L~sL~~~k~~iL~~ 337 (453)
+|..+..|+..+=+.+..|..||.+.+ ++....+...|..|.. -+++..
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~--KG~v~~ 54 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD--KGCLTT 54 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH--CCceee
Confidence 466788888776566788999977765 7888999999999964 366654
No 244
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=23.31 E-value=1.5e+02 Score=27.20 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=36.5
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
..|+-+.-||.++-+ +.|..||++.+++++.+++.++..+.
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 378899999988887 47999999999999999999998886
No 245
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=23.25 E-value=77 Score=27.87 Aligned_cols=47 Identities=11% Similarity=0.208 Sum_probs=40.3
Q ss_pred hhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccc
Q 012914 387 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 441 (453)
Q Consensus 387 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R 441 (453)
.+|-.|.+++.....+++.+|=..| ..+...+.+||..|.+.|.|++
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 4678899999999999998777654 4688899999999999999986
No 246
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=23.21 E-value=1.2e+02 Score=26.79 Aligned_cols=32 Identities=19% Similarity=0.199 Sum_probs=23.9
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhH
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
++++.|- .++|++||++.+|++...++..+..
T Consensus 141 i~~l~~~--~~~s~~eIA~~lgis~~tV~~~l~r 172 (182)
T PRK12537 141 CILHAYV--DGCSHAEIAQRLGAPLGTVKAWIKR 172 (182)
T ss_pred HHHHHHH--cCCCHHHHHHHHCCChhhHHHHHHH
Confidence 3444443 4679999999999999888776653
No 247
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=22.95 E-value=46 Score=31.69 Aligned_cols=46 Identities=20% Similarity=0.437 Sum_probs=39.8
Q ss_pred cceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhcccccc
Q 012914 389 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 442 (453)
Q Consensus 389 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~ 442 (453)
...|+.++++++.++..||.+ +|..+...|.+-|..|-++|.|.|-
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~--------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVE--------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHH--------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 345777889999999988877 4789999999999999999999984
No 248
>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=22.89 E-value=96 Score=25.49 Aligned_cols=57 Identities=9% Similarity=0.175 Sum_probs=40.6
Q ss_pred eeehhcc-CCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEe
Q 012914 392 LVRIMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 451 (453)
Q Consensus 392 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Y 451 (453)
|..+|+. .+.++.++|...+.+. ...++..-|=+.|+.|.+.|.|.+-..+.+...|
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 3444554 4578888998887753 3567889999999999999999997655454444
No 249
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.83 E-value=57 Score=25.96 Aligned_cols=27 Identities=22% Similarity=0.334 Sum_probs=23.6
Q ss_pred CCCCChhHHHHHHHhhhhhccccccCC
Q 012914 418 MFKPDIKAIKKRMEDLITRDYLERDKE 444 (453)
Q Consensus 418 ~F~~~~~~ik~~Ie~LIereyi~R~~~ 444 (453)
+...+.++|..+++.|.+.|+|+|..+
T Consensus 30 ~l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 30 RLKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred HHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 345788999999999999999999874
No 250
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=22.79 E-value=1.3e+02 Score=26.62 Aligned_cols=39 Identities=15% Similarity=0.112 Sum_probs=27.0
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 288 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 288 s~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+.-|-.++.++- .+++|++||++.+|++...++..|..-
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 444444443321 236799999999999999888877543
No 251
>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=22.74 E-value=86 Score=25.67 Aligned_cols=44 Identities=16% Similarity=0.164 Sum_probs=30.9
Q ss_pred eeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccC
Q 012914 392 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 392 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
|...+.....++..+|-.. ...+.+.+-..|..|.++|||+|..
T Consensus 33 iL~~l~~~~~~t~~ela~~--------~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLANQ--------ACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHcCCcCHHHHHHH--------hCCCchhHHHHHHHHHHCCCEEecc
Confidence 4444555666776655553 3345567889999999999999854
No 252
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=22.61 E-value=1.2e+02 Score=25.89 Aligned_cols=58 Identities=9% Similarity=0.138 Sum_probs=47.6
Q ss_pred hhhhhhcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhcccccc
Q 012914 383 DRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 442 (453)
Q Consensus 383 ~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~ 442 (453)
++...+.-+|..++..+ ++=-+|..++.+...+.|.|+...|=..+..|.+.|+|+..
T Consensus 39 ~~~~~~~l~IL~lL~~~--~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~ 96 (135)
T PRK09416 39 EKEEDILLAILQLLMNE--KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSS 96 (135)
T ss_pred cccccHHHHHHHHHhCC--CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEe
Confidence 33456777888888765 78789999988765556899999999999999999999974
No 253
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=22.55 E-value=1.6e+02 Score=27.38 Aligned_cols=44 Identities=20% Similarity=0.210 Sum_probs=34.5
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 293 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 293 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
+.+-.-++...+|..+|++.++++...+.+.|..|.. .+++.+.
