Query 041844
Match_columns 97
No_of_seqs 134 out of 740
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 11:15:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041844.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041844hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08100 Dimerisation: Dimeris 99.7 3.3E-17 7.2E-22 98.1 3.4 49 39-89 1-51 (51)
2 TIGR02716 C20_methyl_CrtF C-20 99.1 7.6E-11 1.6E-15 89.8 5.3 53 37-96 3-55 (306)
3 KOG3178 Hydroxyindole-O-methyl 99.1 1.5E-10 3.2E-15 91.7 6.2 71 17-97 4-76 (342)
4 PF09339 HTH_IclR: IclR helix- 98.0 2.3E-06 4.9E-11 50.2 1.6 45 49-96 6-50 (52)
5 smart00346 HTH_ICLR helix_turn 97.4 0.00023 4.9E-09 44.8 3.8 45 49-96 8-52 (91)
6 TIGR02431 pcaR_pcaU beta-ketoa 97.0 0.00085 1.8E-08 49.8 3.7 45 49-96 12-56 (248)
7 PRK11569 transcriptional repre 97.0 0.00085 1.8E-08 50.8 3.7 44 49-95 31-74 (274)
8 PRK10163 DNA-binding transcrip 96.9 0.0011 2.3E-08 50.3 3.8 45 49-96 28-72 (271)
9 COG1414 IclR Transcriptional r 96.7 0.002 4.2E-08 48.5 3.8 45 49-96 7-51 (246)
10 PF13412 HTH_24: Winged helix- 96.7 0.0027 5.9E-08 36.1 3.3 45 47-95 4-48 (48)
11 PRK09834 DNA-binding transcrip 96.5 0.0028 6E-08 47.7 3.6 44 49-95 14-57 (263)
12 smart00550 Zalpha Z-DNA-bindin 96.5 0.0062 1.3E-07 37.6 4.3 46 47-95 7-53 (68)
13 PRK15090 DNA-binding transcrip 96.5 0.0032 7E-08 47.0 3.5 43 50-96 18-60 (257)
14 PF12840 HTH_20: Helix-turn-he 96.4 0.0033 7.1E-08 37.6 2.8 46 47-96 11-56 (61)
15 PF02082 Rrf2: Transcriptional 96.4 0.006 1.3E-07 38.5 4.0 33 60-95 24-56 (83)
16 PF01022 HTH_5: Bacterial regu 96.4 0.0028 6.1E-08 36.2 2.2 43 48-95 4-46 (47)
17 PF12802 MarR_2: MarR family; 96.2 0.0046 9.9E-08 36.2 2.5 44 50-96 9-53 (62)
18 cd07153 Fur_like Ferric uptake 96.0 0.013 2.8E-07 38.5 4.2 48 49-96 4-53 (116)
19 COG4190 Predicted transcriptio 95.9 0.015 3.1E-07 41.4 4.4 56 34-95 54-109 (144)
20 PRK10857 DNA-binding transcrip 95.9 0.012 2.7E-07 42.1 4.0 36 58-96 22-57 (164)
21 TIGR02944 suf_reg_Xantho FeS a 95.9 0.011 2.3E-07 40.0 3.5 34 59-95 23-56 (130)
22 PF09012 FeoC: FeoC like trans 95.8 0.008 1.7E-07 36.9 2.4 42 51-96 5-46 (69)
23 TIGR02010 IscR iron-sulfur clu 95.7 0.015 3.3E-07 39.8 3.7 34 59-95 23-56 (135)
24 smart00419 HTH_CRP helix_turn_ 95.6 0.015 3.3E-07 32.1 2.9 33 60-95 7-39 (48)
25 smart00347 HTH_MARR helix_turn 95.6 0.025 5.4E-07 35.1 4.2 45 47-95 11-55 (101)
26 smart00418 HTH_ARSR helix_turn 95.6 0.028 6.1E-07 31.8 4.1 40 51-95 2-41 (66)
27 PF08461 HTH_12: Ribonuclease 95.5 0.024 5.3E-07 35.0 3.8 45 51-95 3-49 (66)
28 PF01978 TrmB: Sugar-specific 95.5 0.0076 1.6E-07 36.5 1.5 43 50-96 12-54 (68)
29 smart00344 HTH_ASNC helix_turn 95.4 0.023 5.1E-07 36.8 3.7 45 47-95 4-48 (108)
30 PF04967 HTH_10: HTH DNA bindi 95.4 0.027 5.8E-07 33.8 3.6 42 37-87 5-46 (53)
31 TIGR00738 rrf2_super rrf2 fami 95.3 0.024 5.2E-07 38.0 3.5 34 59-95 23-56 (132)
32 smart00420 HTH_DEOR helix_turn 95.2 0.042 9.1E-07 30.5 3.8 42 51-96 5-46 (53)
33 PRK06474 hypothetical protein; 95.0 0.036 7.8E-07 40.1 4.0 47 47-96 12-59 (178)
34 cd00092 HTH_CRP helix_turn_hel 95.0 0.034 7.4E-07 32.7 3.2 33 60-95 24-56 (67)
35 PF01047 MarR: MarR family; I 95.0 0.02 4.3E-07 33.3 2.0 41 51-95 8-48 (59)
36 PF13463 HTH_27: Winged helix 94.9 0.035 7.6E-07 32.9 3.2 38 55-95 12-49 (68)
37 PRK11014 transcriptional repre 94.9 0.037 8E-07 38.1 3.5 48 39-95 9-56 (141)
38 PF01726 LexA_DNA_bind: LexA D 94.8 0.035 7.6E-07 34.2 3.0 41 53-95 17-57 (65)
39 COG1959 Predicted transcriptio 94.8 0.041 9E-07 38.8 3.7 33 60-95 24-56 (150)
40 PF01325 Fe_dep_repress: Iron 94.7 0.051 1.1E-06 32.9 3.5 35 58-95 19-53 (60)
41 COG3355 Predicted transcriptio 94.7 0.047 1E-06 38.2 3.6 45 48-95 29-73 (126)
42 PF00325 Crp: Bacterial regula 94.5 0.033 7.1E-07 30.3 2.0 31 61-94 2-32 (32)
43 PF04703 FaeA: FaeA-like prote 94.4 0.049 1.1E-06 33.6 2.9 42 51-95 5-46 (62)
44 PRK10141 DNA-binding transcrip 94.3 0.077 1.7E-06 36.3 4.0 45 47-95 17-61 (117)
45 PF08279 HTH_11: HTH domain; 94.3 0.065 1.4E-06 30.9 3.2 40 50-92 4-43 (55)
46 PRK11920 rirA iron-responsive 94.2 0.074 1.6E-06 37.5 3.9 48 38-95 8-55 (153)
47 PRK00215 LexA repressor; Valid 94.1 0.1 2.2E-06 37.6 4.5 41 53-96 15-56 (205)
48 cd00090 HTH_ARSR Arsenical Res 94.1 0.13 2.7E-06 29.8 4.1 41 50-95 11-51 (78)
49 TIGR02702 SufR_cyano iron-sulf 93.7 0.097 2.1E-06 38.0 3.8 42 50-95 5-46 (203)
50 COG2512 Predicted membrane-ass 93.7 0.066 1.4E-06 41.2 3.0 45 48-95 197-241 (258)
51 TIGR00122 birA_repr_reg BirA b 93.6 0.097 2.1E-06 31.7 3.2 42 48-94 2-43 (69)
52 PRK11639 zinc uptake transcrip 93.6 0.13 2.9E-06 36.7 4.3 50 47-96 27-78 (169)
53 PRK11169 leucine-responsive tr 93.6 0.1 2.2E-06 36.8 3.6 45 47-95 15-59 (164)
54 PF08220 HTH_DeoR: DeoR-like h 93.5 0.13 2.8E-06 30.5 3.5 41 51-95 5-45 (57)
55 COG1522 Lrp Transcriptional re 93.5 0.12 2.6E-06 35.1 3.7 45 47-95 9-53 (154)
56 TIGR02337 HpaR homoprotocatech 93.5 0.16 3.5E-06 33.5 4.3 45 48-96 30-74 (118)
57 PRK06266 transcription initiat 93.5 0.11 2.5E-06 37.7 3.8 42 50-95 26-67 (178)
58 PRK11179 DNA-binding transcrip 93.5 0.12 2.7E-06 35.9 3.8 45 47-95 10-54 (153)
59 TIGR01610 phage_O_Nterm phage 93.2 0.18 3.9E-06 32.8 4.1 34 59-95 45-78 (95)
60 PRK03573 transcriptional regul 93.2 0.21 4.6E-06 33.9 4.6 40 53-95 38-77 (144)
61 smart00345 HTH_GNTR helix_turn 93.0 0.15 3.3E-06 28.9 3.2 33 60-95 18-51 (60)
62 TIGR00498 lexA SOS regulatory 92.7 0.25 5.4E-06 35.4 4.6 40 55-96 19-58 (199)
63 PRK09462 fur ferric uptake reg 92.6 0.21 4.5E-06 34.6 4.0 49 47-95 18-69 (148)
64 TIGR00373 conserved hypothetic 92.6 0.2 4.3E-06 35.7 3.9 42 50-95 18-59 (158)
65 PRK03902 manganese transport t 92.5 0.21 4.5E-06 34.2 3.9 35 58-95 19-53 (142)
66 PHA00738 putative HTH transcri 92.4 0.18 4E-06 34.4 3.4 46 47-96 13-58 (108)
67 PRK15431 ferrous iron transpor 92.4 0.24 5.1E-06 32.1 3.7 40 52-95 8-47 (78)
68 PRK11050 manganese transport r 92.4 0.24 5.2E-06 34.7 4.1 40 52-95 43-82 (152)
69 COG0735 Fur Fe2+/Zn2+ uptake r 92.1 0.23 4.9E-06 34.8 3.6 50 47-96 22-73 (145)
70 PF13545 HTH_Crp_2: Crp-like h 92.1 0.15 3.3E-06 30.8 2.4 33 60-95 27-59 (76)
71 TIGR01889 Staph_reg_Sar staphy 92.0 0.26 5.7E-06 32.4 3.7 34 59-95 41-74 (109)
72 COG2345 Predicted transcriptio 91.7 0.19 4.2E-06 38.0 3.1 34 59-95 23-56 (218)
73 PF01475 FUR: Ferric uptake re 91.6 0.11 2.3E-06 34.5 1.5 50 47-96 9-60 (120)
74 PF06163 DUF977: Bacterial pro 91.6 0.32 7E-06 34.1 3.9 44 47-94 13-56 (127)
75 PF03444 HrcA_DNA-bdg: Winged 91.0 0.62 1.3E-05 30.1 4.5 47 39-95 8-54 (78)
76 PRK11512 DNA-binding transcrip 90.8 0.43 9.3E-06 32.6 3.9 40 52-95 46-85 (144)
77 TIGR02787 codY_Gpos GTP-sensin 90.5 0.38 8.2E-06 37.2 3.8 44 50-96 187-230 (251)
78 TIGR01884 cas_HTH CRISPR locus 90.5 0.36 7.8E-06 35.0 3.5 45 48-96 145-189 (203)
79 cd07377 WHTH_GntR Winged helix 90.1 0.65 1.4E-05 26.7 3.8 31 62-95 26-56 (66)
80 PRK14096 pgi glucose-6-phospha 90.1 0.42 9E-06 40.3 3.9 41 51-92 468-508 (528)
81 TIGR03697 NtcA_cyano global ni 90.0 0.34 7.4E-06 33.5 2.9 32 61-95 143-174 (193)
82 PF04182 B-block_TFIIIC: B-blo 90.0 0.48 1E-05 29.5 3.3 46 47-95 3-49 (75)
83 PF02796 HTH_7: Helix-turn-hel 89.2 0.29 6.3E-06 27.6 1.7 22 62-86 22-43 (45)
84 COG3413 Predicted DNA binding 89.1 0.55 1.2E-05 34.3 3.6 36 34-75 157-192 (215)
85 PF02002 TFIIE_alpha: TFIIE al 89.1 0.36 7.9E-06 31.5 2.3 42 50-95 17-58 (105)
86 PRK12423 LexA repressor; Provi 89.0 0.82 1.8E-05 33.3 4.4 41 53-96 17-58 (202)
87 PF13601 HTH_34: Winged helix 89.0 0.24 5.1E-06 31.4 1.4 45 47-95 1-45 (80)
88 COG1378 Predicted transcriptio 88.2 0.67 1.5E-05 35.2 3.6 33 60-95 29-61 (247)
89 COG1321 TroR Mn-dependent tran 88.1 0.98 2.1E-05 32.1 4.2 35 58-95 21-55 (154)
90 PRK11161 fumarate/nitrate redu 88.1 0.52 1.1E-05 33.9 2.8 32 61-95 184-215 (235)
91 PRK11753 DNA-binding transcrip 88.0 0.58 1.3E-05 32.9 3.0 32 61-95 168-199 (211)
92 PRK13918 CRP/FNR family transc 87.8 0.63 1.4E-05 32.6 3.1 32 61-95 149-180 (202)
93 PF00392 GntR: Bacterial regul 87.8 0.51 1.1E-05 28.1 2.3 34 59-95 21-55 (64)
94 smart00529 HTH_DTXR Helix-turn 87.7 0.75 1.6E-05 28.9 3.1 30 64-96 2-31 (96)
95 PRK13509 transcriptional repre 87.5 0.88 1.9E-05 34.2 3.9 42 50-95 9-50 (251)
96 PF13730 HTH_36: Helix-turn-he 87.3 0.79 1.7E-05 26.2 2.8 29 63-94 27-55 (55)
97 PF13404 HTH_AsnC-type: AsnC-t 87.1 0.82 1.8E-05 25.8 2.7 37 47-86 4-40 (42)
98 PRK10870 transcriptional repre 87.1 1.1 2.4E-05 32.0 4.0 35 59-96 69-103 (176)
99 PRK09391 fixK transcriptional 87.0 0.67 1.5E-05 33.8 2.9 32 61-95 179-210 (230)
100 PRK10046 dpiA two-component re 86.8 0.85 1.9E-05 32.7 3.4 43 51-96 167-209 (225)
101 COG1675 TFA1 Transcription ini 85.7 1.1 2.5E-05 32.8 3.5 42 50-95 22-63 (176)
102 COG1725 Predicted transcriptio 85.2 2.4 5.1E-05 29.5 4.7 33 60-95 34-66 (125)
103 PRK09334 30S ribosomal protein 84.6 1.1 2.4E-05 29.4 2.7 33 60-95 40-72 (86)
104 PRK09802 DNA-binding transcrip 84.6 1.3 2.7E-05 33.8 3.4 43 49-95 20-62 (269)
105 COG1846 MarR Transcriptional r 84.5 1.4 3.1E-05 27.7 3.2 45 48-96 24-68 (126)
106 PRK04214 rbn ribonuclease BN/u 84.0 1.4 3.1E-05 35.4 3.7 36 58-96 307-342 (412)
107 COG1510 Predicted transcriptio 83.9 1.5 3.3E-05 32.3 3.5 35 58-95 38-72 (177)
108 COG4565 CitB Response regulato 83.9 1.5 3.2E-05 33.5 3.5 41 52-95 164-204 (224)
109 PF03297 Ribosomal_S25: S25 ri 83.7 1.5 3.3E-05 29.6 3.2 33 60-95 58-90 (105)
110 PRK10906 DNA-binding transcrip 83.3 1.5 3.2E-05 33.1 3.3 42 50-95 9-50 (252)
111 PF08221 HTH_9: RNA polymerase 83.3 3.6 7.7E-05 24.8 4.5 40 52-95 19-58 (62)
112 PF14947 HTH_45: Winged helix- 83.1 1.2 2.6E-05 27.8 2.3 34 59-95 17-50 (77)
113 PF07381 DUF1495: Winged helix 82.9 2.2 4.7E-05 28.1 3.6 45 47-94 10-65 (90)
114 PF00165 HTH_AraC: Bacterial r 82.8 1 2.2E-05 24.6 1.8 27 60-89 7-33 (42)
115 PRK10434 srlR DNA-bindng trans 82.5 1.6 3.4E-05 32.9 3.2 42 50-95 9-50 (256)
116 PF12793 SgrR_N: Sugar transpo 82.4 1.9 4.1E-05 29.3 3.3 33 60-95 18-50 (115)
117 COG4189 Predicted transcriptio 82.1 3.2 6.9E-05 32.6 4.8 53 37-95 16-68 (308)
118 TIGR00331 hrcA heat shock gene 82.0 2.5 5.4E-05 33.4 4.3 47 40-96 7-55 (337)
119 PHA02943 hypothetical protein; 81.9 2.2 4.7E-05 31.1 3.6 42 50-96 15-56 (165)
120 PF08784 RPA_C: Replication pr 81.9 2 4.4E-05 27.7 3.2 44 48-94 49-95 (102)
121 PRK14165 winged helix-turn-hel 81.8 1.9 4.2E-05 32.4 3.5 33 60-95 20-52 (217)
122 PRK10402 DNA-binding transcrip 81.7 1.5 3.3E-05 31.7 2.8 33 60-95 168-200 (226)
123 PRK04424 fatty acid biosynthes 81.5 1.2 2.7E-05 32.2 2.2 42 50-95 11-52 (185)
124 PRK05638 threonine synthase; V 81.5 2.2 4.7E-05 34.6 3.9 42 51-95 376-417 (442)
125 PF01418 HTH_6: Helix-turn-hel 80.9 0.8 1.7E-05 28.5 1.0 30 60-92 33-62 (77)
126 PRK00082 hrcA heat-inducible t 80.2 3.2 6.9E-05 32.9 4.3 36 58-96 22-59 (339)
127 PF12324 HTH_15: Helix-turn-he 80.0 3.5 7.6E-05 26.6 3.7 21 52-73 30-50 (77)
128 PRK11886 bifunctional biotin-- 79.7 2.4 5.3E-05 32.6 3.5 41 49-93 7-47 (319)
129 PRK09954 putative kinase; Prov 79.7 2.8 6.1E-05 32.5 3.8 44 48-95 5-48 (362)
130 COG1349 GlpR Transcriptional r 79.4 2.2 4.8E-05 32.2 3.1 42 50-95 9-50 (253)
131 PF13518 HTH_28: Helix-turn-he 79.1 3.6 7.7E-05 22.8 3.3 28 63-93 14-41 (52)
132 PRK04172 pheS phenylalanyl-tRN 78.9 3 6.5E-05 34.4 3.9 43 49-95 9-51 (489)
133 PRK11511 DNA-binding transcrip 78.8 2.9 6.3E-05 28.1 3.3 36 53-91 16-52 (127)
134 COG4901 Ribosomal protein S25 78.8 2.4 5.3E-05 28.9 2.8 45 48-95 43-90 (107)
135 PF13936 HTH_38: Helix-turn-he 78.6 2.2 4.7E-05 24.0 2.2 24 60-86 19-42 (44)
136 TIGR02698 CopY_TcrY copper tra 78.5 3.6 7.8E-05 28.1 3.7 48 47-95 5-53 (130)
137 TIGR00635 ruvB Holliday juncti 77.9 3.8 8.2E-05 30.7 4.0 35 58-95 252-287 (305)
138 PRK09775 putative DNA-binding 77.9 2.8 6E-05 34.5 3.5 37 52-95 6-42 (442)
139 smart00342 HTH_ARAC helix_turn 77.8 2.5 5.3E-05 24.8 2.4 26 61-89 1-26 (84)
140 PRK11302 DNA-binding transcrip 77.5 1.5 3.4E-05 32.6 1.8 43 47-92 17-62 (284)
141 PF03428 RP-C: Replication pro 76.6 14 0.00029 27.0 6.4 32 62-96 71-103 (177)
142 PRK10411 DNA-binding transcrip 76.6 4.2 9.1E-05 30.4 3.9 43 49-95 7-49 (240)
143 PF10668 Phage_terminase: Phag 76.4 3.1 6.7E-05 25.5 2.5 24 52-75 13-36 (60)
144 PF03965 Penicillinase_R: Peni 76.3 2.7 5.8E-05 27.8 2.5 49 47-96 4-53 (115)
145 PRK11557 putative DNA-binding 76.2 2 4.2E-05 32.1 2.0 42 48-92 14-58 (278)
146 PF01638 HxlR: HxlR-like helix 75.5 3.1 6.7E-05 26.4 2.5 34 60-96 17-51 (90)
147 PRK11534 DNA-binding transcrip 75.1 4.4 9.5E-05 29.2 3.5 34 59-95 28-61 (224)
148 PF03374 ANT: Phage antirepres 75.0 4.3 9.3E-05 26.4 3.2 39 50-94 13-51 (111)
149 smart00531 TFIIE Transcription 75.0 4.5 9.7E-05 28.2 3.4 39 50-92 5-43 (147)
150 PF05584 Sulfolobus_pRN: Sulfo 73.7 8 0.00017 24.6 4.0 42 50-96 9-50 (72)
151 PRK13239 alkylmercury lyase; P 73.7 4.5 9.8E-05 30.3 3.4 35 51-89 27-61 (206)
152 PRK13558 bacterio-opsin activa 73.4 4.4 9.6E-05 33.6 3.6 44 34-86 609-652 (665)
153 TIGR03338 phnR_burk phosphonat 73.3 4.7 0.0001 28.7 3.3 34 59-95 32-65 (212)
154 PRK09392 ftrB transcriptional 73.2 4.2 9.1E-05 29.3 3.0 30 61-93 173-202 (236)
155 TIGR02844 spore_III_D sporulat 72.8 4.3 9.3E-05 26.1 2.7 32 50-86 10-41 (80)
156 PF08222 HTH_CodY: CodY helix- 72.0 2 4.3E-05 26.5 0.9 35 60-97 3-37 (61)
157 PF13384 HTH_23: Homeodomain-l 71.9 2.4 5.1E-05 23.6 1.2 30 61-93 17-46 (50)
158 COG1737 RpiR Transcriptional r 71.8 1.8 4E-05 32.9 0.9 43 48-93 20-65 (281)
159 PF13744 HTH_37: Helix-turn-he 71.5 6 0.00013 24.6 3.1 40 51-92 23-72 (80)
160 PF06971 Put_DNA-bind_N: Putat 71.2 2.2 4.7E-05 25.1 1.0 31 50-83 16-47 (50)
161 PRK11642 exoribonuclease R; Pr 71.1 6.1 0.00013 35.0 4.0 45 51-95 24-69 (813)
162 PRK10430 DNA-binding transcrip 71.0 4.1 8.9E-05 29.4 2.6 34 60-96 177-210 (239)
163 PF00356 LacI: Bacterial regul 70.8 2.8 6E-05 24.1 1.3 31 63-93 1-43 (46)
164 PF00440 TetR_N: Bacterial reg 70.5 4.4 9.6E-05 22.6 2.1 21 60-83 15-35 (47)
165 PRK10219 DNA-binding transcrip 70.4 6.9 0.00015 25.0 3.3 29 60-91 20-48 (107)
166 PRK13777 transcriptional regul 70.3 8.1 0.00017 28.2 4.0 39 53-95 52-90 (185)
167 PF04492 Phage_rep_O: Bacterio 70.2 5.5 0.00012 26.5 2.8 46 47-95 33-85 (100)
168 PRK11414 colanic acid/biofilm 70.0 7.5 0.00016 28.0 3.8 34 59-95 32-65 (221)
169 PF13443 HTH_26: Cro/C1-type H 69.9 3.2 7E-05 24.0 1.5 30 52-86 3-32 (63)
170 PRK11337 DNA-binding transcrip 69.8 3.5 7.5E-05 31.0 2.0 43 47-92 29-74 (292)
171 COG1802 GntR Transcriptional r 69.5 8.4 0.00018 28.0 4.0 34 59-95 37-70 (230)