T Consensus 11 allg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe--~GlI~R~ 54 (217)
T PRK14165 11 ALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLED--EGYITRT 54 (217)
T ss_pred HHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 3344455556899999999999999999999999963 4677654
No 254
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=22.51 E-value=1.2e+02 Score=25.82 Aligned_cols=35 Identities=23% Similarity=0.412 Sum_probs=25.8
Q ss_pred hhcc-CCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhh
Q 012914 395 IMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDL 433 (453)
Q Consensus 395 imK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~L 433 (453)
||+. ++.|++.+|+.+|.+.+. .+.+.+..+|-.|
T Consensus 12 iL~~~~~~m~f~dL~~ev~~~~~----~s~e~~~~~iaq~ 47 (129)
T PRK02363 12 ILKEKKEPMSFYDLVNEIQKYLG----KSDEEIRERIAQF 47 (129)
T ss_pred HHHHcCCcccHHHHHHHHHHHhC----CCHHHHHHHHHHH
Confidence 4545 468999999999999765 4666777766553
No 255
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.44 E-value=1.3e+02 Score=26.91 Aligned_cols=23 Identities=26% Similarity=0.358 Sum_probs=20.0
Q ss_pred CcCHHHHHHHhCCChHHHHHHHh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
++|++||++.+|++...++..|.
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 150 ELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 68999999999999988877654
No 256
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=22.14 E-value=1.5e+02 Score=25.19 Aligned_cols=24 Identities=13% Similarity=0.120 Sum_probs=20.8
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhH
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
++|+.||++.+|++...+...+..
T Consensus 122 ~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 122 GKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 579999999999999988877654
No 257
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=22.04 E-value=66 Score=27.48 Aligned_cols=38 Identities=16% Similarity=0.331 Sum_probs=28.9
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccC
Q 012914 398 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 443 (453)
Q Consensus 398 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 443 (453)
....++..+|-.. +..+.+-+-..|+.|.++|||+|..
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 4568888999999999999999953
No 258
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=21.84 E-value=1e+02 Score=24.32 Aligned_cols=24 Identities=25% Similarity=0.412 Sum_probs=21.7
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHh
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
..+|.++|+..+|++.+.+.++|+
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 479999999999999999998875
No 259
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.77 E-value=1.3e+02 Score=26.54 Aligned_cols=38 Identities=13% Similarity=0.072 Sum_probs=26.6
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
++.-+-.|+.+.- .+++|++||++.+|++...++..|.
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 4455555554432 2467999999999999988876554
No 260
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=21.71 E-value=89 Score=26.31 Aligned_cols=29 Identities=10% Similarity=0.288 Sum_probs=20.6
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCChHHHH
Q 012914 291 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLV 321 (453)
Q Consensus 291 Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~ 321 (453)
+.++.|.+- +++|++||++.+|++...++
T Consensus 113 r~v~~l~~~--~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 113 KKIIYMKFF--EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHCcCHHhhc
Confidence 334444333 35799999999999988764
No 261
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.65 E-value=1.3e+02 Score=25.79 Aligned_cols=38 Identities=16% Similarity=0.198 Sum_probs=26.1
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
+++-+..|+.+. ..+++|++||++.+|++...+...|.
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 344444455442 23468999999999999987766554
No 262
>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=21.65 E-value=1.6e+02 Score=24.84 Aligned_cols=38 Identities=16% Similarity=0.179 Sum_probs=26.9
Q ss_pred cHHHHHHHHh-hcCCCCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 288 STYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 288 s~~Qa~ILll-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+.-+..|+.+ +- .++|+.||++.+|++...+...+...
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 3444444433 43 36799999999999999988777543
No 263
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=21.54 E-value=76 Score=27.54 Aligned_cols=46 Identities=11% Similarity=0.159 Sum_probs=37.9
Q ss_pred hcceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccc
Q 012914 388 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 441 (453)
Q Consensus 388 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R 441 (453)
+|-.|.+.|.....+++.+|-.++ ..+.+.+..||+.|.+.|+|++
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 456677788888888888877654 4688999999999999999985
No 264
>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=21.35 E-value=1.2e+02 Score=19.62 Aligned_cols=21 Identities=24% Similarity=0.303 Sum_probs=17.4
Q ss_pred cCHHHHHHHhCCChHHHHHHH
Q 012914 304 LSYSEIMTQLNLTHDDLVRLL 324 (453)
Q Consensus 304 ~t~~ei~~~t~i~~~~l~~~L 324 (453)
+|..|+++.+|++...+.+-.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 578999999999998876643
No 265
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.10 E-value=2.2e+02 Score=18.94 Aligned_cols=24 Identities=17% Similarity=0.346 Sum_probs=20.3
Q ss_pred CHHHHHHHhCCChHHHHHHHhHhh
Q 012914 305 SYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 305 t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
|+.+++...|++...+.+-+...-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 999999999999988877666553
No 266
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.01 E-value=1.2e+02 Score=23.83 Aligned_cols=23 Identities=43% Similarity=0.469 Sum_probs=21.4
Q ss_pred CcCHHHHHHHhCCChHHHHHHHh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
.+|.++|+..+++++..+.+.|+
T Consensus 23 ~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 23 PLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred cccHHHHHHHhCCCHHHHHHHHH
Confidence 78999999999999999999884
No 267
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=20.91 E-value=64 Score=25.94 Aligned_cols=27 Identities=15% Similarity=0.297 Sum_probs=23.1
Q ss_pred CCCCChhHHHHHHHhhhhhccccccCC
Q 012914 418 MFKPDIKAIKKRMEDLITRDYLERDKE 444 (453)
Q Consensus 418 ~F~~~~~~ik~~Ie~LIereyi~R~~~ 444 (453)
+...+.+.+...|+.|.++|||+|..+
T Consensus 45 ~l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 45 RLGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred HHCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 455788899999999999999999753
No 268
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=20.85 E-value=1.6e+02 Score=25.60 Aligned_cols=23 Identities=22% Similarity=0.316 Sum_probs=19.3
Q ss_pred CcCHHHHHHHhCCChHHHHHHHh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
++|++||++.+|++...++..|.
T Consensus 134 g~s~~EIA~~lgis~~tV~~~l~ 156 (173)
T PRK09645 134 GWSTAQIAADLGIPEGTVKSRLH 156 (173)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 67999999999999988865543
No 269
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=20.71 E-value=2.1e+02 Score=19.87 Aligned_cols=25 Identities=24% Similarity=0.331 Sum_probs=18.8
Q ss_pred CCCCcCHHHHHHHhCCChHHHHHHH
Q 012914 300 TSDRLSYSEIMTQLNLTHDDLVRLL 324 (453)
Q Consensus 300 ~~~~~t~~ei~~~t~i~~~~l~~~L 324 (453)
....++-.+|++.+|++...+++-|
T Consensus 25 G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 25 GVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp T-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred CCeeECHHHHHHHHCCCHHHhcccC
Confidence 3457999999999999999988754
No 270
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=20.58 E-value=1.3e+02 Score=28.10 Aligned_cols=39 Identities=21% Similarity=0.213 Sum_probs=26.5
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhH
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
++.-|-.|+++.- ..++|++||++.+|+|...++..|..
T Consensus 117 Lp~~~R~v~lL~~-~eg~S~~EIAe~LgiS~~tVksrL~R 155 (228)
T PRK06704 117 LNVQQSAILLLKD-VFQYSIADIAKVCSVSEGAVKASLFR 155 (228)
T ss_pred CCHHHhhHhhhHH-hhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444444444422 22589999999999999888776643
No 271
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=20.47 E-value=77 Score=29.52 Aligned_cols=49 Identities=8% Similarity=0.154 Sum_probs=35.1
Q ss_pred hccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEec
Q 012914 396 MKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYL 452 (453)
Q Consensus 396 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yi 452 (453)
++..-.++..+|-.. ...+.+.+-+.|..|.++|||+|....++.+.++
T Consensus 16 l~~~~~IS~~eLA~~--------L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L 64 (217)
T PRK14165 16 VNNTVKISSSEFANH--------TGTSSKTAARILKQLEDEGYITRTIVPRGQLITI 64 (217)
T ss_pred cCCCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence 344445666666553 4468899999999999999999987555555554
No 272
>PRK09483 response regulator; Provisional
Probab=20.45 E-value=1.9e+02 Score=25.66 Aligned_cols=41 Identities=20% Similarity=0.203 Sum_probs=34.9
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 286 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 286 ~vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
..|.-+.-||.++.. +.|..+|++.++++...++.++..+.
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 367888888877754 57899999999999999999998886
No 273
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=20.34 E-value=1.7e+02 Score=27.01 Aligned_cols=40 Identities=18% Similarity=0.157 Sum_probs=35.1
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 287 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 287 vs~~Qa~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
.|.-|.-||.+.-. ++|..||++.+++++..++.++..+.