172 PRK10681 DNA-binding transcrip 69.2 6.4 0.00014 29.5 3.3 39 50-92 11-49 (252)
173 TIGR01764 excise DNA binding d 68.7 5 0.00011 21.5 2.1 22 62-86 2-23 (49)
174 cd04761 HTH_MerR-SF Helix-Turn 67.6 8.1 0.00018 21.0 2.8 27 62-95 1-27 (49)
175 TIGR03879 near_KaiC_dom probab 67.1 3.9 8.5E-05 26.0 1.5 32 60-94 31-62 (73)
176 PF02186 TFIIE_beta: TFIIE bet 66.9 9.2 0.0002 23.5 3.2 33 52-86 11-43 (65)
177 PRK01381 Trp operon repressor; 66.5 8.2 0.00018 25.9 3.1 40 47-91 43-82 (99)
178 PF02319 E2F_TDP: E2F/DP famil 65.7 3.3 7.2E-05 25.5 1.0 35 60-95 23-60 (71)
179 cd04762 HTH_MerR-trunc Helix-T 65.1 6.5 0.00014 20.8 2.1 22 62-86 1-22 (49)
180 PF12728 HTH_17: Helix-turn-he 64.7 6.4 0.00014 22.0 2.0 22 62-86 2-23 (51)
181 PRK15482 transcriptional regul 64.6 5.2 0.00011 30.1 2.1 43 47-92 17-62 (285)
182 PF00376 MerR: MerR family reg 64.5 6.9 0.00015 21.4 2.1 25 63-94 1-25 (38)
183 PRK00080 ruvB Holliday junctio 64.0 11 0.00023 29.0 3.8 34 59-95 274-308 (328)
184 KOG2165 Anaphase-promoting com 63.7 7.6 0.00016 34.3 3.1 34 60-96 615-648 (765)
185 TIGR03882 cyclo_dehyd_2 bacter 63.4 14 0.00031 26.8 4.2 37 59-96 40-76 (193)
186 PF03979 Sigma70_r1_1: Sigma-7 63.4 8.2 0.00018 24.3 2.5 34 60-93 20-53 (82)
187 PRK10572 DNA-binding transcrip 63.3 10 0.00022 28.2 3.4 38 51-91 188-226 (290)
188 PF13022 HTH_Tnp_1_2: Helix-tu 63.1 6.3 0.00014 28.2 2.1 31 53-86 26-56 (142)
189 TIGR01321 TrpR trp operon repr 63.1 9.7 0.00021 25.3 2.9 39 47-90 43-81 (94)
190 PF09269 DUF1967: Domain of un 63.1 4.3 9.2E-05 25.1 1.1 30 64-95 18-47 (69)
191 TIGR03613 RutR pyrimidine util 62.5 11 0.00024 26.2 3.4 23 52-74 18-41 (202)
192 TIGR03384 betaine_BetI transcr 62.5 13 0.00028 25.3 3.6 30 38-74 11-41 (189)
193 PRK09975 DNA-binding transcrip 62.1 13 0.00029 26.0 3.7 22 53-74 22-44 (213)
194 PF04545 Sigma70_r4: Sigma-70, 61.8 7.9 0.00017 21.6 2.1 24 60-86 19-42 (50)
195 PLN02853 Probable phenylalanyl 61.8 11 0.00024 31.8 3.6 46 47-95 4-49 (492)
196 PRK00135 scpB segregation and 61.6 14 0.0003 27.1 3.8 41 49-96 93-133 (188)
197 PRK15121 right oriC-binding tr 61.6 11 0.00023 28.4 3.3 36 53-91 12-48 (289)
198 PF09929 DUF2161: Uncharacteri 61.4 19 0.00042 24.9 4.2 40 32-86 54-93 (118)
199 PTZ00326 phenylalanyl-tRNA syn 61.3 13 0.00028 31.3 4.0 46 47-95 7-52 (494)
200 PHA02591 hypothetical protein; 61.0 14 0.0003 24.1 3.3 31 51-86 51-81 (83)
201 PRK10668 DNA-binding transcrip 60.9 16 0.00034 25.7 3.9 30 38-74 14-44 (215)
202 PF04760 IF2_N: Translation in 60.8 5.4 0.00012 23.0 1.3 29 60-94 2-31 (54)
203 PF08721 Tn7_Tnp_TnsA_C: TnsA 60.6 26 0.00056 20.9 4.4 41 51-95 32-76 (79)
204 PF01381 HTH_3: Helix-turn-hel 60.4 5.5 0.00012 22.3 1.2 24 60-86 8-31 (55)
205 PRK13503 transcriptional activ 60.3 11 0.00023 27.6 3.0 36 51-89 176-212 (278)
206 smart00422 HTH_MERR helix_turn 59.7 13 0.00029 21.6 2.9 27 62-95 1-27 (70)
207 PRK13756 tetracycline represso 59.5 17 0.00037 26.5 4.0 31 38-75 7-38 (205)
208 TIGR02531 yecD_yerC TrpR-relat 59.3 12 0.00026 24.3 2.8 25 61-88 50-74 (88)
209 PRK10225 DNA-binding transcrip 59.2 12 0.00026 27.5 3.2 34 59-95 30-64 (257)
210 COG5631 Predicted transcriptio 59.0 67 0.0015 23.9 6.9 62 30-95 62-130 (199)
211 PF04552 Sigma54_DBD: Sigma-54 58.8 3.2 6.9E-05 29.8 0.0 25 60-87 48-72 (160)
212 COG3703 ChaC Uncharacterized p 58.7 13 0.00028 27.8 3.2 36 60-95 130-169 (190)
213 PF13551 HTH_29: Winged helix- 58.4 16 0.00034 22.9 3.3 27 63-92 14-40 (112)
214 PRK03837 transcriptional regul 58.2 14 0.0003 26.8 3.3 34 59-95 34-68 (241)
215 PRK04984 fatty acid metabolism 58.2 13 0.00028 26.9 3.2 34 59-95 28-62 (239)
216 PF04218 CENP-B_N: CENP-B N-te 58.0 14 0.00031 21.4 2.8 33 48-86 12-44 (53)
217 PF07789 DUF1627: Protein of u 58.0 14 0.0003 26.8 3.1 33 59-94 4-36 (155)
218 PRK10421 DNA-binding transcrip 57.5 14 0.0003 27.3 3.2 34 59-95 23-57 (253)
219 PF05158 RNA_pol_Rpc34: RNA po 57.3 8.3 0.00018 30.5 2.1 43 51-96 89-132 (327)
220 TIGR02812 fadR_gamma fatty aci 57.2 14 0.0003 26.8 3.2 34 59-95 27-61 (235)
221 PF10007 DUF2250: Uncharacteri 57.2 20 0.00042 23.6 3.6 45 48-96 9-53 (92)
222 PRK09990 DNA-binding transcrip 56.9 14 0.00031 27.0 3.2 34 59-95 28-62 (251)
223 PF09286 Pro-kuma_activ: Pro-k 56.9 10 0.00023 25.7 2.3 32 59-93 45-76 (143)
224 PRK15008 HTH-type transcriptio 56.7 18 0.00038 25.8 3.6 31 37-74 20-51 (212)
225 PF13411 MerR_1: MerR HTH fami 56.2 11 0.00023 22.1 2.1 27 62-95 1-27 (69)
226 PRK09464 pdhR transcriptional 56.1 15 0.00033 26.9 3.2 34 59-95 31-65 (254)
227 PRK13626 transcriptional regul 56.0 12 0.00025 31.1 2.8 33 60-95 22-54 (552)
228 PF13542 HTH_Tnp_ISL3: Helix-t 56.0 13 0.00028 20.7 2.3 24 61-87 27-50 (52)
229 COG3682 Predicted transcriptio 55.7 20 0.00044 24.9 3.6 49 47-96 7-56 (123)
230 PF08280 HTH_Mga: M protein tr 55.5 9.4 0.0002 22.5 1.7 38 47-88 6-43 (59)
231 COG3695 Predicted methylated D 55.3 14 0.00031 25.0 2.7 32 58-90 20-51 (103)
232 COG2344 AT-rich DNA-binding pr 55.1 13 0.00029 28.1 2.8 40 50-92 20-60 (211)
233 COG4671 Predicted glycosyl tra 54.5 19 0.00041 29.7 3.8 36 38-75 328-363 (400)
234 PRK09480 slmA division inhibit 54.4 23 0.0005 24.2 3.8 16 59-74 28-43 (194)
235 PRK13502 transcriptional activ 54.4 16 0.00035 26.9 3.1 37 50-89 180-217 (282)
236 PRK05472 redox-sensing transcr 54.4 24 0.00052 25.6 4.0 43 47-92 17-60 (213)
237 COG2390 DeoR Transcriptional r 53.9 14 0.00031 29.3 3.0 33 60-95 25-57 (321)
238 PRK00767 transcriptional regul 53.8 22 0.00048 24.3 3.6 23 52-74 19-42 (197)
239 PF07638 Sigma70_ECF: ECF sigm 53.8 14 0.0003 26.2 2.6 26 60-88 150-175 (185)
240 PF13814 Replic_Relax: Replica 53.3 21 0.00047 24.8 3.5 36 60-95 8-43 (191)
241 COG2378 Predicted transcriptio 53.1 20 0.00043 28.0 3.6 40 50-93 12-51 (311)
242 cd07977 TFIIE_beta_winged_heli 53.1 26 0.00056 22.0 3.5 34 52-87 15-50 (75)
243 PF06413 Neugrin: Neugrin; In 53.0 12 0.00027 28.3 2.4 29 55-86 22-51 (225)
244 COG4465 CodY Pleiotropic trans 52.4 30 0.00065 26.8 4.3 45 50-97 193-237 (261)
245 PRK14996 TetR family transcrip 52.1 23 0.0005 24.5 3.5 22 53-74 19-41 (192)
246 TIGR02297 HpaA 4-hydroxyphenyl 51.8 20 0.00043 26.4 3.3 36 53-91 193-229 (287)
247 PF14394 DUF4423: Domain of un 51.7 49 0.0011 23.7 5.2 51 33-96 21-73 (171)
248 PF04433 SWIRM: SWIRM domain; 51.3 26 0.00056 21.9 3.4 35 58-95 50-85 (86)
249 TIGR02395 rpoN_sigma RNA polym 51.1 12 0.00025 30.7 2.1 24 60-86 317-340 (429)
250 PRK15186 AraC family transcrip 51.1 19 0.00041 27.9 3.2 34 51-87 186-220 (291)
251 PF04539 Sigma70_r3: Sigma-70 50.8 17 0.00038 21.8 2.4 30 57-89 16-45 (78)
252 TIGR03826 YvyF flagellar opero 50.6 22 0.00049 25.0 3.2 32 52-86 36-68 (137)
253 COG1309 AcrR Transcriptional r 50.6 49 0.0011 21.0 4.7 23 58-83 28-51 (201)
254 PF05331 DUF742: Protein of un 50.5 23 0.0005 24.2 3.2 32 60-94 54-85 (114)
255 PRK10371 DNA-binding transcrip 50.4 18 0.00039 27.6 2.9 35 52-89 197-232 (302)
256 PRK09940 transcriptional regul 50.3 18 0.00039 27.7 2.9 34 51-87 139-173 (253)
257 PHA00542 putative Cro-like pro 50.2 20 0.00042 22.5 2.7 23 60-85 30-52 (82)
258 PRK11523 DNA-binding transcrip 50.2 22 0.00047 26.2 3.3 34 59-95 29-63 (253)
259 PRK15340 transcriptional regul 50.1 20 0.00043 27.0 3.0 40 50-92 113-153 (216)
260 smart00354 HTH_LACI helix_turn 50.0 12 0.00026 22.6 1.6 16 78-93 29-44 (70)
261 PLN03238 probable histone acet 49.3 34 0.00075 27.1 4.4 32 58-95 220-251 (290)
262 PRK13501 transcriptional activ 48.8 19 0.00042 26.8 2.9 36 52-90 182-218 (290)
263 PF01710 HTH_Tnp_IS630: Transp 48.6 20 0.00043 23.9 2.6 25 59-86 69-93 (119)
264 PRK15185 transcriptional regul 48.6 22 0.00047 28.2 3.2 35 50-87 210-245 (309)
265 PLN00104 MYST -like histone ac 48.5 34 0.00075 28.6 4.5 33 57-95 370-402 (450)
266 PRK09978 DNA-binding transcrip 48.0 22 0.00048 27.5 3.1 34 51-87 147-181 (274)
267 PRK10736 hypothetical protein; 47.6 22 0.00048 28.9 3.2 42 50-96 312-353 (374)
268 TIGR03070 couple_hipB transcri 47.4 15 0.00032 20.2 1.6 15 60-74 14-28 (58)
269 smart00421 HTH_LUXR helix_turn 47.0 26 0.00057 18.8 2.6 24 60-86 17-40 (58)
270 PF09824 ArsR: ArsR transcript 46.9 37 0.0008 24.7 3.9 42 47-96 18-59 (160)
271 COG0640 ArsR Predicted transcr 46.5 58 0.0013 18.9 4.6 45 47-95 26-70 (110)
272 PRK11552 putative DNA-binding 46.0 41 0.00089 24.4 4.1 30 37-74 15-45 (225)
273 smart00351 PAX Paired Box doma 45.8 33 0.00071 23.1 3.4 33 60-95 32-64 (125)
274 PRK14101 bifunctional glucokin 45.6 15 0.00032 31.2 1.9 42 48-92 358-402 (638)
275 PRK09685 DNA-binding transcrip 45.5 25 0.00054 26.1 3.0 34 51-87 202-237 (302)
276 PF10771 DUF2582: Protein of u 45.5 26 0.00057 21.6 2.6 38 50-91 12-49 (65)
277 PRK05932 RNA polymerase factor 45.5 16 0.00035 30.2 2.1 24 60-86 342-365 (455)
278 PRK09393 ftrA transcriptional 45.3 31 0.00067 26.3 3.5 35 53-90 225-260 (322)
279 COG4977 Transcriptional regula 45.2 20 0.00044 28.6 2.6 27 60-89 235-261 (328)
280 PRK15044 transcriptional regul 45.1 27 0.00058 27.6 3.2 35 50-87 196-231 (295)
281 PRK13500 transcriptional activ 43.9 28 0.00061 26.5 3.1 37 51-90 211-248 (312)
282 COG2169 Ada Adenosine deaminas 43.8 33 0.00072 25.5 3.4 34 53-89 89-122 (187)
283 PF09079 Cdc6_C: CDC6, C termi 43.6 30 0.00064 21.4 2.7 32 64-95 25-56 (85)
284 PF05402 PqqD: Coenzyme PQQ sy 43.5 17 0.00037 21.3 1.6 41 51-94 22-67 (68)
285 PRK13824 replication initiatio 43.5 24 0.00052 28.8 2.8 32 62-96 83-115 (404)
286 cd06171 Sigma70_r4 Sigma70, re 43.1 28 0.0006 18.2 2.3 25 60-87 25-49 (55)
287 PF03551 PadR: Transcriptional 42.9 16 0.00034 22.1 1.3 37 60-96 8-49 (75)
288 TIGR03595 Obg_CgtA_exten Obg f 42.8 35 0.00075 21.0 2.9 31 63-95 17-47 (69)
289 TIGR02063 RNase_R ribonuclease 42.4 36 0.00077 29.4 3.8 45 51-95 7-53 (709)
290 PF02387 IncFII_repA: IncFII R 42.4 34 0.00075 26.8 3.4 37 60-96 94-137 (281)
291 COG2207 AraC AraC-type DNA-bin 42.3 36 0.00078 21.2 3.0 28 60-90 35-62 (127)
292 PRK00118 putative DNA-binding 41.8 25 0.00054 23.6 2.3 24 60-86 32-55 (104)
293 cd06445 ATase The DNA repair p 41.5 45 0.00098 20.6 3.3 28 58-86 14-41 (79)
294 PF05732 RepL: Firmicute plasm 41.3 28 0.00061 24.9 2.6 33 61-96 75-107 (165)
295 PF13560 HTH_31: Helix-turn-he 40.8 17 0.00037 21.2 1.2 23 60-85 13-35 (64)
296 COG0664 Crp cAMP-binding prote 40.8 43 0.00092 22.6 3.4 33 60-95 170-202 (214)
297 cd04764 HTH_MlrA-like_sg1 Heli 40.7 37 0.0008 19.8 2.7 14 62-75 1-14 (67)
298 COG3645 Uncharacterized phage- 40.7 34 0.00073 24.3 2.8 39 50-94 36-74 (135)
299 COG2186 FadR Transcriptional r 40.3 34 0.00074 25.4 3.1 32 62-96 35-66 (241)
300 PRK11202 DNA-binding transcrip 40.3 38 0.00083 23.9 3.2 21 55-75 25-46 (203)
301 cd04763 HTH_MlrA-like Helix-Tu 40.1 40 0.00087 19.8 2.8 25 63-94 2-27 (68)
302 PF13591 MerR_2: MerR HTH fami 40.0 32 0.00069 21.7 2.5 27 62-95 1-27 (84)
303 PF13986 DUF4224: Domain of un 39.9 61 0.0013 18.5 3.4 28 62-94 3-30 (47)
304 PF00196 GerE: Bacterial regul 39.7 25 0.00055 20.1 1.8 26 47-75 7-32 (58)
305 PRK12469 RNA polymerase factor 39.6 25 0.00054 29.5 2.4 24 60-86 368-391 (481)
306 PF09441 Abp2: ARS binding pro 39.6 21 0.00045 26.3 1.7 31 60-90 69-112 (175)
307 PRK11640 putative transcriptio 39.5 47 0.001 23.5 3.5 22 53-74 12-34 (191)
308 COG1733 Predicted transcriptio 39.3 52 0.0011 22.3 3.6 34 60-96 35-69 (120)
309 cd01105 HTH_GlnR-like Helix-Tu 38.8 41 0.00089 21.2 2.8 27 62-95 2-28 (88)
310 PRK04217 hypothetical protein; 38.7 30 0.00064 23.4 2.2 25 60-87 57-81 (110)
311 COG2188 PhnF Transcriptional r 38.5 27 0.00058 25.8 2.2 32 62-96 32-63 (236)
312 TIGR00180 parB_part ParB-like 38.2 36 0.00079 24.2 2.8 27 60-89 119-145 (187)
313 PF08281 Sigma70_r4_2: Sigma-7 38.0 26 0.00055 19.6 1.6 22 60-84 25-46 (54)
314 PRK15418 transcriptional regul 37.9 41 0.00088 26.3 3.2 33 60-95 28-60 (318)
315 cd08768 Cdc6_C Winged-helix do 37.9 48 0.001 20.1 3.0 32 64-95 32-63 (87)
316 cd06170 LuxR_C_like C-terminal 37.8 45 0.00097 18.0 2.6 24 60-86 14-37 (57)
317 PRK10265 chaperone-modulator p 37.8 29 0.00062 22.7 2.0 28 61-95 7-34 (101)
318 KOG2747 Histone acetyltransfer 37.7 41 0.0009 27.7 3.3 46 34-95 312-357 (396)
319 PF14502 HTH_41: Helix-turn-he 37.5 59 0.0013 19.1 3.1 33 60-95 5-37 (48)
320 COG2524 Predicted transcriptio 37.3 73 0.0016 25.3 4.5 41 53-96 17-57 (294)
321 PF08535 KorB: KorB domain; I 37.0 20 0.00042 22.8 1.1 25 61-88 3-27 (93)
322 PRK15435 bifunctional DNA-bind 36.7 49 0.0011 26.3 3.5 33 53-89 92-124 (353)
323 TIGR02404 trehalos_R_Bsub treh 36.6 37 0.00081 24.5 2.7 31 63-96 26-56 (233)
324 PF05066 HARE-HTH: HB1, ASXL, 36.6 19 0.0004 21.7 0.9 21 52-72 8-28 (72)
325 PRK10130 transcriptional regul 36.4 38 0.00082 26.9 2.9 34 53-89 247-281 (350)
326 cd00131 PAX Paired Box domain 36.2 28 0.00062 23.6 1.9 41 48-94 23-63 (128)
327 PF09743 DUF2042: Uncharacteri 36.1 52 0.0011 25.4 3.5 38 51-91 60-97 (272)
328 COG3432 Predicted transcriptio 36.0 20 0.00044 23.8 1.1 41 51-94 20-61 (95)
329 PHA01976 helix-turn-helix prot 36.0 29 0.00064 20.1 1.7 15 60-74 14-28 (67)
330 PF01853 MOZ_SAS: MOZ/SAS fami 35.8 43 0.00093 24.9 2.9 29 61-95 150-178 (188)
331 COG4742 Predicted transcriptio 35.8 77 0.0017 24.6 4.4 45 47-96 14-58 (260)
332 TIGR02937 sigma70-ECF RNA poly 35.7 40 0.00086 21.3 2.5 24 60-86 125-148 (158)
333 TIGR02366 DHAK_reg probable di 35.6 45 0.00098 22.6 2.9 23 52-74 13-36 (176)
334 PF01371 Trp_repressor: Trp re 35.2 56 0.0012 21.2 3.1 38 47-90 37-75 (87)
335 smart00530 HTH_XRE Helix-turn- 35.1 57 0.0012 16.4 2.7 13 61-73 10-22 (56)
336 PF10078 DUF2316: Uncharacteri 35.0 34 0.00074 22.5 2.0 23 60-85 22-44 (89)
337 PF05344 DUF746: Domain of Unk 34.9 52 0.0011 20.5 2.8 26 59-87 11-36 (65)
338 PF10975 DUF2802: Protein of u 34.8 20 0.00043 22.3 0.9 24 61-84 44-67 (70)
339 cd02420 Peptidase_C39D A sub-f 34.6 1.2E+02 0.0026 19.2 5.0 35 58-93 24-58 (125)
340 PRK01905 DNA-binding protein F 34.5 97 0.0021 19.1 4.0 32 51-87 42-73 (77)
341 cd02424 Peptidase_C39E A sub-f 34.3 1.3E+02 0.0028 19.4 4.9 35 58-93 25-59 (129)
342 PRK03911 heat-inducible transc 34.1 1.2E+02 0.0027 23.6 5.3 49 40-96 8-56 (260)
343 TIGR03433 padR_acidobact trans 34.1 81 0.0018 20.2 3.7 41 53-95 11-56 (100)
344 TIGR02392 rpoH_proteo alternat 33.9 37 0.00081 25.5 2.4 24 60-86 235-258 (270)
345 TIGR02325 C_P_lyase_phnF phosp 33.9 44 0.00095 24.0 2.7 31 63-96 34-64 (238)
346 PRK08558 adenine phosphoribosy 33.8 36 0.00079 25.6 2.3 36 47-85 9-44 (238)
347 PRK09492 treR trehalose repres 33.8 31 0.00067 25.3 1.9 23 61-86 4-26 (315)
348 PF00888 Cullin: Cullin family 33.7 15 0.00032 30.0 0.2 34 59-95 532-565 (588)
349 TIGR03337 phnR transcriptional 33.6 43 0.00093 24.0 2.6 31 63-96 27-57 (231)
350 PRK11303 DNA-binding transcrip 33.4 29 0.00063 25.7 1.7 32 62-93 1-47 (328)
351 TIGR02277 PaaX_trns_reg phenyl 33.3 55 0.0012 25.2 3.3 43 53-95 9-51 (280)
352 PF04157 EAP30: EAP30/Vps36 fa 33.2 36 0.00078 25.0 2.2 40 52-94 180-220 (223)
353 smart00088 PINT motif in prote 33.0 79 0.0017 19.2 3.4 33 60-95 23-55 (88)
354 smart00753 PAM PCI/PINT associ 33.0 79 0.0017 19.2 3.4 33 60-95 23-55 (88)
355 TIGR02607 antidote_HigA addict 33.0 51 0.0011 19.5 2.5 13 61-73 18-30 (78)
356 PF04079 DUF387: Putative tran 32.9 40 0.00087 24.0 2.3 28 58-89 10-37 (159)
357 PHA02701 ORF020 dsRNA-binding 32.5 82 0.0018 23.4 3.9 40 47-86 5-45 (183)
358 PF11972 HTH_13: HTH DNA bindi 32.5 68 0.0015 19.2 2.9 34 51-89 4-38 (54)
359 PRK10014 DNA-binding transcrip 32.0 33 0.00071 25.5 1.8 24 60-86 5-28 (342)
360 PF14357 DUF4404: Domain of un 32.0 41 0.00089 21.5 2.0 20 74-93 66-85 (85)
361 COG2865 Predicted transcriptio 31.9 59 0.0013 27.3 3.4 39 53-95 409-447 (467)
362 COG3978 Acetolactate synthase 31.7 32 0.00069 22.6 1.4 18 77-94 13-30 (86)
363 PRK09526 lacI lac repressor; R 31.5 34 0.00074 25.4 1.8 24 60-86 4-27 (342)
364 TIGR00589 ogt O-6-methylguanin 31.5 87 0.0019 19.7 3.5 28 58-86 16-43 (80)
365 PF01035 DNA_binding_1: 6-O-me 31.4 38 0.00081 21.4 1.8 28 58-86 16-43 (85)
366 COG4367 Uncharacterized protei 31.4 46 0.001 22.2 2.2 23 60-85 22-44 (97)
367 cd01104 HTH_MlrA-CarA Helix-Tu 31.2 35 0.00076 19.7 1.5 19 63-84 2-20 (68)
368 cd04895 ACT_ACR_1 ACT domain-c 31.2 46 0.001 20.7 2.1 17 77-93 11-27 (72)
369 PRK14999 histidine utilization 30.6 52 0.0011 24.0 2.7 33 60-95 34-67 (241)
370 COG3655 Predicted transcriptio 30.6 38 0.00082 21.6 1.6 24 49-74 5-28 (73)
371 PRK15481 transcriptional regul 30.5 62 0.0013 25.5 3.2 34 59-95 26-60 (431)
372 TIGR01481 ccpA catabolite cont 30.4 35 0.00076 25.2 1.7 32 62-93 2-45 (329)
373 cd00569 HTH_Hin_like Helix-tur 30.4 40 0.00087 15.5 1.5 21 61-84 21-41 (42)
374 PRK15002 redox-sensitivie tran 30.4 61 0.0013 22.9 2.9 29 60-95 10-38 (154)
375 PF13309 HTH_22: HTH domain 30.3 46 0.00099 20.0 1.9 36 40-86 29-64 (64)
376 PRK13890 conjugal transfer pro 30.3 48 0.001 22.3 2.2 14 60-73 17-30 (120)
377 PF05930 Phage_AlpA: Prophage 29.7 35 0.00077 19.3 1.3 22 62-86 4-25 (51)
378 PRK11063 metQ DL-methionine tr 29.6 43 0.00094 25.5 2.1 35 60-95 120-156 (271)
379 COG2412 Uncharacterized conser 29.4 1E+02 0.0023 20.8 3.7 42 4-53 40-81 (101)
380 COG4567 Response regulator con 29.2 92 0.002 23.0 3.6 55 33-92 88-155 (182)
381 TIGR00475 selB selenocysteine- 29.2 63 0.0014 27.4 3.2 32 60-94 487-518 (581)
382 PF02954 HTH_8: Bacterial regu 29.1 81 0.0018 17.1 2.7 29 53-86 12-40 (42)
383 cd04896 ACT_ACR-like_3 ACT dom 29.0 49 0.0011 20.8 2.0 17 77-93 10-26 (75)
384 COG1164 Oligoendopeptidase F [ 28.9 2.7E+02 0.0059 23.8 7.0 65 22-89 512-586 (598)
385 PF09940 DUF2172: Domain of un 28.9 37 0.00079 28.0 1.7 44 49-95 343-386 (386)
386 TIGR02018 his_ut_repres histid 28.5 61 0.0013 23.4 2.7 33 60-95 23-56 (230)
387 TIGR03859 PQQ_PqqD coenzyme PQ 28.5 1.1E+02 0.0024 19.0 3.6 40 51-94 36-80 (81)
388 PRK05658 RNA polymerase sigma 28.4 65 0.0014 27.4 3.2 56 24-87 436-506 (619)
389 PF02787 CPSase_L_D3: Carbamoy 28.3 54 0.0012 22.3 2.2 29 52-86 17-45 (123)
390 PF06224 HTH_42: Winged helix 28.3 1.1E+02 0.0024 23.1 4.2 44 51-95 90-138 (327)
391 PRK09726 antitoxin HipB; Provi 28.2 43 0.00093 20.9 1.6 15 60-74 24-38 (88)
392 TIGR02985 Sig70_bacteroi1 RNA 28.1 57 0.0012 21.3 2.3 22 60-84 128-149 (161)
393 PRK13752 putative transcriptio 28.0 71 0.0015 22.2 2.8 29 60-95 6-34 (144)
394 PRK14987 gluconate operon tran 28.0 40 0.00087 25.1 1.7 24 60-86 4-27 (331)
395 PRK05901 RNA polymerase sigma 28.0 76 0.0017 26.8 3.5 56 24-87 327-397 (509)
396 cd01392 HTH_LacI Helix-turn-he 27.9 29 0.00062 19.0 0.7 33 62-94 9-42 (52)
397 TIGR02147 Fsuc_second hypothet 27.7 1.9E+02 0.0041 22.3 5.4 53 33-96 119-171 (271)
398 TIGR02719 repress_PhaQ poly-be 27.6 2.2E+02 0.0047 19.9 5.5 47 47-95 25-74 (138)
399 PRK00135 scpB segregation and 27.5 80 0.0017 23.1 3.1 29 58-89 16-45 (188)
400 PF03704 BTAD: Bacterial trans 27.4 85 0.0018 20.6 3.1 40 53-92 70-110 (146)
401 cd00093 HTH_XRE Helix-turn-hel 27.2 95 0.0021 15.6 2.7 13 61-73 12-24 (58)
402 PRK09764 DNA-binding transcrip 27.2 66 0.0014 23.5 2.7 34 59-95 26-60 (240)
403 PRK10703 DNA-binding transcrip 26.8 43 0.00094 24.9 1.7 22 62-86 2-23 (341)
404 PRK11402 DNA-binding transcrip 26.7 67 0.0014 23.4 2.6 31 62-95 34-64 (241)
405 PLN03239 histone acetyltransfe 26.5 1.3E+02 0.0027 24.6 4.3 48 34-95 265-312 (351)
406 TIGR02216 phage_TIGR02216 phag 26.3 91 0.002 19.1 2.7 27 61-87 24-56 (60)
407 PRK07037 extracytoplasmic-func 26.3 64 0.0014 21.6 2.3 16 60-75 124-139 (163)
408 cd06459 M3B_Oligoendopeptidase 26.1 3.1E+02 0.0067 21.3 6.4 31 58-88 396-426 (427)
409 COG3620 Predicted transcriptio 25.9 85 0.0018 23.3 3.0 29 61-90 18-59 (187)
410 PF11761 CbiG_mid: Cobalamin b 25.8 51 0.0011 20.1 1.6 30 63-92 3-32 (93)
411 PRK07921 RNA polymerase sigma 25.6 58 0.0013 25.6 2.2 23 59-84 280-302 (324)
412 PRK07405 RNA polymerase sigma 25.5 66 0.0014 25.0 2.5 23 59-84 274-296 (317)
413 PF02042 RWP-RK: RWP-RK domain 25.3 71 0.0015 18.9 2.1 23 61-86 15-37 (52)
414 PRK04158 transcriptional repre 25.1 25 0.00055 27.3 0.1 45 50-97 190-234 (256)
415 COG1497 Predicted transcriptio 25.0 1E+02 0.0023 24.1 3.5 36 58-96 22-57 (260)
416 PRK06596 RNA polymerase factor 25.0 63 0.0014 24.6 2.3 24 60-86 247-270 (284)
417 cd02418 Peptidase_C39B A sub-f 24.8 1.9E+02 0.0042 18.3 4.6 35 58-93 24-58 (136)
418 PRK10401 DNA-binding transcrip 24.8 48 0.001 24.9 1.6 13 62-74 2-14 (346)
419 KOG1767 40S ribosomal protein 24.7 60 0.0013 22.2 1.9 33 60-95 59-91 (110)
420 PF07848 PaaX: PaaX-like prote 24.6 99 0.0021 19.0 2.8 43 53-95 12-54 (70)
421 PF10376 Mei5: Double-strand r 24.3 1.1E+02 0.0025 23.0 3.5 36 36-75 179-215 (221)
422 TIGR02885 spore_sigF RNA polym 24.2 68 0.0015 23.1 2.3 23 60-85 198-220 (231)
423 cd02419 Peptidase_C39C A sub-f 24.0 2E+02 0.0043 18.2 4.8 35 58-93 24-58 (127)
424 PF07900 DUF1670: Protein of u 23.7 3.4E+02 0.0073 20.7 6.5 34 58-94 102-136 (220)
425 PRK10339 DNA-binding transcrip 23.6 50 0.0011 24.5 1.5 13 62-74 2-14 (327)
426 TIGR02997 Sig70-cyanoRpoD RNA 23.5 78 0.0017 24.1 2.6 25 59-86 267-291 (298)
427 cd02423 Peptidase_C39G A sub-f 23.4 2E+02 0.0044 18.1 4.9 35 58-93 24-59 (129)
428 PF07106 TBPIP: Tat binding pr 23.1 1.5E+02 0.0032 20.7 3.8 45 51-96 6-50 (169)
429 PF12200 DUF3597: Domain of un 22.8 72 0.0016 22.4 2.0 29 64-92 88-123 (127)
430 PRK10079 phosphonate metabolis 22.7 90 0.0019 22.7 2.7 31 62-95 36-66 (241)
431 PRK10727 DNA-binding transcrip 22.6 55 0.0012 24.5 1.6 31 63-93 3-45 (343)
432 PF06056 Terminase_5: Putative 22.4 86 0.0019 18.6 2.1 15 60-74 12-26 (58)
433 PRK13413 mpi multiple promoter 22.1 1E+02 0.0023 21.9 2.9 24 60-86 171-194 (200)
434 PRK12427 flagellar biosynthesi 21.9 92 0.002 22.9 2.6 26 60-88 198-223 (231)
435 COG3398 Uncharacterized protei 21.8 1.8E+02 0.004 22.5 4.2 44 48-95 103-146 (240)
436 PRK15411 rcsA colanic acid cap 21.8 1.1E+02 0.0023 22.0 2.9 40 47-89 141-181 (207)
437 PRK11924 RNA polymerase sigma 21.7 96 0.0021 20.6 2.5 16 60-75 140-155 (179)
438 TIGR02405 trehalos_R_Ecol treh 21.7 67 0.0015 23.7 1.8 21 62-85 2-22 (311)
439 TIGR02393 RpoD_Cterm RNA polym 21.5 91 0.002 22.7 2.5 23 59-84 194-216 (238)
440 PRK15201 fimbriae regulatory p 21.4 1.1E+02 0.0023 23.1 2.8 40 47-89 137-177 (198)
441 TIGR02850 spore_sigG RNA polym 21.4 85 0.0018 23.2 2.3 24 60-86 221-244 (254)
442 PRK09863 putative frv operon r 21.3 99 0.0021 25.8 2.9 36 48-88 6-41 (584)
443 PRK09333 30S ribosomal protein 21.2 2.7E+02 0.006 19.9 4.8 36 60-95 66-112 (150)
444 COG5027 SAS2 Histone acetyltra 21.1 1.3E+02 0.0028 24.8 3.5 45 34-95 314-359 (395)
445 PF15467 SGIII: Secretogranin- 21.0 1.1E+02 0.0024 25.4 3.0 45 52-96 120-168 (453)
446 cd04897 ACT_ACR_3 ACT domain-c 20.7 90 0.0019 19.6 2.0 17 77-93 11-27 (75)
447 cd04773 HTH_TioE_rpt2 Second H 20.7 74 0.0016 20.8 1.7 14 62-75 1-14 (108)
448 PF04297 UPF0122: Putative hel 20.6 69 0.0015 21.4 1.5 24 60-86 32-55 (101)
449 PF00126 HTH_1: Bacterial regu 20.5 1E+02 0.0022 17.7 2.2 37 48-90 3-39 (60)
450 PRK10512 selenocysteinyl-tRNA- 20.5 1.2E+02 0.0026 26.0 3.3 32 60-94 505-536 (614)
451 cd00592 HTH_MerR-like Helix-Tu 20.4 90 0.002 19.5 2.0 14 62-75 1-14 (100)
452 PRK07500 rpoH2 RNA polymerase 20.4 90 0.0019 23.8 2.3 24 60-86 244-267 (289)
453 PRK12529 RNA polymerase sigma 20.3 1.1E+02 0.0024 21.0 2.6 16 60-75 142-157 (178)
454 COG3357 Predicted transcriptio 20.3 1.9E+02 0.0041 19.4 3.5 25 50-74 7-31 (97)
455 PRK05949 RNA polymerase sigma 20.2 97 0.0021 24.3 2.5 23 59-84 284-306 (327)
No 1
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=99.67 E-value=3.3e-17 Score=98.09 Aligned_cols=49 Identities=39% Similarity=0.731 Sum_probs=44.5
Q ss_pred HHHHHHHHHhcChhHHHhhCC-CCCCHHHHHHHhC-CCCCCcccHHHHHHHHH
Q 041844 39 MSLKCVKLIQVGIPDIIHNHT-KPMTLNQLLGALQ-IHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 39 ~aL~~a~~veLgI~D~La~~~-gp~s~~ELA~~~g-~~~~~~~~L~RlLR~La 89 (97)
|+|||| |||||||+|+++| +|+|++||+++++ .+|+++..|+|+||+|+
T Consensus 1 MaLk~a--veLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~ 51 (51)
T PF08100_consen 1 MALKCA--VELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV 51 (51)
T ss_dssp HHHHHH--HHTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred CcHHHH--HHcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence 799999 9999999999997 9999999999999 78878899999999996
No 2
>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=99.13 E-value=7.6e-11 Score=89.76 Aligned_cols=53 Identities=21% Similarity=0.262 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 37 NSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 37 ~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
..++|++| ++|||||+|++ +|+|++|||+++|++| ..++|+||+|+++|+|++
T Consensus 3 ~~~~l~aa--~~Lglfd~L~~--gp~t~~eLA~~~~~~~---~~~~~lL~~L~~lgll~~ 55 (306)
T TIGR02716 3 EFSCMKAA--IELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETLRQMRVINL 55 (306)
T ss_pred hHHHHHHH--HHcCcHHHHhc--CCCCHHHHHHHcCCCh---HHHHHHHHHHHhCCCeEe
Confidence 46899999 99999999976 8999999999999965 899999999999999975
No 3
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.10 E-value=1.5e-10 Score=91.71 Aligned_cols=71 Identities=23% Similarity=0.273 Sum_probs=60.6
Q ss_pred HHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhC--CCCCCcccHHHHHHHHHhcCcc
Q 041844 17 LQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ--IHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 17 ~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g--~~~~~~~~L~RlLR~Laa~gif 94 (97)
-++...+ +++.+++..+|++++| +||||||+|+++++ .+|+|..+. ..|.+|..++|+||.|++.+++
T Consensus 4 ~~~~l~~-----~~l~~~~~~~~~lk~A--~eL~v~d~l~~~~~---p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~ 73 (342)
T KOG3178|consen 4 NEASLRA-----MRLANGFALPMVLKAA--CELGVFDILANAGS---PSEIASLLPTPKNPEAPVLLDRILRLLVSYSIL 73 (342)
T ss_pred hHHHHHH-----HHHHhhhhhHHHHHHH--HHcChHHHHHhCCC---HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhc
Confidence 3455666 8889999999999999 99999999998655 778887776 5666889999999999999999
Q ss_pred ccC
Q 041844 95 NLR 97 (97)
Q Consensus 95 ~e~ 97 (97)
+++
T Consensus 74 k~~ 76 (342)
T KOG3178|consen 74 KCR 76 (342)
T ss_pred eee
Confidence 863
No 4
>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=98.04 E-value=2.3e-06 Score=50.18 Aligned_cols=45 Identities=24% Similarity=0.437 Sum_probs=39.3
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.|.+.++.+++++|+.|||+++|.+. ..++|+|+.|+..|++..
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~---stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPK---STVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCcCeec
Confidence 367788988888999999999999954 899999999999999864
No 5
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.42 E-value=0.00023 Score=44.82 Aligned_cols=45 Identities=18% Similarity=0.284 Sum_probs=38.9
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.|.+.|+++++++|+.|||+.+|++. ..++|+|+.|...|++..
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~---~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSK---STAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeee
Confidence 467788887657999999999999954 899999999999998863
No 6
>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=96.99 E-value=0.00085 Score=49.84 Aligned_cols=45 Identities=13% Similarity=0.229 Sum_probs=39.2
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.|.+.++.+.+|+|+.|||+.+|.+. ..++|+|..|+..|++..
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpk---sT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTR---AAARRFLLTLVELGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEe
Confidence 367788877678999999999999955 899999999999998863
No 7
>PRK11569 transcriptional repressor IclR; Provisional
Probab=96.99 E-value=0.00085 Score=50.82 Aligned_cols=44 Identities=16% Similarity=0.297 Sum_probs=38.8
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|.|.+.++++.+++|++|||+.+|.+. ..++|+|+.|+..|++.
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpk---sTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPN---STTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 366788887778999999999999955 89999999999999985
No 8
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=96.92 E-value=0.0011 Score=50.31 Aligned_cols=45 Identities=11% Similarity=0.116 Sum_probs=39.2
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.|.+.++.+++++|+.|||+.+|.+. ..++|+|..|+..|++..
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpk---Stv~RlL~tL~~~G~l~~ 72 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPL---STTFRLLKVLQAADFVYQ 72 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence 367788887778899999999999955 899999999999999853
No 9
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=96.71 E-value=0.002 Score=48.54 Aligned_cols=45 Identities=22% Similarity=0.380 Sum_probs=39.0
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|.|.|.|++++.++++.|||+++|.++ ..++|+|..|+..|+++.