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 67888888877766 68999999999999999999998875
No 274
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.32 E-value=1.2e+02 Score=26.54 Aligned_cols=24 Identities=29% Similarity=0.526 Sum_probs=20.5
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHh
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
.++|++||++.+|++...++..|.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 467999999999999988877664
No 275
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. 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 RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=20.30 E-value=1.6e+02 Score=28.47 Aligned_cols=35 Identities=11% Similarity=0.178 Sum_probs=25.8
Q ss_pred HHHHHHhh--cCCCCcCHHHHHHHhCCChHHHHHHHh
Q 012914 291 QAATLLLF--NTSDRLSYSEIMTQLNLTHDDLVRLLH 325 (453)
Q Consensus 291 Qa~ILllF--n~~~~~t~~ei~~~t~i~~~~l~~~L~ 325 (453)
+.++.+.| ...+.+|+.||++.+|++...++..+.
T Consensus 228 R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~ 264 (285)
T TIGR02394 228 REVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQV 264 (285)
T ss_pred HHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 33444443 456689999999999999988777654
No 276
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=20.30 E-value=1.4e+02 Score=27.37 Aligned_cols=42 Identities=14% Similarity=0.230 Sum_probs=32.9
Q ss_pred HHHHhhcCC-CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceee
Q 012914 293 ATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 336 (453)
Q Consensus 293 ~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~ 336 (453)
-||.++.+. ...|.+||++.+++++.++++++..|.. .+++.
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 456566554 2689999999999999999999999974 34554
No 277
>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=20.30 E-value=2.4e+02 Score=22.72 Aligned_cols=44 Identities=20% Similarity=0.224 Sum_probs=33.7
Q ss_pred HHHHhhcC-CCCcCHHHHHHHh-----CCChHHHHHHHhHhhhcccceeecC
Q 012914 293 ATLLLFNT-SDRLSYSEIMTQL-----NLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 293 ~ILllFn~-~~~~t~~ei~~~t-----~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
.||..+.+ ...+|.+||.+.+ +++...+-++|..|.. .+++.+.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~--~Gli~~~ 54 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEE--AGLVREI 54 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHh--CCCEEEE
Confidence 45555544 4579999999998 6899999999999974 4677653
No 278
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=20.19 E-value=73 Score=33.25 Aligned_cols=56 Identities=14% Similarity=0.285 Sum_probs=48.1
Q ss_pred cceeeehhccCCCCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhccccccCCCCCceEec
Q 012914 389 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYL 452 (453)
Q Consensus 389 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yi 452 (453)
+.+|++.++....++-.+|-+. |..+...+-+.|..|+.+|++++-.....-+.||
T Consensus 404 ~~~il~~~~en~~~T~~~L~~~--------l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v 459 (467)
T COG2865 404 QEKILELIKENGKVTARELREI--------LGISSETIRRRIANLVKRGLLKQLGSSGRGTWYV 459 (467)
T ss_pred HHHHHHHHhhccccCHHHHHHH--------hCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEe
Confidence 4899999999999998887764 4478889999999999999999988777777776
No 279
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=20.16 E-value=1.5e+02 Score=28.90 Aligned_cols=35 Identities=14% Similarity=0.152 Sum_probs=30.5
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHhHhhhcccceeecC
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 338 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~~iL~~~ 338 (453)
...|.+||++.+|+++..+.+-|..|+. .++|.+.
T Consensus 22 gp~t~~eLA~~~~~~~~~~~~lL~~L~~--lgll~~~ 56 (306)
T TIGR02716 22 GPKDLATLAADTGSVPPRLEMLLETLRQ--MRVINLE 56 (306)
T ss_pred CCCCHHHHHHHcCCChHHHHHHHHHHHh--CCCeEec
Confidence 5789999999999999999999999975 5788753
No 280
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=20.13 E-value=1.7e+02 Score=26.12 Aligned_cols=24 Identities=29% Similarity=0.314 Sum_probs=20.5
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhH
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHS 326 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~s 326 (453)
++|++||++.+|++...++..|..
T Consensus 147 g~s~~EIA~~lgis~~tV~~~l~R 170 (191)
T PRK12520 147 ELETEEICQELQITATNAWVLLYR 170 (191)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 579999999999999888776653
No 281
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=20.13 E-value=1.3e+02 Score=21.94 Aligned_cols=26 Identities=19% Similarity=0.381 Sum_probs=22.0
Q ss_pred CcCHHHHHHHhCCChHHHHHHHhHhh
Q 012914 303 RLSYSEIMTQLNLTHDDLVRLLHSLS 328 (453)
Q Consensus 303 ~~t~~ei~~~t~i~~~~l~~~L~sL~ 328 (453)
.+|+++|++.+|++...+.+.+....
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 37899999999999999888876653
No 282
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=20.08 E-value=1.4e+02 Score=27.65 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=21.9
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHhHh
Q 012914 302 DRLSYSEIMTQLNLTHDDLVRLLHSL 327 (453)
Q Consensus 302 ~~~t~~ei~~~t~i~~~~l~~~L~sL 327 (453)
+.+|++||++.+|++...++..|.--
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RA 174 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARA 174 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 36899999999999999888877543
Done!