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpk---sT~~RlL~tL~~~G~v~~ 51 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPK---STVHRLLQTLVELGYVEQ 51 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEE
Confidence 467888988556678999999999965 899999999999999874
No 10
>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=96.66 E-value=0.0027 Score=36.06 Aligned_cols=45 Identities=18% Similarity=0.236 Sum_probs=36.2
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+..|.+.|.++ +.+|..|||..+|++ ...+.+.++-|...|+++
T Consensus 4 ~~~~Il~~l~~~-~~~t~~ela~~~~is---~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLREN-PRITQKELAEKLGIS---RSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHC-TTS-HHHHHHHHTS----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHhCCC---HHHHHHHHHHHHHCcCcC
Confidence 355677888774 469999999999994 489999999999999874
No 11
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=96.55 E-value=0.0028 Score=47.69 Aligned_cols=44 Identities=14% Similarity=0.187 Sum_probs=38.2
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.|.+.+..+++++|+.|||+.+|++. ..++|+++.|+..|++.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~k---stv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHR---TTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 366788877777899999999999955 89999999999999985
No 12
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=96.48 E-value=0.0062 Score=37.58 Aligned_cols=46 Identities=20% Similarity=0.216 Sum_probs=38.1
Q ss_pred HhcChhHHHhhCCC-CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTK-PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~g-p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+=.|.+.|..+++ ++|+.|||..+|++. ..++|+|-.|...|++.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~---~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPK---KEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 34456777877765 399999999999955 78999999999999875
No 13
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=96.46 E-value=0.0032 Score=47.05 Aligned_cols=43 Identities=9% Similarity=0.233 Sum_probs=36.7
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|.+.+..+ +++|++|||+.+|++. ..++|+|+.|+..|++..
T Consensus 18 ~IL~~l~~~-~~l~l~eia~~lgl~k---stv~Rll~tL~~~G~l~~ 60 (257)
T PRK15090 18 GILQALGEE-REIGITELSQRVMMSK---STVYRFLQTMKTLGYVAQ 60 (257)
T ss_pred HHHHHhhcC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence 566777654 5899999999999955 899999999999999853
No 14
>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=96.43 E-value=0.0033 Score=37.58 Aligned_cols=46 Identities=20% Similarity=0.398 Sum_probs=38.4
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
..+.|.+.|.. ++|+|+.|||+.+|+++ ..+++=|+.|...|+++.
T Consensus 11 ~R~~Il~~L~~-~~~~t~~ela~~l~~~~---~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 11 TRLRILRLLAS-NGPMTVSELAEELGISQ---STVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HHHHHHHHHHH-CSTBEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHhc-CCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEE
Confidence 56677888833 48999999999999954 889999999999999863
No 15
>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=96.40 E-value=0.006 Score=38.53 Aligned_cols=33 Identities=24% Similarity=0.490 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+++|..|||+.+++++ ..++++|+.|...|+++
T Consensus 24 ~~~s~~eiA~~~~i~~---~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 24 KPVSSKEIAERLGISP---SYLRKILQKLKKAGLIE 56 (83)
T ss_dssp C-BEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHHHhhCCeeE
Confidence 5799999999999955 99999999999999976
No 16
>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=96.38 E-value=0.0028 Score=36.22 Aligned_cols=43 Identities=16% Similarity=0.354 Sum_probs=36.3
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++.|...|.+ ||.++.||++.+|+++ ..+.+-|+.|...|+++
T Consensus 4 R~~Il~~L~~--~~~~~~el~~~l~~s~---~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSE--GPLTVSELAEELGLSQ---STVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHTT--SSEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHh--CCCchhhHHHhccccc---hHHHHHHHHHHHCcCee
Confidence 4556677765 8999999999999954 89999999999999875
No 17
>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=96.21 E-value=0.0046 Score=36.25 Aligned_cols=44 Identities=18% Similarity=0.228 Sum_probs=34.7
Q ss_pred ChhHHHhhCCCC-CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 50 GIPDIIHNHTKP-MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 50 gI~D~La~~~gp-~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|.-.|..++++ +|..|||+.+++++ ..+.|+++.|...|++..
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~---~~vs~~v~~L~~~Glv~r 53 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISK---STVSRIVKRLEKKGLVER 53 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence 344556555543 89999999999954 899999999999998863
No 18
>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=96.03 E-value=0.013 Score=38.51 Aligned_cols=48 Identities=10% Similarity=0.144 Sum_probs=38.1
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCC--CCCcccHHHHHHHHHhcCcccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIH--PTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~--~~~~~~L~RlLR~Laa~gif~e 96 (97)
..|.+.|...+++.|++||.+.+.-. ..+...++|.|..|+..|++.+
T Consensus 4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 4 LAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 45678887777899999999998531 1155889999999999998763
No 19
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=95.93 E-value=0.015 Score=41.42 Aligned_cols=56 Identities=14% Similarity=0.265 Sum_probs=43.3
Q ss_pred hHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 34 ~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+|-..+.+-+= -.+.+...|+. .+|.|+.|||+.+|= |...++|=||.|...|++.
T Consensus 54 Sye~la~vLsp--~nleLl~~Ia~-~~P~Si~ElAe~vgR---dv~nvhr~Ls~l~~~GlI~ 109 (144)
T COG4190 54 SYEDLARVLSP--RNLELLELIAQ-EEPASINELAELVGR---DVKNVHRTLSTLADLGLIF 109 (144)
T ss_pred cHHHHHHHhCh--hHHHHHHHHHh-cCcccHHHHHHHhCc---chHHHHHHHHHHHhcCeEE
Confidence 44444444444 55677788865 479999999999998 4489999999999999865
No 20
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=95.91 E-value=0.012 Score=42.13 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=32.0
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.++|+|++|||+++++++ ..|.+||+.|...|++..
T Consensus 22 ~~~~vs~~eIA~~~~ip~---~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 22 EAGPVPLADISERQGISL---SYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred CCCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEe
Confidence 347999999999999965 899999999999999863
No 21
>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=95.89 E-value=0.011 Score=40.00 Aligned_cols=34 Identities=9% Similarity=0.234 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++++|+.|||+++++++ ..+.++|+.|...|++.
T Consensus 23 ~~~~s~~eia~~l~is~---~~v~~~l~~L~~~Gli~ 56 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNA---PTVSKILKQLSLAGIVT 56 (130)
T ss_pred CCCccHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence 47899999999999955 89999999999999985
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=95.83 E-value=0.008 Score=36.88 Aligned_cols=42 Identities=21% Similarity=0.462 Sum_probs=33.4
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|-+.|.++ +..|+.|||..++++| +.+.-+|..|..+|.+..
T Consensus 5 i~~~l~~~-~~~S~~eLa~~~~~s~---~~ve~mL~~l~~kG~I~~ 46 (69)
T PF09012_consen 5 IRDYLRER-GRVSLAELAREFGISP---EAVEAMLEQLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHS--SEEHHHHHHHTT--H---HHHHHHHHHHHCCTSCEE
T ss_pred HHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEE
Confidence 45777663 7999999999999955 999999999999998763
No 23
>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=95.71 E-value=0.015 Score=39.84 Aligned_cols=34 Identities=26% Similarity=0.364 Sum_probs=31.0
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+++.|++|||+.+++++ ..+.+||+.|+..|++.
T Consensus 23 ~~~~s~~~ia~~~~ip~---~~l~kil~~L~~~glv~ 56 (135)
T TIGR02010 23 TGPVTLADISERQGISL---SYLEQLFAKLRKAGLVK 56 (135)
T ss_pred CCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCceE
Confidence 46899999999999965 89999999999999875
No 24
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=95.62 E-value=0.015 Score=32.12 Aligned_cols=33 Identities=15% Similarity=0.269 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-++|..|||+.+|+++ ..+.|.|+.|...|++.
T Consensus 7 ~~~s~~~la~~l~~s~---~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 7 LPLTRQEIAELLGLTR---ETVSRTLKRLEKEGLIS 39 (48)
T ss_pred eccCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 3689999999999954 88999999999999875
No 25
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.61 E-value=0.025 Score=35.14 Aligned_cols=45 Identities=18% Similarity=0.346 Sum_probs=37.1
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.++.|+..|..+ +++|..+|+..+++++ ..+.|.++.|...|++.
T Consensus 11 ~~~~il~~l~~~-~~~~~~~la~~~~~s~---~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 11 TQFLVLRILYEE-GPLSVSELAKRLGVSP---STVTRVLDRLEKKGLIR 55 (101)
T ss_pred HHHHHHHHHHHc-CCcCHHHHHHHHCCCc---hhHHHHHHHHHHCCCeE
Confidence 355666777654 5799999999999955 88999999999999986
No 26
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=95.60 E-value=0.028 Score=31.84 Aligned_cols=40 Identities=13% Similarity=0.227 Sum_probs=33.3
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|...|. .++.|..||++.+++++ ..+.+.++.|...|++.
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~---~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQ---STVSHHLKKLREAGLVE 41 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCH---HHHHHHHHHHHHCCCee
Confidence 344554 47899999999999955 78999999999999875
No 27
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=95.55 E-value=0.024 Score=34.96 Aligned_cols=45 Identities=20% Similarity=0.324 Sum_probs=36.9
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCC--cccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTK--TRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~--~~~L~RlLR~Laa~gif~ 95 (97)
|.++|.++++|++..+|+..+.....+ ...++|-||.|-..|+..
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~ 49 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTR 49 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcc
Confidence 567788888999999999999764334 378999999999999543
No 28
>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=95.51 E-value=0.0076 Score=36.50 Aligned_cols=43 Identities=16% Similarity=0.145 Sum_probs=34.5
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|.-.|.. .+++|+.|||..+|++. ..+++.|+.|...|++..
T Consensus 12 ~vy~~Ll~-~~~~t~~eIa~~l~i~~---~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 12 KVYLALLK-NGPATAEEIAEELGISR---STVYRALKSLEEKGLVER 54 (68)
T ss_dssp HHHHHHHH-HCHEEHHHHHHHHTSSH---HHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence 34444432 28999999999999954 899999999999998863
No 29
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=95.44 E-value=0.023 Score=36.78 Aligned_cols=45 Identities=20% Similarity=0.316 Sum_probs=38.4
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+..|...|..+ +++|..|||+.+|+++ ..+.|.++.|...|++.
T Consensus 4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~---~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKD-ARISLAELAKKVGLSP---STVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence 466777888764 6899999999999955 89999999999999875
No 30
>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=95.42 E-value=0.027 Score=33.76 Aligned_cols=42 Identities=21% Similarity=0.267 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 37 NSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 37 ~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
.-.+|++| .++|-||. +...|+.|||+.+|+.+ ..+..-||-
T Consensus 5 Q~e~L~~A--~~~GYfd~----PR~~tl~elA~~lgis~---st~~~~LRr 46 (53)
T PF04967_consen 5 QREILKAA--YELGYFDV----PRRITLEELAEELGISK---STVSEHLRR 46 (53)
T ss_pred HHHHHHHH--HHcCCCCC----CCcCCHHHHHHHhCCCH---HHHHHHHHH
Confidence 45688999 99999984 36799999999999954 555555553
No 31
>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=95.30 E-value=0.024 Score=37.99 Aligned_cols=34 Identities=18% Similarity=0.354 Sum_probs=30.9
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+++.|..|||+.+++++ ..++++|+.|+..|++.
T Consensus 23 ~~~~s~~eia~~~~i~~---~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 23 EGPVSVKEIAERQGISR---SYLEKILRTLRRAGLVE 56 (132)
T ss_pred CCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence 35999999999999965 89999999999999885
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.19 E-value=0.042 Score=30.51 Aligned_cols=42 Identities=12% Similarity=0.230 Sum_probs=34.2
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|.+.|.++ ++.|..+|++.+++.+ ..++|.|..|...|++..
T Consensus 5 il~~l~~~-~~~s~~~l~~~l~~s~---~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 5 ILELLAQQ-GKVSVEELAELLGVSE---MTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEE
Confidence 44555554 5799999999999954 889999999999998753
No 33
>PRK06474 hypothetical protein; Provisional
Probab=95.05 E-value=0.036 Score=40.06 Aligned_cols=47 Identities=17% Similarity=0.306 Sum_probs=39.0
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhC-CCCCCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQ-IHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g-~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
..+.|.+.|..+++++|+.||+..++ ++ ...++|.|+.|+..|++..
T Consensus 12 ~R~~Il~~L~~~~~~~ta~el~~~l~~is---~aTvYrhL~~L~e~GLI~~ 59 (178)
T PRK06474 12 VRMKICQVLMRNKEGLTPLELVKILKDVP---QATLYRHLQTMVDSGILHV 59 (178)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhcCCC---HHHHHHHHHHHHHCCCEEE
Confidence 67778888877666799999999984 53 3789999999999999863
No 34
>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=95.01 E-value=0.034 Score=32.70 Aligned_cols=33 Identities=15% Similarity=0.249 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.++|..|||+.+|+++ ..+.|+|+.|...|++.
T Consensus 24 ~~~s~~ela~~~g~s~---~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 24 LPLTRQEIADYLGLTR---ETVSRTLKELEEEGLIS 56 (67)
T ss_pred CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 6899999999999954 89999999999999886
No 35
>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=94.95 E-value=0.02 Score=33.34 Aligned_cols=41 Identities=20% Similarity=0.284 Sum_probs=33.1
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+...|.++ +++|..|||..+++++ ..+.|+++.|...|++.
T Consensus 8 iL~~l~~~-~~~~~~~la~~~~~~~---~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 8 ILRILYEN-GGITQSELAEKLGISR---STVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HHHHHHHH-SSEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHc-CCCCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEE
Confidence 33445444 5799999999999954 89999999999999876
No 36
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=94.95 E-value=0.035 Score=32.89 Aligned_cols=38 Identities=21% Similarity=0.334 Sum_probs=29.3
Q ss_pred HhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 55 IHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 55 La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|....+++|..+|++.++.+ ...+.|+++.|...|+++
T Consensus 12 l~~~~~~~t~~~l~~~~~~~---~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 12 LAHSDGPMTQSDLAERLGIS---KSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp HT--TS-BEHHHHHHHTT-----HHHHHHHHHHHHHTTSEE
T ss_pred HHccCCCcCHHHHHHHHCcC---HHHHHHHHHHHHHCCCEE
Confidence 43235899999999999994 489999999999999984
No 37
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=94.88 E-value=0.037 Score=38.09 Aligned_cols=48 Identities=10% Similarity=0.260 Sum_probs=36.9
Q ss_pred HHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 39 MSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 39 ~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.++++. +.++.. ..+.+.|..|||+..|+++ ..++++|+.|...|++.
T Consensus 9 YAl~~~--i~la~~----~~g~~~s~~~ia~~~~is~---~~vrk~l~~L~~~Glv~ 56 (141)
T PRK11014 9 YGLRAL--IYMASL----PEGRMTSISEVTEVYGVSR---NHMVKIINQLSRAGYVT 56 (141)
T ss_pred HHHHHH--HHHhcC----CCCCccCHHHHHHHHCcCH---HHHHHHHHHHHhCCEEE
Confidence 355666 554422 2346889999999999955 89999999999999875
No 38
>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=94.83 E-value=0.035 Score=34.25 Aligned_cols=41 Identities=22% Similarity=0.377 Sum_probs=31.8
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.+.++|-|-|+.|||+.+|+. .+..+++.|+.|...|+++
T Consensus 17 ~~~~~~G~~Pt~rEIa~~~g~~--S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 17 EYIEENGYPPTVREIAEALGLK--STSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHHHHHSS---HHHHHHHHTSS--SHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHcCCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCcCcc
Confidence 4455567778999999999995 2489999999999999886
No 39
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=94.79 E-value=0.041 Score=38.78 Aligned_cols=33 Identities=18% Similarity=0.389 Sum_probs=30.5
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++.|+++||+..+++| ..|.|||..|...|+++
T Consensus 24 ~~~s~~~IA~~~~is~---~~L~kil~~L~kaGlV~ 56 (150)
T COG1959 24 GPVSSAEIAERQGISP---SYLEKILSKLRKAGLVK 56 (150)
T ss_pred CcccHHHHHHHhCcCH---HHHHHHHHHHHHcCCEE
Confidence 4899999999999965 99999999999999986
No 40
>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=94.72 E-value=0.051 Score=32.88 Aligned_cols=35 Identities=14% Similarity=0.319 Sum_probs=31.3
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+++.+..+||+.+++.| +.+..+++-|...|++.
T Consensus 19 ~~~~v~~~~iA~~L~vs~---~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSP---PTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp CTSSBBHHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred CCCCccHHHHHHHHCCCh---HHHHHHHHHHHHCCCEE
Confidence 568999999999999955 89999999999999875
No 41
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.68 E-value=0.047 Score=38.17 Aligned_cols=45 Identities=16% Similarity=0.280 Sum_probs=36.3
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..++-+|-+..+|.|++|||+.++. +.+.++|-++-|...|++.
T Consensus 29 Dv~v~~~LL~~~~~~tvdelae~lnr---~rStv~rsl~~L~~~GlV~ 73 (126)
T COG3355 29 DVEVYKALLEENGPLTVDELAEILNR---SRSTVYRSLQNLLEAGLVE 73 (126)
T ss_pred HHHHHHHHHhhcCCcCHHHHHHHHCc---cHHHHHHHHHHHHHcCCee
Confidence 44455555433489999999999999 4489999999999999876
No 42
>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=94.54 E-value=0.033 Score=30.27 Aligned_cols=31 Identities=23% Similarity=0.374 Sum_probs=25.3
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
|+|-.|||..+|+.+ +.+.|+|..|...|++
T Consensus 2 ~mtr~diA~~lG~t~---ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGLTR---ETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS-H---HHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCCcH---HHHHHHHHHHHHcCCC
Confidence 578899999999955 8999999999998874
No 43
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.40 E-value=0.049 Score=33.59 Aligned_cols=42 Identities=17% Similarity=0.292 Sum_probs=33.5
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|-+.|....+|.|..|||+.+|++. ...++.|..|...|.+.
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~---~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSI---YQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-H---HHHHHHHHHHHHCTSEE
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence 4566655458999999999999944 88999999999999765
No 44
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=94.32 E-value=0.077 Score=36.32 Aligned_cols=45 Identities=18% Similarity=0.226 Sum_probs=39.1
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.+.|.+.|.+ +++.++.||++.+++.+ ..+.+-|+.|...|++.
T Consensus 17 tRl~IL~~L~~-~~~~~v~ela~~l~lsq---stvS~HL~~L~~AGLV~ 61 (117)
T PRK10141 17 TRLGIVLLLRE-SGELCVCDLCTALDQSQ---PKISRHLALLRESGLLL 61 (117)
T ss_pred HHHHHHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCceE
Confidence 67788888864 36899999999999955 88999999999999986
No 45
>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=94.32 E-value=0.065 Score=30.89 Aligned_cols=40 Identities=20% Similarity=0.288 Sum_probs=32.4
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
.|...|.++++++|+.|||+.++++. ..++|-+..|...|
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~---rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSR---RTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-H---HHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCH---HHHHHHHHHHHHCC
Confidence 34566755667899999999999954 89999999998877
No 46
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=94.23 E-value=0.074 Score=37.49 Aligned_cols=48 Identities=15% Similarity=0.264 Sum_probs=37.0
Q ss_pred HHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 38 SMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 38 s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-.++++. +.|-. ..+++.|+.|||+..++++ ..|.+||+.|+..|+++
T Consensus 8 ~YAlr~L--~~LA~-----~~~~~~s~~eIA~~~~is~---~~L~kIl~~L~~aGlv~ 55 (153)
T PRK11920 8 NYAIRML--MYCAA-----NDGKLSRIPEIARAYGVSE---LFLFKILQPLVEAGLVE 55 (153)
T ss_pred hHHHHHH--HHHHh-----CCCCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 3466666 54321 1246789999999999965 89999999999999876
No 47
>PRK00215 LexA repressor; Validated
Probab=94.11 E-value=0.1 Score=37.64 Aligned_cols=41 Identities=27% Similarity=0.408 Sum_probs=34.2
Q ss_pred HHHhhCCCCCCHHHHHHHhCC-CCCCcccHHHHHHHHHhcCcccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQI-HPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~-~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.+.+++.+.|..|||+.+|. ++ ..+.|+++.|...|+++.
T Consensus 15 ~~~~~~~~~~s~~ela~~~~~~~~---~tv~~~l~~L~~~g~i~~ 56 (205)
T PRK00215 15 DHIEETGYPPSRREIADALGLRSP---SAVHEHLKALERKGFIRR 56 (205)
T ss_pred HHHHHhCCCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEEe
Confidence 334455678999999999999 65 789999999999998853
No 48
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=94.08 E-value=0.13 Score=29.77 Aligned_cols=41 Identities=17% Similarity=0.295 Sum_probs=32.8
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|.+.+.. ++.+..||+..++++. ..+.|.++.|...|++.
T Consensus 11 ~il~~l~~--~~~~~~ei~~~~~i~~---~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 11 RILRLLLE--GPLTVSELAERLGLSQ---STVSRHLKKLEEAGLVE 51 (78)
T ss_pred HHHHHHHH--CCcCHHHHHHHHCcCH---hHHHHHHHHHHHCCCeE
Confidence 34455555 3399999999999954 88999999999999875
No 49
>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=93.70 E-value=0.097 Score=38.00 Aligned_cols=42 Identities=21% Similarity=0.274 Sum_probs=35.3
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|...|..+ +++|..|||+.+|+++ ..+.|.|+.|...|++.
T Consensus 5 ~IL~~L~~~-~~~t~~eLA~~lgis~---~tV~~~L~~Le~~GlV~ 46 (203)
T TIGR02702 5 DILSYLLKQ-GQATAAALAEALAISP---QAVRRHLKDLETEGLIE 46 (203)
T ss_pred HHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence 355666554 6799999999999955 89999999999999885
No 50
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=93.65 E-value=0.066 Score=41.18 Aligned_cols=45 Identities=20% Similarity=0.293 Sum_probs=40.0
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..|-|+|.++||-++-+||.+++|.+. ..+.|++|-|..+|+++
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lglsk---tTvsR~L~~LEk~GlIe 241 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGLSK---TTVSRILRRLEKRGLIE 241 (258)
T ss_pred HHHHHHHHHHhCCEEeHHHHHHhhCCCh---HHHHHHHHHHHhCCceE
Confidence 4567788888999999999999999954 78999999999999986
No 51
>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=93.64 E-value=0.097 Score=31.69 Aligned_cols=42 Identities=14% Similarity=0.196 Sum_probs=34.6
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
++.|...+.+ ++.|..|||+.+|+.. ..++|-++.|...|+.
T Consensus 2 ~~~il~~L~~--~~~~~~eLa~~l~vS~---~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 2 PLRLLALLAD--NPFSGEKLGEALGMSR---TAVNKHIQTLREWGVD 43 (69)
T ss_pred hHHHHHHHHc--CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCe
Confidence 4556777765 6899999999999954 8899999999988873
No 52
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=93.59 E-value=0.13 Score=36.68 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=40.4
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCC-C-CCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIH-P-TKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~-~-~~~~~L~RlLR~Laa~gif~e 96 (97)
.+.-|.+.|...+++.|+.||.+.+.-. | .+...++|.|+.|+..|++.+
T Consensus 27 qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~ 78 (169)
T PRK11639 27 QRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHK 78 (169)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEE
Confidence 5566788887777899999999998642 1 256789999999999999863
No 53
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=93.55 E-value=0.1 Score=36.85 Aligned_cols=45 Identities=20% Similarity=0.220 Sum_probs=38.2
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+|..|.++|.+ ++.+|..|||+++|+++ ..+.|=++-|...|+++
T Consensus 15 ~D~~IL~~Lq~-d~R~s~~eiA~~lglS~---~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 15 IDRNILNELQK-DGRISNVELSKRVGLSP---TPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHhcc-CCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence 67888888876 47999999999999965 77888888899999875
No 54
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=93.49 E-value=0.13 Score=30.53 Aligned_cols=41 Identities=10% Similarity=0.267 Sum_probs=34.7
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|.+.|..+ +.+|+.|||+.+++.+ ..++|=+..|...|++.
T Consensus 5 Il~~l~~~-~~~s~~ela~~~~VS~---~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 5 ILELLKEK-GKVSVKELAEEFGVSE---MTIRRDLNKLEKQGLIK 45 (57)
T ss_pred HHHHHHHc-CCEEHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 45667553 7999999999999955 89999999999999864
No 55
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=93.47 E-value=0.12 Score=35.14 Aligned_cols=45 Identities=13% Similarity=0.224 Sum_probs=37.4
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++..|-+.|..+ +++|..|||+++|+++ ..+.+-++-|...|++.
T Consensus 9 ~D~~IL~~L~~d-~r~~~~eia~~lglS~---~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 9 IDRRILRLLQED-ARISNAELAERVGLSP---STVLRRIKRLEEEGVIK 53 (154)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCcee
Confidence 566777888764 6799999999999965 78888889999999875
No 56
>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=93.47 E-value=0.16 Score=33.50 Aligned_cols=45 Identities=24% Similarity=0.259 Sum_probs=36.1
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+..|...|..+ +++|..|||..+++++ ..+.|+++-|...|++..
T Consensus 30 q~~iL~~l~~~-~~~t~~ela~~~~~~~---~tvs~~l~~Le~~GlI~r 74 (118)
T TIGR02337 30 QWRILRILAEQ-GSMEFTQLANQACILR---PSLTGILARLERDGLVTR 74 (118)
T ss_pred HHHHHHHHHHc-CCcCHHHHHHHhCCCc---hhHHHHHHHHHHCCCEEe
Confidence 33455556553 6899999999999955 789999999999998863
No 57
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=93.46 E-value=0.11 Score=37.72 Aligned_cols=42 Identities=7% Similarity=0.090 Sum_probs=36.2
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|.++|-.+ |++|.+|||..+|++. ..++|+|..|...|++.
T Consensus 26 ~Vl~~L~~~-g~~tdeeLA~~Lgi~~---~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 26 EVLKALIKK-GEVTDEEIAEQTGIKL---NTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeE
Confidence 467877665 5999999999999954 89999999999999876
No 58
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.46 E-value=0.12 Score=35.93 Aligned_cols=45 Identities=16% Similarity=0.347 Sum_probs=37.9
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+..|.+.|..+ +..|.+|||+++|+++ ..++|=++-|...|++.
T Consensus 10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~---~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 10 LDRGILEALMEN-ARTPYAELAKQFGVSP---GTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence 577888888764 7999999999999965 77888888899999875
No 59
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=93.17 E-value=0.18 Score=32.77 Aligned_cols=34 Identities=12% Similarity=0.041 Sum_probs=30.8
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..++|..|||+.+|+++ ..+.|++..|...|++.
T Consensus 45 ~~~is~~eLa~~~g~sr---~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 45 QDRVTATVIAELTGLSR---THVSDAIKSLARRRIIF 78 (95)
T ss_pred CCccCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence 36899999999999955 89999999999999886
No 60
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=93.17 E-value=0.21 Score=33.86 Aligned_cols=40 Identities=23% Similarity=0.193 Sum_probs=33.1
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..|...+++.|..|||..+++++ ..+.|++.-|...|++.
T Consensus 38 ~~l~~~~~~~t~~eLa~~l~~~~---~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 38 HNIHQLPPEQSQIQLAKAIGIEQ---PSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHHHHHHCCCEe
Confidence 34444445789999999999955 89999999999999886
No 61
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=93.02 E-value=0.15 Score=28.86 Aligned_cols=33 Identities=12% Similarity=0.213 Sum_probs=29.1
Q ss_pred CCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.+ |..|||+.++++. ..++|.++.|...|++.
T Consensus 18 ~~l~s~~~la~~~~vs~---~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 18 DKLPSERELAAQLGVSR---TTVREALSRLEAEGLVQ 51 (60)
T ss_pred CcCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 456 8999999999954 89999999999999875
No 62
>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=92.69 E-value=0.25 Score=35.42 Aligned_cols=40 Identities=15% Similarity=0.275 Sum_probs=32.7
Q ss_pred HhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 55 IHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 55 La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.+++-|.|..|||+.+|.+ .+..+++.|+.|...|++..
T Consensus 19 ~~~~~~~~~~~ela~~~~~~--s~~tv~~~l~~L~~~g~i~~ 58 (199)
T TIGR00498 19 IESTGYPPSIREIARAVGLR--SPSAAEEHLKALERKGYIER 58 (199)
T ss_pred HHhcCCCCcHHHHHHHhCCC--ChHHHHHHHHHHHHCCCEec
Confidence 33445688999999999995 13889999999999998763
No 63
>PRK09462 fur ferric uptake regulator; Provisional
Probab=92.64 E-value=0.21 Score=34.60 Aligned_cols=49 Identities=8% Similarity=0.109 Sum_probs=38.4
Q ss_pred HhcChhHHHhhC-CCCCCHHHHHHHhCC-CC-CCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNH-TKPMTLNQLLGALQI-HP-TKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~-~gp~s~~ELA~~~g~-~~-~~~~~L~RlLR~Laa~gif~ 95 (97)
.+.-|.+.|... +++.|+.||-+.+.- .| .+...++|.|..|+..|++.
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~ 69 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVT 69 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEE
Confidence 455677888765 479999999998853 22 25688999999999999885
No 64
>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=92.57 E-value=0.2 Score=35.66 Aligned_cols=42 Identities=12% Similarity=0.017 Sum_probs=35.5
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|+|+|-.+ +.+|-+|||..+|++. ..++|++..|...|++.
T Consensus 18 ~Vl~aL~~~-~~~tdEeLa~~Lgi~~---~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 18 LVLFSLGIK-GEFTDEEISLELGIKL---NEVRKALYALYDAGLAD 59 (158)
T ss_pred HHHHHHhcc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCce
Confidence 456777644 5899999999999954 88999999999999874
No 65
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=92.52 E-value=0.21 Score=34.23 Aligned_cols=35 Identities=17% Similarity=0.315 Sum_probs=31.2
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+++.+++|||..+++++ +.+.+.++.|...|++.
T Consensus 19 ~~~~~~~~ela~~l~vs~---~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 19 EKGYARVSDIAEALSVHP---SSVTKMVQKLDKDEYLI 53 (142)
T ss_pred cCCCcCHHHHHHHhCCCh---hHHHHHHHHHHHCCCEE
Confidence 457889999999999955 89999999999999875
No 66
>PHA00738 putative HTH transcription regulator
Probab=92.40 E-value=0.18 Score=34.42 Aligned_cols=46 Identities=13% Similarity=0.183 Sum_probs=38.4
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.++.|.+.|.. ++++++.||++.+++. .+.+.+-|+.|...|++..
T Consensus 13 tRr~IL~lL~~-~e~~~V~eLae~l~lS---QptVS~HLKvLreAGLV~s 58 (108)
T PHA00738 13 LRRKILELIAE-NYILSASLISHTLLLS---YTTVLRHLKILNEQGYIEL 58 (108)
T ss_pred HHHHHHHHHHH-cCCccHHHHHHhhCCC---HHHHHHHHHHHHHCCceEE
Confidence 55677888865 3479999999999994 3799999999999999864
No 67
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=92.38 E-value=0.24 Score=32.06 Aligned_cols=40 Identities=15% Similarity=0.121 Sum_probs=34.4
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
=|.|+.+ |-+++.|||..+++++ +.++=+|-.|+++|-++
T Consensus 8 Rd~l~~~-gr~s~~~Ls~~~~~p~---~~VeaMLe~l~~kGkve 47 (78)
T PRK15431 8 RDLLALR-GRMEAAQISQTLNTPQ---PMINAMLQQLESMGKAV 47 (78)
T ss_pred HHHHHHc-CcccHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence 3788775 6999999999999955 89999999999999654
No 68
>PRK11050 manganese transport regulator MntR; Provisional
Probab=92.38 E-value=0.24 Score=34.71 Aligned_cols=40 Identities=15% Similarity=0.256 Sum_probs=33.5
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
...+.. +++.+..|||+.+++++ ..+.|.++.|...|++.
T Consensus 43 ~~~l~~-~~~~t~~eLA~~l~is~---stVsr~l~~Le~~GlI~ 82 (152)
T PRK11050 43 ADLIAE-VGEARQVDIAARLGVSQ---PTVAKMLKRLARDGLVE 82 (152)
T ss_pred HHHHHh-cCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 345543 47899999999999955 89999999999999885
No 69
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=92.08 E-value=0.23 Score=34.78 Aligned_cols=50 Identities=10% Similarity=0.171 Sum_probs=40.5
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCC-CC-CCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQI-HP-TKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~-~~-~~~~~L~RlLR~Laa~gif~e 96 (97)
-++.|.++|.+++++.|+.||=..+.- .| ..+..++|.|..|+..|++.+
T Consensus 22 qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~ 73 (145)
T COG0735 22 QRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHR 73 (145)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEE
Confidence 456778999888888999999988774 22 256789999999999999863
No 70
>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=92.08 E-value=0.15 Score=30.81 Aligned_cols=33 Identities=15% Similarity=0.299 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-++|-.+||..+|++. ..+.|+|+.|...|+++
T Consensus 27 ~~lt~~~iA~~~g~sr---~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSR---ETVSRILKRLKDEGIIE 59 (76)
T ss_dssp EESSHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred ecCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 4789999999999965 88999999999999875
No 71
>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=92.01 E-value=0.26 Score=32.40 Aligned_cols=34 Identities=18% Similarity=0.420 Sum_probs=31.0
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++++|..|||..++.++ ..+.|+++.|...|++.
T Consensus 41 ~~~~t~~eL~~~l~~~~---stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 41 EGKLTLKEIIKEILIKQ---SALVKIIKKLSKKGYLS 74 (109)
T ss_pred CCcCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCEe
Confidence 47899999999999955 89999999999999876
No 72
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=91.75 E-value=0.19 Score=37.98 Aligned_cols=34 Identities=21% Similarity=0.361 Sum_probs=31.2
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+|+|+.|||+.+|+++ ..++|-|-.|+..|+++
T Consensus 23 ~g~~sa~elA~~Lgis~---~avR~HL~~Le~~Glv~ 56 (218)
T COG2345 23 SGPVSADELAEELGISP---MAVRRHLDDLEAEGLVE 56 (218)
T ss_pred cCCccHHHHHHHhCCCH---HHHHHHHHHHHhCccee
Confidence 37999999999999976 89999999999999875
No 73
>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=91.62 E-value=0.11 Score=34.50 Aligned_cols=50 Identities=10% Similarity=0.174 Sum_probs=38.6
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCC--CCCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIH--PTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~--~~~~~~L~RlLR~Laa~gif~e 96 (97)
.+.-|.+.|.+.+++.|+.||-..+... ..+...++|.|..|+..|++..
T Consensus 9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~ 60 (120)
T PF01475_consen 9 QRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRK 60 (120)
T ss_dssp HHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEE
Confidence 4456778888877899999999998631 1145679999999999998753
No 74
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=91.57 E-value=0.32 Score=34.10 Aligned_cols=44 Identities=18% Similarity=0.321 Sum_probs=37.0
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
+...|.+.+.++ |.+|..|++..+|++- ..+.+.+|.|++.|-+
T Consensus 13 Lk~rIvElVRe~-GRiTi~ql~~~TGasR---~Tvk~~lreLVa~G~l 56 (127)
T PF06163_consen 13 LKARIVELVREH-GRITIKQLVAKTGASR---NTVKRYLRELVARGDL 56 (127)
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHCCCH---HHHHHHHHHHHHcCCe
Confidence 566778877665 7999999999999954 7899999999998854
No 75
>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=91.00 E-value=0.62 Score=30.11 Aligned_cols=47 Identities=17% Similarity=0.247 Sum_probs=37.6
Q ss_pred HHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 39 MSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 39 ~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+|++. |+ +.+. .+.|+...+||+.++.+| ..++..|..|..+|+++
T Consensus 8 ~IL~al--V~----~Y~~-~~~PVgSk~ia~~l~~s~---aTIRN~M~~Le~lGlve 54 (78)
T PF03444_consen 8 EILKAL--VE----LYIE-TGEPVGSKTIAEELGRSP---ATIRNEMADLEELGLVE 54 (78)
T ss_pred HHHHHH--HH----HHHh-cCCCcCHHHHHHHHCCCh---HHHHHHHHHHHHCCCcc
Confidence 455555 54 3343 468999999999999965 89999999999999985
No 76
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=90.84 E-value=0.43 Score=32.56 Aligned_cols=40 Identities=20% Similarity=0.159 Sum_probs=33.5
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.-.|.. .+++|..|||..+++++ ..+.|++.-|...|++.
T Consensus 46 L~~l~~-~~~~t~~eLa~~l~i~~---~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 46 LCSIRC-AACITPVELKKVLSVDL---GALTRMLDRLVCKGWVE 85 (144)
T ss_pred HHHHHH-cCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 444544 36899999999999955 89999999999999886
No 77
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=90.54 E-value=0.38 Score=37.19 Aligned_cols=44 Identities=9% Similarity=0.110 Sum_probs=37.3
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|++.|...++-++..+||+++|+.+ ..+++-+|.|.+.|+++-
T Consensus 187 ~IL~~L~~~egrlse~eLAerlGVSR---s~ireAlrkLE~aGvIe~ 230 (251)
T TIGR02787 187 HIFEELDGNEGLLVASKIADRVGITR---SVIVNALRKLESAGVIES 230 (251)
T ss_pred HHHHHhccccccccHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence 56777765458999999999999965 789999999999999863
No 78
>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=90.46 E-value=0.36 Score=35.00 Aligned_cols=45 Identities=7% Similarity=0.167 Sum_probs=36.2
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+..|...|.++ +++|..|||+.+++++ ..++|.++.|...|++..
T Consensus 145 ~~~IL~~l~~~-g~~s~~eia~~l~is~---stv~r~L~~Le~~GlI~r 189 (203)
T TIGR01884 145 ELKVLEVLKAE-GEKSVKNIAKKLGKSL---STISRHLRELEKKGLVEQ 189 (203)
T ss_pred HHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence 34555666554 5799999999999955 889999999999998863
No 79
>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=90.07 E-value=0.65 Score=26.68 Aligned_cols=31 Identities=13% Similarity=0.142 Sum_probs=27.6
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|..|||..+++++ ..+.+.+..|...|++.
T Consensus 26 ~~~~~la~~~~is~---~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 26 PSERELAEELGVSR---TTVREALRELEAEGLVE 56 (66)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 45999999999954 89999999999999875
No 80
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=90.06 E-value=0.42 Score=40.33 Aligned_cols=41 Identities=7% Similarity=0.250 Sum_probs=33.2
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
|-..+...+++.|++||++++|... +...++.|||+|++++
T Consensus 468 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~n~ 508 (528)
T PRK14096 468 VEELLKEDGGELSIEEIAAALGAPE-QVETIYKILRHLAANN 508 (528)
T ss_pred HHHHHhccCCCCCHHHHHHHcCCCc-cHHHHHHHHHHHhcCC
Confidence 4455545568999999999999844 6789999999999874
No 81
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=89.99 E-value=0.34 Score=33.53 Aligned_cols=32 Identities=9% Similarity=0.134 Sum_probs=29.5
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|+|-.|||+.+|+.+ ..+.|+|+.|...|+++
T Consensus 143 ~~t~~~iA~~lG~tr---etvsR~l~~l~~~g~I~ 174 (193)
T TIGR03697 143 RLSHQAIAEAIGSTR---VTITRLLGDLRKKKLIS 174 (193)
T ss_pred CCCHHHHHHHhCCcH---HHHHHHHHHHHHCCCEE
Confidence 689999999999955 89999999999999886
No 82
>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=89.97 E-value=0.48 Score=29.50 Aligned_cols=46 Identities=24% Similarity=0.351 Sum_probs=37.5
Q ss_pred HhcChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++..+.+.|+++. ...+..||+..+|.|| ..+...++.|...|++.
T Consensus 3 ~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~---r~i~~~~k~L~~~gLI~ 49 (75)
T PF04182_consen 3 IQYCLLERIARSRYNGITQSDLSKLLGIDP---RSIFYRLKKLEKKGLIV 49 (75)
T ss_pred hHHHHHHHHHhcCCCCEehhHHHHHhCCCc---hHHHHHHHHHHHCCCEE
Confidence 3445667777655 7789999999999955 99999999999999875
No 83
>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=89.16 E-value=0.29 Score=27.63 Aligned_cols=22 Identities=5% Similarity=0.138 Sum_probs=16.6
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+|+.|||..+|++. ..++|+++
T Consensus 22 ~si~~IA~~~gvsr---~TvyR~l~ 43 (45)
T PF02796_consen 22 MSIAEIAKQFGVSR---STVYRYLN 43 (45)
T ss_dssp --HHHHHHHTTS-H---HHHHHHHC
T ss_pred CCHHHHHHHHCcCH---HHHHHHHh
Confidence 99999999999954 78888875
No 84
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=89.11 E-value=0.55 Score=34.35 Aligned_cols=36 Identities=19% Similarity=0.211 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCC
Q 041844 34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHP 75 (97)
Q Consensus 34 ~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~ 75 (97)
.-.+-.+|+.| .++|-||. +...++.|||+.+|+.+
T Consensus 157 TdrQ~~vL~~A--~~~GYFd~----PR~~~l~dLA~~lGISk 192 (215)
T COG3413 157 TDRQLEVLRLA--YKMGYFDY----PRRVSLKDLAKELGISK 192 (215)
T ss_pred CHHHHHHHHHH--HHcCCCCC----CccCCHHHHHHHhCCCH
Confidence 34567799999 99999985 36789999999999954
No 85
>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=89.05 E-value=0.36 Score=31.50 Aligned_cols=42 Identities=19% Similarity=0.316 Sum_probs=30.8
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|+|.|..+ |.++-+|||..+|+++ .-++++|..|...|+++
T Consensus 17 ~Il~~L~~~-~~l~de~la~~~~l~~---~~vRkiL~~L~~~~lv~ 58 (105)
T PF02002_consen 17 RILDALLRK-GELTDEDLAKKLGLKP---KEVRKILYKLYEDGLVS 58 (105)
T ss_dssp HHHHHHHHH---B-HHHHHHTT-S-H---HHHHHHHHHHHHHSS-E
T ss_pred HHHHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeE
Confidence 356777654 6899999999999954 88999999999999875
No 86
>PRK12423 LexA repressor; Provisional
Probab=89.03 E-value=0.82 Score=33.27 Aligned_cols=41 Identities=17% Similarity=0.276 Sum_probs=32.3
Q ss_pred HHHhhCCCCCCHHHHHHHhCC-CCCCcccHHHHHHHHHhcCcccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQI-HPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~-~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.+.+++-+-|..|||+++|+ .+ ..+++-|+.|+..|+++.
T Consensus 17 ~~i~~~g~~Ps~~eia~~~g~~s~---~~v~~~l~~L~~~G~l~~ 58 (202)
T PRK12423 17 ERIAQAGQPPSLAEIAQAFGFASR---SVARKHVQALAEAGLIEV 58 (202)
T ss_pred HHHHHcCCCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEEe
Confidence 344444556799999999995 44 789999999999998863
No 87
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=89.02 E-value=0.24 Score=31.42 Aligned_cols=45 Identities=16% Similarity=0.269 Sum_probs=35.9
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|+|+|...|.. .+.++..||.+.+|++. ..|.+-|+.|...|+++
T Consensus 1 vRl~Il~~L~~-~~~~~f~~L~~~l~lt~---g~Ls~hL~~Le~~GyV~ 45 (80)
T PF13601_consen 1 VRLAILALLYA-NEEATFSELKEELGLTD---GNLSKHLKKLEEAGYVE 45 (80)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT--H---HHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHhh-cCCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEE
Confidence 35666677755 36899999999999944 89999999999999886
No 88
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=88.24 E-value=0.67 Score=35.25 Aligned_cols=33 Identities=15% Similarity=0.116 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|+.|+.||++.+|++- ..++.+||.|...|++.
T Consensus 29 g~~tA~eis~~sgvP~---~kvY~vl~sLe~kG~v~ 61 (247)
T COG1378 29 GEATAKEISEASGVPR---PKVYDVLRSLEKKGLVE 61 (247)
T ss_pred CCccHHHHHHHcCCCc---hhHHHHHHHHHHCCCEE
Confidence 7999999999999954 68999999999999875
No 89
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=88.10 E-value=0.98 Score=32.09 Aligned_cols=35 Identities=14% Similarity=0.230 Sum_probs=31.5
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..++....+||+.++++| +.+..+++-|...|++.
T Consensus 21 ~~~~~~~~diA~~L~Vsp---~sVt~ml~rL~~~GlV~ 55 (154)
T COG1321 21 EKGFARTKDIAERLKVSP---PSVTEMLKRLERLGLVE 55 (154)
T ss_pred ccCcccHHHHHHHhCCCc---HHHHHHHHHHHHCCCeE
Confidence 458999999999999966 88999999999999875
No 90
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=88.06 E-value=0.52 Score=33.93 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=29.3
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|+|-.+||+.+|+.+ ..+.|+|+.|...|+++
T Consensus 184 ~lt~~~iA~~lG~sr---~tvsR~l~~l~~~g~I~ 215 (235)
T PRK11161 184 TMTRGDIGNYLGLTV---ETISRLLGRFQKSGMLA 215 (235)
T ss_pred cccHHHHHHHhCCcH---HHHHHHHHHHHHCCCEE
Confidence 689999999999965 89999999999999886
No 91
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=87.96 E-value=0.58 Score=32.92 Aligned_cols=32 Identities=9% Similarity=0.090 Sum_probs=29.5
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++|-.|||+.+|+.+ ..+.|+|+.|...|+++
T Consensus 168 ~~t~~~lA~~lG~tr---~tvsR~l~~l~~~gii~ 199 (211)
T PRK11753 168 KITRQEIGRIVGCSR---EMVGRVLKMLEDQGLIS 199 (211)
T ss_pred CCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence 788999999999965 89999999999999886
No 92
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=87.84 E-value=0.63 Score=32.58 Aligned_cols=32 Identities=19% Similarity=0.258 Sum_probs=29.4
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|+|-.|||..+|+.+ +.+.|+|+-|...|+++
T Consensus 149 ~~t~~~iA~~lG~tr---etvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 149 YATHDELAAAVGSVR---ETVTKVIGELSREGYIR 180 (202)
T ss_pred cCCHHHHHHHhCccH---HHHHHHHHHHHHCCCEE
Confidence 689999999999965 89999999999999886
No 93
>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=87.82 E-value=0.51 Score=28.07 Aligned_cols=34 Identities=9% Similarity=0.126 Sum_probs=28.6
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |..+||+..+++. ..+++.|+.|...|++.
T Consensus 21 g~~lps~~~la~~~~vsr---~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSR---TTVREALRRLEAEGLIE 55 (64)
T ss_dssp TSBE--HHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred CCEeCCHHHHHHHhccCC---cHHHHHHHHHHHCCcEE
Confidence 4567 9999999999954 88999999999999875
No 94
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=87.65 E-value=0.75 Score=28.89 Aligned_cols=30 Identities=13% Similarity=0.346 Sum_probs=26.5
Q ss_pred HHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 64 LNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 64 ~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
..|||+.+++++ ..+.|+++.|...|++..
T Consensus 2 ~~ela~~l~is~---stvs~~l~~L~~~glI~r 31 (96)
T smart00529 2 TSEIAERLNVSP---PTVTQMLKKLEKDGLVEY 31 (96)
T ss_pred HHHHHHHhCCCh---HHHHHHHHHHHHCCCEEE
Confidence 579999999955 899999999999998863
No 95
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=87.55 E-value=0.88 Score=34.23 Aligned_cols=42 Identities=17% Similarity=0.210 Sum_probs=35.5
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|-+.|.+ .+.+++.|||+.+|+.+ ..++|-|+.|...|++.
T Consensus 9 ~Il~~l~~-~~~~~~~ela~~l~vS~---~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 9 ILLELLAQ-LGFVTVEKVIERLGISP---ATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 45677765 47999999999999955 88999999999999874
No 96
>PF13730 HTH_36: Helix-turn-helix domain
Probab=87.31 E-value=0.79 Score=26.19 Aligned_cols=29 Identities=17% Similarity=0.263 Sum_probs=26.3
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
|.+.||+.+|+.. ..+.|.++.|...|++
T Consensus 27 S~~~la~~~g~s~---~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSR---RTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCH---HHHHHHHHHHHHCcCC
Confidence 8999999999954 8999999999999974
No 97
>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=87.12 E-value=0.82 Score=25.75 Aligned_cols=37 Identities=8% Similarity=0.106 Sum_probs=25.7
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
++..|.+.|..+ +..|..|||+.+|+++ .....|+-|
T Consensus 4 ~D~~Il~~Lq~d-~r~s~~~la~~lglS~--~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQED-GRRSYAELAEELGLSE--STVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHH--TTS-HHHHHHHHTS-H--HHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHCcCH--HHHHHHHHH
Confidence 566778888764 7999999999999964 245555544
No 98
>PRK10870 transcriptional repressor MprA; Provisional
Probab=87.12 E-value=1.1 Score=32.02 Aligned_cols=35 Identities=14% Similarity=0.139 Sum_probs=31.0
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
++++|..|||..+++++ ..+.|++.-|...|++..
T Consensus 69 ~~~it~~eLa~~l~l~~---~tvsr~v~rLe~kGlV~R 103 (176)
T PRK10870 69 NHSIQPSELSCALGSSR---TNATRIADELEKRGWIER 103 (176)
T ss_pred CCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence 46899999999999955 899999999999998863
No 99
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=86.97 E-value=0.67 Score=33.79 Aligned_cols=32 Identities=16% Similarity=0.272 Sum_probs=29.3
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++|-.|||+.+|+.+ ..+.|+++.|...|+++
T Consensus 179 ~lt~~~IA~~lGisr---etlsR~L~~L~~~GlI~ 210 (230)
T PRK09391 179 PMSRRDIADYLGLTI---ETVSRALSQLQDRGLIG 210 (230)
T ss_pred cCCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEE
Confidence 578899999999965 89999999999999886
No 100
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=86.85 E-value=0.85 Score=32.72 Aligned_cols=43 Identities=9% Similarity=0.017 Sum_probs=34.2
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|.+.+++..+..|..|||+++++.+ ..+++-+.+|+.+|++..
T Consensus 167 Vl~~~~~g~~g~s~~eIa~~l~iS~---~Tv~~~~~~~~~~~~~~~ 209 (225)
T PRK10046 167 VRKLFKEPGVQHTAETVAQALTISR---TTARRYLEYCASRHLIIA 209 (225)
T ss_pred HHHHHHcCCCCcCHHHHHHHhCccH---HHHHHHHHHHHhCCeEEE
Confidence 4455654224689999999999955 889999999999998753
No 101
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=85.74 E-value=1.1 Score=32.81 Aligned_cols=42 Identities=19% Similarity=0.260 Sum_probs=35.1
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-|+|++-.. |..|-.|||..+|+ +..-++|+|+.|...|++.
T Consensus 22 ~v~~~l~~k-ge~tDeela~~l~i---~~~~vrriL~~L~e~~li~ 63 (176)
T COG1675 22 LVVDALLEK-GELTDEELAELLGI---KKNEVRRILYALYEDGLIS 63 (176)
T ss_pred HHHHHHHhc-CCcChHHHHHHhCc---cHHHHHHHHHHHHhCCceE
Confidence 345777654 48999999999999 4488999999999999886
No 102
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=85.17 E-value=2.4 Score=29.53 Aligned_cols=33 Identities=21% Similarity=0.313 Sum_probs=29.0
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.=-|+.|||..+|++| ..+.|.-+.|...|++.
T Consensus 34 kLPSvRelA~~~~VNp---nTv~raY~eLE~eG~i~ 66 (125)
T COG1725 34 KLPSVRELAKDLGVNP---NTVQRAYQELEREGIVE 66 (125)
T ss_pred CCCcHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence 3458999999999966 89999999999999874
No 103
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=84.63 E-value=1.1 Score=29.39 Aligned_cols=33 Identities=18% Similarity=0.158 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.-+|.+.|++++++. .++-+++||.|...|++.
T Consensus 40 K~ITps~lserlkI~---~SlAr~~Lr~L~~kG~Ik 72 (86)
T PRK09334 40 KIVTPYTLASKYGIK---ISVAKKVLRELEKRGVLV 72 (86)
T ss_pred cEEcHHHHHHHhcch---HHHHHHHHHHHHHCCCEE
Confidence 568999999999994 489999999999999874
No 104
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=84.58 E-value=1.3 Score=33.83 Aligned_cols=43 Identities=12% Similarity=0.113 Sum_probs=36.0
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..|.+.|.++ +.+|+.|||+.+++++ ..++|=++.|...|++.
T Consensus 20 ~~Il~~L~~~-~~vtv~eLa~~l~VS~---~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 20 EQIIQRLRQQ-GSVQVNDLSALYGVST---VTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHc-CCEeHHHHHHHHCCCH---HHHHHHHHHHHhCCCeE
Confidence 3567778664 5799999999999955 89999999999999874
No 105
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=84.53 E-value=1.4 Score=27.71 Aligned_cols=45 Identities=16% Similarity=0.159 Sum_probs=33.4
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+..+...|...+ +.+..|||..+++++ ..+.|+++-|...|++..
T Consensus 24 q~~~L~~l~~~~-~~~~~~la~~l~i~~---~~vt~~l~~Le~~glv~r 68 (126)
T COG1846 24 QYQVLLALYEAG-GITVKELAERLGLDR---STVTRLLKRLEDKGLIER 68 (126)
T ss_pred HHHHHHHHHHhC-CCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCeee
Confidence 444445555543 333399999999955 899999999999998863
No 106
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=83.99 E-value=1.4 Score=35.41 Aligned_cols=36 Identities=22% Similarity=0.361 Sum_probs=31.8
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.++|.|.+||++++++++ +.+++++..|...|++.+
T Consensus 307 ~g~~~t~~~La~~l~~~~---~~v~~iL~~L~~agLI~~ 342 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGY---DELGELLCELARIGLLRR 342 (412)
T ss_pred cCCCCCHHHHHHHhCCCH---HHHHHHHHHHHhCCCeEe
Confidence 568999999999999855 899999999999998753
No 107
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=83.88 E-value=1.5 Score=32.30 Aligned_cols=35 Identities=20% Similarity=0.283 Sum_probs=29.5
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.+|+|++||++++|.+- +.+.--||.|-..|++.
T Consensus 38 s~~Pmtl~Ei~E~lg~Sk---s~vS~~lkkL~~~~lV~ 72 (177)
T COG1510 38 SRKPLTLDEIAEALGMSK---SNVSMGLKKLQDWNLVK 72 (177)
T ss_pred cCCCccHHHHHHHHCCCc---chHHHHHHHHHhcchHH
Confidence 458999999999999954 67888999998888764
No 108
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=83.87 E-value=1.5 Score=33.46 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=33.7
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-+.+..-+.+.|++|+|+++|++- ...+|-|-+|++.|++.
T Consensus 164 ~~~~~~~~~~~Taeela~~~giSR---vTaRRYLeyl~~~~~l~ 204 (224)
T COG4565 164 REALKEPDQELTAEELAQALGISR---VTARRYLEYLVSNGILE 204 (224)
T ss_pred HHHHhCcCCccCHHHHHHHhCccH---HHHHHHHHHHHhcCeee
Confidence 355653358999999999999943 78999999999999875
No 109
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=83.67 E-value=1.5 Score=29.63 Aligned_cols=33 Identities=21% Similarity=0.189 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.-+|+..||+++++. -++-+++||.|...|++.
T Consensus 58 K~ITp~~lserlkI~---~SlAr~~Lr~L~~kG~Ik 90 (105)
T PF03297_consen 58 KLITPSVLSERLKIN---GSLARKALRELESKGLIK 90 (105)
T ss_dssp SCECHHHHHHHHCCS---CHHHHHHHHHHHHCCSSE
T ss_pred cEeeHHHHHHhHhhH---HHHHHHHHHHHHHCCCEE
Confidence 568999999999994 489999999999999875
No 110
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=83.29 E-value=1.5 Score=33.14 Aligned_cols=42 Identities=10% Similarity=0.211 Sum_probs=35.5
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|-+.|.+ .+.+++.|||+.+++++ ..++|=|..|...|++.
T Consensus 9 ~Il~~l~~-~~~~~~~ela~~l~vS~---~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 9 AIIELVKQ-QGYVSTEELVEHFSVSP---QTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHH-cCCEeHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence 45677755 46899999999999954 89999999999999875
No 111
>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=83.29 E-value=3.6 Score=24.83 Aligned_cols=40 Identities=10% Similarity=0.313 Sum_probs=30.1
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++.|.++ |..|+.+|+..++.++ +.++.-|-.|...|++.
T Consensus 19 ~~~Ll~~-G~ltl~~i~~~t~l~~---~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 19 GEVLLSR-GRLTLREIVRRTGLSP---KQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHHC--SEEHHHHHHHHT--H---HHHHHHHHHHHHTTSEE
T ss_pred HHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHcCCee
Confidence 4555443 7999999999999854 88999999999988764
No 112
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=83.08 E-value=1.2 Score=27.80 Aligned_cols=34 Identities=9% Similarity=0.113 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.++.+..+|+..++++. ..+.+.+..|...|+++
T Consensus 17 ~~~~~~t~i~~~~~L~~---~~~~~yL~~L~~~gLI~ 50 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLNY---STLKKYLKELEEKGLIK 50 (77)
T ss_dssp TT-B-HHHHHTTST--H---HHHHHHHHHHHHTTSEE
T ss_pred cCCCCHHHHHHHhCcCH---HHHHHHHHHHHHCcCee
Confidence 48999999999999954 89999999999999875
No 113
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=82.92 E-value=2.2 Score=28.11 Aligned_cols=45 Identities=9% Similarity=0.105 Sum_probs=34.4
Q ss_pred HhcChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHH----------HHhcCcc
Q 041844 47 IQVGIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCS----------LVRSGFF 94 (97)
Q Consensus 47 veLgI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~----------Laa~gif 94 (97)
+...|+.-|.+. +.+.++.|||..+++++ ..+.-.|+- |+.+|++
T Consensus 10 ~R~~vl~~L~~~yp~~~~~~eIar~v~~~~---snV~GaL~G~g~rY~~e~SLv~lGLV 65 (90)
T PF07381_consen 10 VRKKVLEYLCSIYPEPAYPSEIARSVGSDY---SNVLGALRGDGKRYNKEDSLVGLGLV 65 (90)
T ss_pred HHHHHHHHHHHcCCCcCCHHHHHHHHCCCH---HHHHHHHhcCCCCcCcchhHHHcCCe
Confidence 566778888776 68999999999999965 666666653 6667766
No 114
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=82.85 E-value=1 Score=24.58 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
.++|++|||..+|.++ ..+.|+.+...
T Consensus 7 ~~~~l~~iA~~~g~S~---~~f~r~Fk~~~ 33 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSP---SYFSRLFKKET 33 (42)
T ss_dssp SS--HHHHHHHHTS-H---HHHHHHHHHHT
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHHHHH
Confidence 5799999999999954 89999988543
No 115
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=82.52 E-value=1.6 Score=32.94 Aligned_cols=42 Identities=10% Similarity=0.119 Sum_probs=35.8
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|.+.|.++ +.+++.|||+.+++++ ..++|=++.|...|++.
T Consensus 9 ~Il~~L~~~-~~v~v~eLa~~l~VS~---~TIRRDL~~Le~~g~l~ 50 (256)
T PRK10434 9 AILEYLQKQ-GKTSVEELAQYFDTTG---TTIRKDLVILEHAGTVI 50 (256)
T ss_pred HHHHHHHHc-CCEEHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 566778664 6899999999999955 89999999999999764
No 116
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=82.44 E-value=1.9 Score=29.26 Aligned_cols=33 Identities=21% Similarity=0.270 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.++|++|||+.+.+.+ ...+++|+-|...|.++
T Consensus 18 ~~vtl~elA~~l~cS~---Rn~r~lLkkm~~~gWi~ 50 (115)
T PF12793_consen 18 VEVTLDELAELLFCSR---RNARTLLKKMQEEGWIT 50 (115)
T ss_pred cceeHHHHHHHhCCCH---HHHHHHHHHHHHCCCee
Confidence 5789999999999965 89999999999998764
No 117
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=82.10 E-value=3.2 Score=32.56 Aligned_cols=53 Identities=19% Similarity=0.363 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 37 NSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 37 ~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.-.++... +++.|...|+.. +|+.+.|||+++|.+. ..+.-=+..|...|+++
T Consensus 16 v~kalaS~--vRv~Il~lL~~k-~plNvneiAe~lgLpq---st~s~~ik~Le~aGlir 68 (308)
T COG4189 16 VLKALASK--VRVAILQLLHRK-GPLNVNEIAEALGLPQ---STMSANIKVLEKAGLIR 68 (308)
T ss_pred HHHHHHHH--HHHHHHHHHHHh-CCCCHHHHHHHhCCch---hhhhhhHHHHHhcCcee
Confidence 34566677 888999999864 7999999999999943 55666677788888764
No 118
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=82.05 E-value=2.5 Score=33.43 Aligned_cols=47 Identities=21% Similarity=0.363 Sum_probs=37.1
Q ss_pred HHHHHHHHhcChhHHHhhCCCCCCHHHHHHH--hCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 40 SLKCVKLIQVGIPDIIHNHTKPMTLNQLLGA--LQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 40 aL~~a~~veLgI~D~La~~~gp~s~~ELA~~--~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|++. |+ +.+. .++|.+..+|++. +++++ ..++|-|..|...|++..
T Consensus 7 il~aI--V~----~~l~-~~~pv~s~~l~~~~~~~vS~---aTiR~d~~~Le~~G~l~~ 55 (337)
T TIGR00331 7 ILKAI--VE----EYIK-TGQPVGSKTLLEKYNLGLSS---ATIRNDMADLEDLGFIEK 55 (337)
T ss_pred HHHHH--HH----HHHh-cCCCcCHHHHHhhcCCCCCh---HHHHHHHHHHHHCCCccC
Confidence 45555 54 4454 4689999999999 77755 899999999999998853
No 119
>PHA02943 hypothetical protein; Provisional
Probab=81.91 E-value=2.2 Score=31.12 Aligned_cols=42 Identities=10% Similarity=0.086 Sum_probs=33.8
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|-+.| ..|..|.+|||+++|++- ...+=+|+.|...|.+.+
T Consensus 15 eILE~L--k~G~~TtseIAkaLGlS~---~qa~~~LyvLErEG~Vkr 56 (165)
T PHA02943 15 KTLRLL--ADGCKTTSRIANKLGVSH---SMARNALYQLAKEGMVLK 56 (165)
T ss_pred HHHHHH--hcCCccHHHHHHHHCCCH---HHHHHHHHHHHHcCceEE
Confidence 445666 348999999999999943 778999999999997753
No 120
>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=81.85 E-value=2 Score=27.72 Aligned_cols=44 Identities=11% Similarity=0.168 Sum_probs=33.4
Q ss_pred hcChhHHHhh---CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 48 QVGIPDIIHN---HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 48 eLgI~D~La~---~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
.-.|++.|.. ....+++++|+++++.+ ..-++-.+..|+..|.+
T Consensus 49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~---~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMS---ENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHC----TTTEEHHHHHHHSTS----HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHhcCCCCCcccHHHHHHHhCcC---HHHHHHHHHHHHhCCeE
Confidence 3355666655 23679999999999884 47899999999999964
No 121
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=81.83 E-value=1.9 Score=32.37 Aligned_cols=33 Identities=6% Similarity=0.144 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+|..|||+.+++++ ..+.|+++.|...|+++
T Consensus 20 ~~IS~~eLA~~L~iS~---~Tvsr~Lk~LEe~GlI~ 52 (217)
T PRK14165 20 VKISSSEFANHTGTSS---KTAARILKQLEDEGYIT 52 (217)
T ss_pred CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 5689999999999954 89999999999999885
No 122
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=81.70 E-value=1.5 Score=31.70 Aligned_cols=33 Identities=15% Similarity=0.305 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-+.|-.|||+.+|+.+ ..|.|+|+-|...|+++
T Consensus 168 ~~~t~~~lA~~lG~sr---etvsR~L~~L~~~G~I~ 200 (226)
T PRK10402 168 YHEKHTQAAEYLGVSY---RHLLYVLAQFIQDGYLK 200 (226)
T ss_pred ccchHHHHHHHHCCcH---HHHHHHHHHHHHCCCEE
Confidence 3568899999999965 89999999999999875
No 123
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=81.54 E-value=1.2 Score=32.16 Aligned_cols=42 Identities=10% Similarity=0.117 Sum_probs=34.9
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|.+.|..+ +..++.|||+.+++++ ..++|=++.|...|.+.
T Consensus 11 ~Il~~l~~~-~~~~~~~La~~~~vS~---~TiRRDl~~L~~~g~~~ 52 (185)
T PRK04424 11 ALQELIEEN-PFITDEELAEKFGVSI---QTIRLDRMELGIPELRE 52 (185)
T ss_pred HHHHHHHHC-CCEEHHHHHHHHCcCH---HHHHHHHHHHhcchHHH
Confidence 456677653 6899999999999955 89999999999988764
No 124
>PRK05638 threonine synthase; Validated
Probab=81.48 E-value=2.2 Score=34.59 Aligned_cols=42 Identities=19% Similarity=0.168 Sum_probs=32.4
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|...|.+ ++++..||++.++.+. ....+++.|+.|...|+++
T Consensus 376 IL~~L~~--~~~~~~el~~~l~~~~-s~~~v~~hL~~Le~~GLV~ 417 (442)
T PRK05638 376 ILKILSE--REMYGYEIWKALGKPL-KYQAVYQHIKELEELGLIE 417 (442)
T ss_pred HHHHHhh--CCccHHHHHHHHcccC-CcchHHHHHHHHHHCCCEE
Confidence 4445543 6899999999998211 3379999999999999885
No 125
>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=80.87 E-value=0.8 Score=28.46 Aligned_cols=30 Identities=20% Similarity=0.217 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
..+|+.|||+.+++++ ..+.|+.|.|--.|
T Consensus 33 ~~~si~elA~~~~vS~---sti~Rf~kkLG~~g 62 (77)
T PF01418_consen 33 AFMSISELAEKAGVSP---STIVRFCKKLGFSG 62 (77)
T ss_dssp CT--HHHHHHHCTS-H---HHHHHHHHHCTTTC
T ss_pred HHccHHHHHHHcCCCH---HHHHHHHHHhCCCC
Confidence 5789999999999955 78888888665544
No 126
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=80.20 E-value=3.2 Score=32.87 Aligned_cols=36 Identities=14% Similarity=0.194 Sum_probs=31.2
Q ss_pred CCCCCCHHHHHHH--hCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 58 HTKPMTLNQLLGA--LQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 58 ~~gp~s~~ELA~~--~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.++|.+..+||+. +++.| ..++|-|..|...|++..
T Consensus 22 ~~~pv~s~~l~~~~~l~~S~---aTIR~dm~~Le~~G~l~~ 59 (339)
T PRK00082 22 TGEPVGSKTLSKRYGLGVSS---ATIRNDMADLEELGLLEK 59 (339)
T ss_pred cCCCcCHHHHHHHhCCCCCh---HHHHHHHHHHHhCCCcCC
Confidence 4689999999977 77755 899999999999998863
No 127
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=80.00 E-value=3.5 Score=26.55 Aligned_cols=21 Identities=29% Similarity=0.436 Sum_probs=15.1
Q ss_pred hHHHhhCCCCCCHHHHHHHhCC
Q 041844 52 PDIIHNHTKPMTLNQLLGALQI 73 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~ 73 (97)
...|+. |+|.|..+||+++|.
T Consensus 30 Lr~LA~-G~PVt~~~LA~a~g~ 50 (77)
T PF12324_consen 30 LRLLAK-GQPVTVEQLAAALGW 50 (77)
T ss_dssp HHHHTT-TS-B-HHHHHHHHT-
T ss_pred HHHHHc-CCCcCHHHHHHHHCC
Confidence 456765 799999999999997
No 128
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=79.73 E-value=2.4 Score=32.62 Aligned_cols=41 Identities=15% Similarity=0.126 Sum_probs=34.4
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
..|-+.|.+ +.+.|..|||+++|++. ..+.|.++.|...|+
T Consensus 7 ~~il~~L~~-~~~~s~~~LA~~lgvsr---~tV~~~l~~L~~~G~ 47 (319)
T PRK11886 7 LQLLSLLAD-GDFHSGEQLGEELGISR---AAIWKHIQTLEEWGL 47 (319)
T ss_pred HHHHHHHHc-CCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCC
Confidence 455667765 46899999999999955 899999999999997
No 129
>PRK09954 putative kinase; Provisional
Probab=79.66 E-value=2.8 Score=32.46 Aligned_cols=44 Identities=20% Similarity=0.276 Sum_probs=36.2
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+..|.+.|.++ +++|..|||+.+++.. ..+.+.++.|...|++.
T Consensus 5 ~~~il~~l~~~-~~~s~~~la~~l~~s~---~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 5 EKEILAILRRN-PLIQQNEIADILQISR---SRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCcC
Confidence 34566777664 5999999999999954 88999999999999874
No 130
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=79.39 E-value=2.2 Score=32.20 Aligned_cols=42 Identities=10% Similarity=0.204 Sum_probs=36.0
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|.+.|.++ |.++++|||+.+++.+ ..++|=|+.|...|++.
T Consensus 9 ~Il~~l~~~-g~v~v~eLa~~~~VS~---~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 9 KILELLKEK-GKVSVEELAELFGVSE---MTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHHHc-CcEEHHHHHHHhCCCH---HHHHHhHHHHHHCCcEE
Confidence 456777663 7999999999999955 89999999999999875
No 131
>PF13518 HTH_28: Helix-turn-helix domain
Probab=79.15 E-value=3.6 Score=22.78 Aligned_cols=28 Identities=7% Similarity=0.137 Sum_probs=24.2
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
|..++|...|+++ ..++|.++..-..|+
T Consensus 14 s~~~~a~~~gis~---~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 14 SVREIAREFGISR---STVYRWIKRYREGGI 41 (52)
T ss_pred CHHHHHHHHCCCH---hHHHHHHHHHHhcCH
Confidence 9999999999955 889999988877764
No 132
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=78.87 E-value=3 Score=34.38 Aligned_cols=43 Identities=19% Similarity=0.223 Sum_probs=34.8
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..|-..|.. .+++|..|||+.+++++ ..+.|++..|.+.|++.
T Consensus 9 ~~vL~~L~~-~~~~s~~eLA~~l~l~~---~tVt~~i~~Le~kGlV~ 51 (489)
T PRK04172 9 KKVLKALKE-LKEATLEELAEKLGLPP---EAVMRAAEWLEEKGLVK 51 (489)
T ss_pred HHHHHHHHh-CCCCCHHHHHHHhCcCH---HHHHHHHHHHHhCCCEE
Confidence 344455644 35899999999999954 89999999999999876
No 133
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=78.81 E-value=2.9 Score=28.11 Aligned_cols=36 Identities=14% Similarity=0.158 Sum_probs=27.0
Q ss_pred HHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844 53 DIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS 91 (97)
Q Consensus 53 D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~ 91 (97)
+.|..+- .+.|++|||+.+|+++ ..|.|+++.-..+
T Consensus 16 ~~I~~~~~~~~sl~~lA~~~g~S~---~~l~r~Fk~~~G~ 52 (127)
T PRK11511 16 DWIEDNLESPLSLEKVSERSGYSK---WHLQRMFKKETGH 52 (127)
T ss_pred HHHHHhcCCCCCHHHHHHHHCcCH---HHHHHHHHHHHCc
Confidence 4444432 6899999999999965 8899998865543
No 134
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=78.80 E-value=2.4 Score=28.88 Aligned_cols=45 Identities=16% Similarity=0.180 Sum_probs=34.7
Q ss_pred hcChhHHHhhC---CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 48 QVGIPDIIHNH---TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 48 eLgI~D~La~~---~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+=.++|.+.+. ..-+|...||++.|+. -+.-+++||+|...|++.
T Consensus 43 dee~~~ki~KEV~~~r~VTpy~la~r~gI~---~SvAr~vLR~LeeeGvv~ 90 (107)
T COG4901 43 DEELLDKIRKEVPRERVVTPYVLASRYGIN---GSVARIVLRHLEEEGVVQ 90 (107)
T ss_pred cHHHHHHHHHhcccceeecHHHHHHHhccc---hHHHHHHHHHHHhCCcee
Confidence 33455655442 2568999999999994 488999999999999875
No 135
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=78.64 E-value=2.2 Score=23.95 Aligned_cols=24 Identities=8% Similarity=0.055 Sum_probs=16.4
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
..+|..|||..+|.++ ..+.|.++
T Consensus 19 ~G~s~~~IA~~lg~s~---sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSR---STVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT--H---HHHHHHHH
T ss_pred cCCCHHHHHHHHCcCc---HHHHHHHh
Confidence 4599999999999965 88888776
No 136
>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=78.49 E-value=3.6 Score=28.14 Aligned_cols=48 Identities=13% Similarity=0.157 Sum_probs=34.8
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCC-CCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQI-HPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~-~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|+.|-++|... ++.|+.||.+.++- .+-+...+.++|+.|...|++.
T Consensus 5 ~E~~VM~vlW~~-~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~ 53 (130)
T TIGR02698 5 AEWEVMRVVWTL-GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLT 53 (130)
T ss_pred HHHHHHHHHHcC-CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCcee
Confidence 355566666553 68999998887642 1114478999999999999886
No 137
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=77.92 E-value=3.8 Score=30.72 Aligned_cols=35 Identities=23% Similarity=0.326 Sum_probs=30.3
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHH-HHHhcCccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVC-SLVRSGFFN 95 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR-~Laa~gif~ 95 (97)
.+++.+++++|+.+|.++ ..+.++++ .|...|++.
T Consensus 252 ~~~~~~~~~ia~~lg~~~---~~~~~~~e~~Li~~~li~ 287 (305)
T TIGR00635 252 QGGPVGLKTLAAALGEDA---DTIEDVYEPYLLQIGFLQ 287 (305)
T ss_pred CCCcccHHHHHHHhCCCc---chHHHhhhHHHHHcCCcc
Confidence 357899999999999955 88999999 799999875
No 138
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=77.89 E-value=2.8 Score=34.51 Aligned_cols=37 Identities=16% Similarity=0.279 Sum_probs=28.9
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-..|.+ ||.|+.||++.+|++ ...+.|.|+.| .|++.
T Consensus 6 ~~~L~~--g~~~~~eL~~~l~~s---q~~~s~~L~~L--~~~V~ 42 (442)
T PRK09775 6 TTLLLQ--GPLSAAELAARLGVS---QATLSRLLAAL--GDQVV 42 (442)
T ss_pred HHHHhc--CCCCHHHHHHHhCCC---HHHHHHHHHHh--hccee
Confidence 345644 899999999999993 37899999988 56543
No 139
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=77.82 E-value=2.5 Score=24.77 Aligned_cols=26 Identities=38% Similarity=0.514 Sum_probs=20.8
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
+.|+++||+.+|+++ ..|.|+++...
T Consensus 1 ~~~~~~la~~~~~s~---~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSP---RHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCH---HHHHHHHHHHh
Confidence 478999999999954 78888887654
No 140
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=77.54 E-value=1.5 Score=32.55 Aligned_cols=43 Identities=12% Similarity=0.142 Sum_probs=31.8
Q ss_pred HhcChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 47 IQVGIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 47 veLgI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
.|-.|++.|-++. .-+|+.|||+++++++ ..+-|+.|.|--.|
T Consensus 17 ~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~---aTv~Rf~kklG~~g 62 (284)
T PRK11302 17 SERKVAEVILASPQTAIHSSIATLAKMANVSE---PTVNRFCRSLDTKG 62 (284)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHcCCCC
Confidence 3455667666654 4589999999999965 78888888776555
No 141
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=76.63 E-value=14 Score=27.03 Aligned_cols=32 Identities=25% Similarity=0.258 Sum_probs=28.3
Q ss_pred CCHHHHHHHh-CCCCCCcccHHHHHHHHHhcCcccc
Q 041844 62 MTLNQLLGAL-QIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 62 ~s~~ELA~~~-g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|-.+|+..+ |+.+ ..|+|.++.|+..|++..
T Consensus 71 pSN~~La~r~~G~s~---~tlrR~l~~LveaGLI~r 103 (177)
T PF03428_consen 71 PSNAQLAERLNGMSE---RTLRRHLARLVEAGLIVR 103 (177)
T ss_pred cCHHHHHHHHcCCCH---HHHHHHHHHHHHCCCeee
Confidence 4889999999 9955 899999999999998753
No 142
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=76.61 E-value=4.2 Score=30.43 Aligned_cols=43 Identities=21% Similarity=0.261 Sum_probs=34.9
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..|.+.|.++ +..+..|||+.+++.+ ..++|-|..|...|.+.
T Consensus 7 ~~Il~~l~~~-~~~~~~eLa~~l~VS~---~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 7 QAIVDLLLNH-TSLTTEALAEQLNVSK---ETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 3466777654 6999999999999954 89999999999887653
No 143
>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=76.40 E-value=3.1 Score=25.53 Aligned_cols=24 Identities=13% Similarity=0.230 Sum_probs=19.3
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCC
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHP 75 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~ 75 (97)
|++--+++|.+++.|||+.+|+++
T Consensus 13 ~e~y~~~~g~i~lkdIA~~Lgvs~ 36 (60)
T PF10668_consen 13 FEIYKESNGKIKLKDIAEKLGVSE 36 (60)
T ss_pred HHHHHHhCCCccHHHHHHHHCCCH
Confidence 445555779999999999999954
No 144
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=76.32 E-value=2.7 Score=27.77 Aligned_cols=49 Identities=20% Similarity=0.306 Sum_probs=37.0
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCC-CCCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIH-PTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~-~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|+.|-++|.+.+ ++|+.||.+.++-+ +-....+.-+|+-|+..|+++.
T Consensus 4 ~E~~IM~~lW~~~-~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~ 53 (115)
T PF03965_consen 4 LELEIMEILWESG-EATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTR 53 (115)
T ss_dssp HHHHHHHHHHHHS-SEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhCC-CCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeE
Confidence 3556667776654 59999999998864 2256789999999999999863
No 145
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=76.24 E-value=2 Score=32.09 Aligned_cols=42 Identities=12% Similarity=0.135 Sum_probs=31.4
Q ss_pred hcChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 48 QVGIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 48 eLgI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
|-.|+|.|-++. .-+|+.|||+++++++ ..+.|+.|.|--.|
T Consensus 14 e~~ia~yil~n~~~v~~~si~elA~~~~vS~---aTv~Rf~kklG~~G 58 (278)
T PRK11557 14 DRKLADYLLLQPDTARHLSSQQLANEAGVSQ---SSVVKFAQKLGYKG 58 (278)
T ss_pred HHHHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHcCCCC
Confidence 445566665554 4689999999999965 78888888776555
No 146
>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=75.48 E-value=3.1 Score=26.38 Aligned_cols=34 Identities=26% Similarity=0.416 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHh-CCCCCCcccHHHHHHHHHhcCcccc
Q 041844 60 KPMTLNQLLGAL-QIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 60 gp~s~~ELA~~~-g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|+....||.+.+ |+++ ..|.+-|+.|...|+++.
T Consensus 17 g~~rf~el~~~l~~is~---~~L~~~L~~L~~~GLv~r 51 (90)
T PF01638_consen 17 GPMRFSELQRRLPGISP---KVLSQRLKELEEAGLVER 51 (90)
T ss_dssp SSEEHHHHHHHSTTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred CCCcHHHHHHhcchhHH---HHHHHHHHHHHHcchhhc
Confidence 899999999999 6754 899999999999999853
No 147
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=75.13 E-value=4.4 Score=29.24 Aligned_cols=34 Identities=12% Similarity=0.132 Sum_probs=30.1
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..++..|||+.+|++. ..++--|+.|.+.|+++
T Consensus 28 G~~L~e~eLae~lgVSR---tpVREAL~~L~~eGlv~ 61 (224)
T PRK11534 28 DEKLRMSLLTSRYALGV---GPLREALSQLVAERLVT 61 (224)
T ss_pred CCcCCHHHHHHHHCCCh---HHHHHHHHHHHHCCCEE
Confidence 46789999999999954 77999999999999885
No 148
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=75.04 E-value=4.3 Score=26.38 Aligned_cols=39 Identities=15% Similarity=0.140 Sum_probs=30.1
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
.-+|.+..+++.+|+.|.|..+|+.+ .-|.++|| ..|++
T Consensus 13 ~~~d~~~~~~~~~ti~~~AK~L~i~~---~~l~~~Lr---~~g~l 51 (111)
T PF03374_consen 13 EFYDAFVDSDGLYTIREAAKLLGIGR---NKLFQWLR---EKGWL 51 (111)
T ss_pred HHHHHHHcCCCCccHHHHHHHhCCCH---HHHHHHHH---hCCce
Confidence 44687777778999999999999954 66777766 56665
No 149
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.00 E-value=4.5 Score=28.15 Aligned_cols=39 Identities=18% Similarity=0.136 Sum_probs=32.1
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
-|+|+|-.+ +.+|-+|||..+|++. ..++++|..|..-+
T Consensus 5 ~v~d~L~~~-~~~~dedLa~~l~i~~---n~vRkiL~~L~ed~ 43 (147)
T smart00531 5 LVLDALMRN-GCVTEEDLAELLGIKQ---KQLRKILYLLYDEK 43 (147)
T ss_pred eehHHHHhc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHhhh
Confidence 467877665 5899999999999954 88999999998833
No 150
>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=73.74 E-value=8 Score=24.60 Aligned_cols=42 Identities=21% Similarity=0.244 Sum_probs=33.7
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|-..++. +..|++||-+.+|++. ..|-..|--|+..|++..
T Consensus 9 ~IL~~ls~--~c~TLeeL~ekTgi~k---~~LlV~LsrL~k~GiI~R 50 (72)
T PF05584_consen 9 KILIILSK--RCCTLEELEEKTGISK---NTLLVYLSRLAKRGIIER 50 (72)
T ss_pred HHHHHHHh--ccCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeee
Confidence 34555665 5999999999999944 788888999999998764
No 151
>PRK13239 alkylmercury lyase; Provisional
Probab=73.69 E-value=4.5 Score=30.35 Aligned_cols=35 Identities=11% Similarity=0.249 Sum_probs=27.0
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
|+..|+ +|+|.|..+||+.+|.+ .+.++++|+.|.
T Consensus 27 llr~la-~G~pvt~~~lA~~~~~~---~~~v~~~L~~l~ 61 (206)
T PRK13239 27 LLRLLA-KGRPVSVTTLAAALGWP---VEEVEAVLEAMP 61 (206)
T ss_pred HHHHHH-cCCCCCHHHHHHHhCCC---HHHHHHHHHhCC
Confidence 456676 68999999999999984 367777777654
No 152
>PRK13558 bacterio-opsin activator; Provisional
Probab=73.37 E-value=4.4 Score=33.59 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 34 ~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
..-+-.+|++| .+.|-||. +...|..|||+.+|+.+ ..+...||
T Consensus 609 t~~q~e~l~~a--~~~gyf~~----pr~~~~~e~a~~l~is~---~t~~~~lr 652 (665)
T PRK13558 609 TDRQLTALQKA--YVSGYFEW----PRRVEGEELAESMGISR---STFHQHLR 652 (665)
T ss_pred CHHHHHHHHHH--HHcCCCCC----CccCCHHHHHHHhCCCH---HHHHHHHH
Confidence 34566799999 99999984 36789999999999954 45555444
No 153
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=73.34 E-value=4.7 Score=28.71 Aligned_cols=34 Identities=9% Similarity=0.115 Sum_probs=30.3
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..++-.+||+.+|++. ..++.-|+.|.+.|+++
T Consensus 32 G~~L~e~~La~~lgVSR---tpVReAL~~L~~eGlv~ 65 (212)
T TIGR03338 32 GAKLNESDIAARLGVSR---GPVREAFRALEEAGLVR 65 (212)
T ss_pred CCEecHHHHHHHhCCCh---HHHHHHHHHHHHCCCEE
Confidence 56789999999999954 78999999999999985
No 154
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=73.20 E-value=4.2 Score=29.25 Aligned_cols=30 Identities=23% Similarity=0.311 Sum_probs=26.7
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
|.|-.|||+.+|+.+ +.+.|+++.|...|+
T Consensus 173 ~~t~~~iA~~lG~tr---etvsR~l~~L~~~gl 202 (236)
T PRK09392 173 PYEKRVLASYLGMTP---ENLSRAFAALASHGV 202 (236)
T ss_pred eCCHHHHHHHhCCCh---hHHHHHHHHHHhCCe
Confidence 566789999999965 889999999999996
No 155
>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=72.75 E-value=4.3 Score=26.07 Aligned_cols=32 Identities=16% Similarity=0.126 Sum_probs=24.9
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|.+.|.+ +..|+.+||+..|+.. ..++|.+.
T Consensus 10 ~I~e~l~~--~~~ti~dvA~~~gvS~---~TVsr~L~ 41 (80)
T TIGR02844 10 EIGKYIVE--TKATVRETAKVFGVSK---STVHKDVT 41 (80)
T ss_pred HHHHHHHH--CCCCHHHHHHHhCCCH---HHHHHHhc
Confidence 45677876 7899999999999954 67777553
No 156
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=71.95 E-value=2 Score=26.54 Aligned_cols=35 Identities=11% Similarity=0.163 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccccC
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR 97 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e~ 97 (97)
|-+++++||.+.|+-. +.+-.-||-|.+.|+++.|
T Consensus 3 g~lvas~iAd~~GiTR---SvIVNALRKleSaGvIesr 37 (61)
T PF08222_consen 3 GRLVASKIADRVGITR---SVIVNALRKLESAGVIESR 37 (61)
T ss_dssp EEE-HHHHHHHHT--H---HHHHHHHHHHHHTTSEEEE
T ss_pred ceehHHHHHHHhCccH---HHHHHHHHHHHhcCceeec
Confidence 4567899999999843 7899999999999998753
No 157
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=71.89 E-value=2.4 Score=23.64 Aligned_cols=30 Identities=7% Similarity=0.123 Sum_probs=18.5
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
..|..+||+.+|+++ ..++|.++-....|+
T Consensus 17 G~s~~~ia~~lgvs~---~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 17 GWSIREIAKRLGVSR---STVYRWIKRYREEGL 46 (50)
T ss_dssp T--HHHHHHHHTS-H---HHHHHHHT-------
T ss_pred CCCHHHHHHHHCcCH---HHHHHHHHHcccccc
Confidence 789999999999955 899999987766664
No 158
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=71.78 E-value=1.8 Score=32.93 Aligned_cols=43 Identities=19% Similarity=0.252 Sum_probs=31.4
Q ss_pred hcChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 48 QVGIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 48 eLgI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
|-.|+|.|-++. .-.|+.|||+++|++| ..+-|+-|.|--.|+
T Consensus 20 er~iA~yil~~~~~~~~~si~elA~~a~VS~---aTv~Rf~~kLGf~Gf 65 (281)
T COG1737 20 ERKIADYILANPDEVALLSIAELAERAGVSP---ATVVRFARKLGFEGF 65 (281)
T ss_pred HHHHHHHHHhCHHHHHHHHHHHHHHHhCCCH---HHHHHHHHHcCCCCH
Confidence 445566665543 4579999999999965 788888887766653
No 159
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=71.52 E-value=6 Score=24.62 Aligned_cols=40 Identities=23% Similarity=0.244 Sum_probs=23.0
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCC----------CcccHHHHHHHHHhcC
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPT----------KTRCLHFLVCSLVRSG 92 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~----------~~~~L~RlLR~Laa~g 92 (97)
|-+.+.. ..+|-.|+|+.+|++.+ +.-.+.++++++.+.|
T Consensus 23 i~~~~~~--~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG 72 (80)
T PF13744_consen 23 IRELREE--RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG 72 (80)
T ss_dssp HHHHHHC--CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred HHHHHHH--cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence 4566654 67899999999997421 1123556666666666
No 160
>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=71.24 E-value=2.2 Score=25.15 Aligned_cols=31 Identities=16% Similarity=0.205 Sum_probs=20.5
Q ss_pred ChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHH
Q 041844 50 GIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHF 83 (97)
Q Consensus 50 gI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~R 83 (97)
.+.+.+...| .-+|..|||+.+|++| ..++|
T Consensus 16 r~L~~l~~~G~~~vSS~~La~~~gi~~---~qVRK 47 (50)
T PF06971_consen 16 RYLEQLKEEGVERVSSQELAEALGITP---AQVRK 47 (50)
T ss_dssp HHHHHHHHTT-SEE-HHHHHHHHTS-H---HHHHH
T ss_pred HHHHHHHHcCCeeECHHHHHHHHCCCH---HHhcc
Confidence 3445565555 5789999999999955 55554
No 161
>PRK11642 exoribonuclease R; Provisional
Probab=71.15 E-value=6.1 Score=34.97 Aligned_cols=45 Identities=20% Similarity=0.267 Sum_probs=35.4
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCC-CCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHP-TKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~-~~~~~L~RlLR~Laa~gif~ 95 (97)
|.+.|...++|++..||+..++++. .+...|.++|+.|...|.+.
T Consensus 24 Il~~l~~~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~ 69 (813)
T PRK11642 24 ILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLV 69 (813)
T ss_pred HHHHHHhcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEE
Confidence 4455655568999999999999954 23456999999999999764
No 162
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=70.98 E-value=4.1 Score=29.37 Aligned_cols=34 Identities=15% Similarity=0.104 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
..+|..|||+++++.+ ..++.-++.|+..|++.+
T Consensus 177 ~g~s~~eIA~~l~iS~---~Tv~~~~~~~~~~~~~~~ 210 (239)
T PRK10430 177 YEFSTDELANAVNISR---VSCRKYLIWLVNCHILFT 210 (239)
T ss_pred CCcCHHHHHHHhCchH---HHHHHHHHHHHhCCEEEE
Confidence 6789999999999955 899999999999998854
No 163
>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=70.79 E-value=2.8 Score=24.09 Aligned_cols=31 Identities=6% Similarity=0.133 Sum_probs=16.8
Q ss_pred CHHHHHHHhCCCC------------CCcccHHHHHHHHHhcCc
Q 041844 63 TLNQLLGALQIHP------------TKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 63 s~~ELA~~~g~~~------------~~~~~L~RlLR~Laa~gi 93 (97)
|+.|||+.+|+++ ..++.-.||+......|+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY 43 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGY 43 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCC
Confidence 4566676666532 133445556665555554
No 164
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=70.48 E-value=4.4 Score=22.56 Aligned_cols=21 Identities=0% Similarity=0.072 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHF 83 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~R 83 (97)
...|+.+||+++|++. ..+++
T Consensus 15 ~~~s~~~Ia~~~gvs~---~~~y~ 35 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSK---GSFYR 35 (47)
T ss_dssp TTSSHHHHHHHHTSCH---HHHHH
T ss_pred HhCCHHHHHHHHccch---hhHHH
Confidence 7899999999999953 55554
No 165
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=70.43 E-value=6.9 Score=25.03 Aligned_cols=29 Identities=7% Similarity=0.175 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS 91 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~ 91 (97)
.+.|++|||+.+++++ ..|.|+.+....+
T Consensus 20 ~~~~~~~lA~~~~~S~---~~l~r~f~~~~g~ 48 (107)
T PRK10219 20 QPLNIDVVAKKSGYSK---WYLQRMFRTVTHQ 48 (107)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHHHHHCc
Confidence 6899999999999955 8899988865433
No 166
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=70.34 E-value=8.1 Score=28.23 Aligned_cols=39 Identities=13% Similarity=0.101 Sum_probs=32.1
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-.|..+ +++|..|||..++.++ ..+.|++.-|...|++.
T Consensus 52 ~~L~~~-~~itq~eLa~~l~l~~---sTvtr~l~rLE~kGlI~ 90 (185)
T PRK13777 52 WIAYHL-KGASISEIAKFGVMHV---STAFNFSKKLEERGYLT 90 (185)
T ss_pred HHHHhC-CCcCHHHHHHHHCCCH---hhHHHHHHHHHHCCCEE
Confidence 344433 6899999999999954 78999999999999886
No 167
>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=70.21 E-value=5.5 Score=26.48 Aligned_cols=46 Identities=15% Similarity=0.117 Sum_probs=35.4
Q ss_pred HhcChhHHHhhC-------CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNH-------TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~-------~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+++|+..+..- ..-+|.+++++.+|+++ ..+.+.+..|..+|++.
T Consensus 33 rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~---~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 33 RQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSR---DHVSKALNELIRRGVII 85 (100)
T ss_pred HHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 344555555442 24689999999999966 78999999999999875
No 168
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=69.99 E-value=7.5 Score=27.99 Aligned_cols=34 Identities=12% Similarity=0.059 Sum_probs=29.9
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..++..+||+.+|++. ..++.-|+.|...|+++
T Consensus 32 G~~L~e~~La~~lgVSR---tpVREAL~~L~~eGLV~ 65 (221)
T PRK11414 32 GARLITKNLAEQLGMSI---TPVREALLRLVSVNALS 65 (221)
T ss_pred CCccCHHHHHHHHCCCc---hhHHHHHHHHHHCCCEE
Confidence 46788899999999954 77999999999999885
No 169
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=69.88 E-value=3.2 Score=24.05 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=18.0
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
-+.+.+ ..+|..+||..+|+++ ..+.|+++
T Consensus 3 ~~~m~~--~~it~~~La~~~gis~---~tl~~~~~ 32 (63)
T PF13443_consen 3 KELMAE--RGITQKDLARKTGISR---STLSRILN 32 (63)
T ss_dssp HHHHHH--TT--HHHHHHHHT--H---HHHHHHHT
T ss_pred HHHHHH--cCCCHHHHHHHHCcCH---HHHHHHHh
Confidence 355655 5678999999999843 66666654
No 170
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=69.82 E-value=3.5 Score=31.04 Aligned_cols=43 Identities=14% Similarity=0.175 Sum_probs=31.4
Q ss_pred HhcChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 47 IQVGIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 47 veLgI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
.|-.|+|.|-++. .-+|+.|||+++++++ ..+.|+-|.|--.|
T Consensus 29 ~e~~Ia~yil~~~~~v~~~si~~lA~~~~vS~---aTi~Rf~kkLGf~g 74 (292)
T PRK11337 29 LESRVVEWLLKPGDLSEATALKDIAEALAVSE---AMIVKVAKKLGFSG 74 (292)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCh---HHHHHHHHHcCCCC
Confidence 3455667665554 4589999999999965 78888888766555
No 171
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=69.52 E-value=8.4 Score=27.96 Aligned_cols=34 Identities=12% Similarity=0.149 Sum_probs=30.6
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|.+++-.+||+.+|++. ..++.-|+.|++.|++.
T Consensus 37 G~~l~e~~La~~~gvSr---tPVReAL~rL~~eGlv~ 70 (230)
T COG1802 37 GERLSEEELAEELGVSR---TPVREALRRLEAEGLVE 70 (230)
T ss_pred CCCccHHHHHHHhCCCC---ccHHHHHHHHHHCCCeE
Confidence 57899999999999955 77999999999999876
No 172
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=69.16 E-value=6.4 Score=29.54 Aligned_cols=39 Identities=5% Similarity=0.021 Sum_probs=32.0
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
.|.+.|.++ |.+++.|||+.+++.+ ..++|=|+.|...+
T Consensus 11 ~I~~~l~~~-~~v~v~eLa~~~~VS~---~TIRRDL~~Le~~~ 49 (252)
T PRK10681 11 QLLQALKRS-DKLHLKDAAALLGVSE---MTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHc-CCCcHHHHHHHhCCCH---HHHHHHHHHhhcCe
Confidence 467778664 6899999999999954 89999999988544
No 173
>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=68.68 E-value=5 Score=21.49 Aligned_cols=22 Identities=14% Similarity=0.169 Sum_probs=17.3
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+|..|+|+.+|+++ ..++++++
T Consensus 2 lt~~e~a~~lgis~---~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSK---DTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHH
Confidence 58899999999954 67777664
No 174
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=67.59 E-value=8.1 Score=20.99 Aligned_cols=27 Identities=19% Similarity=0.305 Sum_probs=19.6
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+|+.|+|+.+|+++ . -+|.....|++.
T Consensus 1 ~~~~e~a~~~gv~~---~----tlr~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSP---S----TLRYYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCH---H----HHHHHHHCCCCC
Confidence 47899999999954 4 566667777653
No 175
>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=67.12 E-value=3.9 Score=25.96 Aligned_cols=32 Identities=9% Similarity=0.037 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
..+|..|||+.+|+++ ..++..++.+-..|++
T Consensus 31 eGlS~kEIAe~LGIS~---~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 31 AGKTASEIAEELGRTE---QTVRNHLKGETKAGGL 62 (73)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHhcCcccchH
Confidence 6789999999999955 8899988877777654
No 176
>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=66.90 E-value=9.2 Score=23.53 Aligned_cols=33 Identities=18% Similarity=0.339 Sum_probs=21.4
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|.|.+.+.|+|++||.+.+..+. + ..+.++|+
T Consensus 11 VeymK~r~~Plt~~eI~d~l~~d~-~-~~~~~~Lk 43 (65)
T PF02186_consen 11 VEYMKKRDHPLTLEEILDYLSLDI-G-KKLKQWLK 43 (65)
T ss_dssp HHHHHHH-S-B-HHHHHHHHTSSS---HHHHHHHH
T ss_pred HHHHHhcCCCcCHHHHHHHHcCCC-C-HHHHHHHH
Confidence 477877789999999999999754 2 23444554
No 177
>PRK01381 Trp operon repressor; Provisional
Probab=66.52 E-value=8.2 Score=25.95 Aligned_cols=40 Identities=13% Similarity=0.069 Sum_probs=32.6
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS 91 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~ 91 (97)
..++|+..|.+ |.+|-.|||+.+|+.. ..+.|.=|.|-.+
T Consensus 43 ~R~~I~~~L~~--g~~sQREIa~~lGvSi---aTITRgsn~Lk~~ 82 (99)
T PRK01381 43 TRVRIVEELLR--GELSQREIKQELGVGI---ATITRGSNSLKTA 82 (99)
T ss_pred HHHHHHHHHHc--CCcCHHHHHHHhCCce---eeehhhHHHhccC
Confidence 67889988866 8999999999999954 7788887777543
No 178
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=65.69 E-value=3.3 Score=25.54 Aligned_cols=35 Identities=23% Similarity=0.392 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHh---CCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGAL---QIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~---g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.+++.++|..+ +... ....|+-+.-+|.+.|+++
T Consensus 23 ~~i~l~~ia~~l~~~~~k~-~~RRlYDI~NVLealgli~ 60 (71)
T PF02319_consen 23 KSISLNEIADKLISENVKT-QRRRLYDIINVLEALGLIE 60 (71)
T ss_dssp TEEEHHHHHHHCHHHCCHH-HCHHHHHHHHHHHHCTSEE
T ss_pred CcccHHHHHHHHccccccc-ccchhhHHHHHHHHhCcee
Confidence 889999999999 7721 2278999999999999986
No 179
>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=65.15 E-value=6.5 Score=20.81 Aligned_cols=22 Identities=23% Similarity=0.247 Sum_probs=16.0
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+|..|+|+.+|+++ ..+++..+
T Consensus 1 ~s~~e~a~~lgvs~---~tl~~~~~ 22 (49)
T cd04762 1 LTTKEAAELLGVSP---STLRRWVK 22 (49)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHH
Confidence 47889999999954 65665544
No 180
>PF12728 HTH_17: Helix-turn-helix domain
Probab=64.68 E-value=6.4 Score=22.02 Aligned_cols=22 Identities=14% Similarity=0.108 Sum_probs=17.4
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+|+.|+|+.+|+++ ..++++++
T Consensus 2 lt~~e~a~~l~is~---~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISR---STVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHH
Confidence 58899999999954 66777665
No 181
>PRK15482 transcriptional regulator MurR; Provisional
Probab=64.57 E-value=5.2 Score=30.07 Aligned_cols=43 Identities=16% Similarity=0.219 Sum_probs=31.3
Q ss_pred HhcChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 47 IQVGIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 47 veLgI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
.|-.|+|.|-++. .-+|+.|||+++|+++ ..+-|+-|.|--.|
T Consensus 17 ~e~~Ia~yIl~n~~~v~~~si~elA~~~~vS~---aTv~Rf~kkLGf~G 62 (285)
T PRK15482 17 NEQKIADFLRANVSELKSVSSRKMAKQLGISQ---SSIVKFAQKLGAQG 62 (285)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHhCCCC
Confidence 3445567665554 5689999999999965 77888887766555
No 182
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. 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; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=64.54 E-value=6.9 Score=21.43 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=20.1
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
|+.|+|+.+|+++ +-||+....|++
T Consensus 1 ti~e~A~~~gvs~-------~tlR~ye~~Gll 25 (38)
T PF00376_consen 1 TIGEVAKLLGVSP-------RTLRYYEREGLL 25 (38)
T ss_dssp EHHHHHHHHTS-H-------HHHHHHHHTTSS
T ss_pred CHHHHHHHHCCCH-------HHHHHHHHCCCC
Confidence 5789999999954 578888888987
No 183
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=63.98 E-value=11 Score=29.00 Aligned_cols=34 Identities=24% Similarity=0.348 Sum_probs=30.3
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHH-HHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVC-SLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR-~Laa~gif~ 95 (97)
++|.+++.+|+.+|.++ ..+.++++ +|...|++.
T Consensus 274 ~~~~~~~~~a~~lg~~~---~~~~~~~e~~Li~~~li~ 308 (328)
T PRK00080 274 GGPVGLDTLAAALGEER---DTIEDVYEPYLIQQGFIQ 308 (328)
T ss_pred CCceeHHHHHHHHCCCc---chHHHHhhHHHHHcCCcc
Confidence 58999999999999955 78999999 999999875
No 184
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=63.71 E-value=7.6 Score=34.28 Aligned_cols=34 Identities=21% Similarity=0.231 Sum_probs=31.2
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
...|+.||++.+|+++ +.|+|-|-++...|++.+
T Consensus 615 ~twt~eelse~l~ip~---~~lrrrL~fWi~~GvL~e 648 (765)
T KOG2165|consen 615 NTWTLEELSESLGIPV---PALRRRLSFWIQKGVLRE 648 (765)
T ss_pred ccccHHHHHHHhCCCH---HHHHHHHHHHHHcCeeec
Confidence 6799999999999965 899999999999999875
No 185
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=63.43 E-value=14 Score=26.78 Aligned_cols=37 Identities=19% Similarity=0.238 Sum_probs=29.9
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+|..|.+||.+++.-.- .+..+..+++.|...|++.+
T Consensus 40 dG~rt~~eI~~~l~~~~-p~~~v~~~L~~L~~~G~l~~ 76 (193)
T TIGR03882 40 DGRRTLDEIIAALAGRF-PAEEVLYALDRLERRGYLVE 76 (193)
T ss_pred cCCCCHHHHHHHhhccC-CHHHHHHHHHHHHHCCCEec
Confidence 47999999999876521 24669999999999998875
No 186
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=63.37 E-value=8.2 Score=24.28 Aligned_cols=34 Identities=15% Similarity=0.142 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
|.+|.+||...++-..-+++.+..|+..|...||
T Consensus 20 G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 20 GYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp SS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred CcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 7899999999999543467899999999999985
No 187
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=63.26 E-value=10 Score=28.19 Aligned_cols=38 Identities=13% Similarity=0.183 Sum_probs=29.0
Q ss_pred hhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844 51 IPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS 91 (97)
Q Consensus 51 I~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~ 91 (97)
+.+.|..+- +++|+++||+.+++++ ..|.|+.|--+.+
T Consensus 188 ~~~~i~~~~~~~isl~~lA~~~~lS~---~~l~r~Fk~~~G~ 226 (290)
T PRK10572 188 ACQYISDHLASEFDIESVAQHVCLSP---SRLAHLFRQQLGI 226 (290)
T ss_pred HHHHHHhcccCCCCHHHHHHHHCCCH---HHHHHHHHHHHCc
Confidence 344554443 8999999999999965 8999999866543
No 188
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=63.15 E-value=6.3 Score=28.16 Aligned_cols=31 Identities=10% Similarity=0.068 Sum_probs=19.8
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
|.+...++..|..|||+.+|+++ ..|+|-.+
T Consensus 26 e~~~~~~~r~T~~eiAee~Gis~---~tLYrWr~ 56 (142)
T PF13022_consen 26 ELMPENGERRTQAEIAEEVGISR---STLYRWRQ 56 (142)
T ss_dssp HHS------S-HHHHHHHHTS-H---HHHHHHHH
T ss_pred HHhhhccccchHHHHHHHhCCCH---HHHHHHHh
Confidence 55555567899999999999955 89999875
No 189
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=63.08 E-value=9.7 Score=25.31 Aligned_cols=39 Identities=13% Similarity=0.082 Sum_probs=31.6
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa 90 (97)
...||+..|-+ +++|=.|||+.+|+.. ..+.|.=|.|..
T Consensus 43 ~R~~i~~~Ll~--~~~tQrEIa~~lGiS~---atIsR~sn~lk~ 81 (94)
T TIGR01321 43 DRIRIVNELLN--GNMSQREIASKLGVSI---ATITRGSNNLKT 81 (94)
T ss_pred HHHHHHHHHHh--CCCCHHHHHHHhCCCh---hhhhHHHhhccc
Confidence 56788887755 7999999999999954 788888887763
No 190
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=63.06 E-value=4.3 Score=25.07 Aligned_cols=30 Identities=13% Similarity=0.218 Sum_probs=23.9
Q ss_pred HHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 64 LNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 64 ~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+..++..++.+ +++.+.|+.|.|..+|+.+
T Consensus 18 ie~~~~~~~~~--~~e~~~rf~~~L~~~Gv~~ 47 (69)
T PF09269_consen 18 IERLVAMTNFD--DEESLRRFQRKLKKMGVEK 47 (69)
T ss_dssp HHHHHTTEEE---TGGGHHHHHHHHHHTTHHH
T ss_pred HHHHHHhcCCC--CHHHHHHHHHHHHHCCHHH
Confidence 56777787764 5689999999999999764
No 191
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=62.53 E-value=11 Score=26.15 Aligned_cols=23 Identities=13% Similarity=0.140 Sum_probs=17.9
Q ss_pred hHHHhhCC-CCCCHHHHHHHhCCC
Q 041844 52 PDIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 52 ~D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
.+.+.+.| ...|+.+||+++|++
T Consensus 18 ~~lf~e~G~~~~s~~~IA~~agvs 41 (202)
T TIGR03613 18 LDTFSRFGFHGTSLEQIAELAGVS 41 (202)
T ss_pred HHHHHHhCcccCCHHHHHHHhCCC
Confidence 35555666 779999999999984
No 192
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=62.47 E-value=13 Score=25.26 Aligned_cols=30 Identities=10% Similarity=0.106 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhcChhHHHhhCC-CCCCHHHHHHHhCCC
Q 041844 38 SMSLKCVKLIQVGIPDIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 38 s~aL~~a~~veLgI~D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
...+.+| .+.+.++| ...|+++||++.|++
T Consensus 11 ~~Il~aA-------~~lf~~~G~~~~s~~~IA~~agvs 41 (189)
T TIGR03384 11 AELIDAT-------IESIGERGSLDVTIAQIARRAGVS 41 (189)
T ss_pred HHHHHHH-------HHHHHhcCcccCCHHHHHHHhCCC
Confidence 4455666 35566666 789999999999984
No 193
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=62.14 E-value=13 Score=25.99 Aligned_cols=22 Identities=18% Similarity=0.164 Sum_probs=17.2
Q ss_pred HHHhhCC-CCCCHHHHHHHhCCC
Q 041844 53 DIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 53 D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
+.+.+.| ...|++|||++.|++
T Consensus 22 ~lf~~~G~~~~ti~~Ia~~agvs 44 (213)
T PRK09975 22 AQFALRGVSNTTLNDIADAANVT 44 (213)
T ss_pred HHHHHcCcccCCHHHHHHHcCCC
Confidence 4455555 679999999999984
No 194
>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=61.78 E-value=7.9 Score=21.62 Aligned_cols=24 Identities=17% Similarity=0.250 Sum_probs=18.6
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
..+|..|||..+|++. ..++++.+
T Consensus 19 ~~~t~~eIa~~lg~s~---~~V~~~~~ 42 (50)
T PF04545_consen 19 EGLTLEEIAERLGISR---STVRRILK 42 (50)
T ss_dssp ST-SHHHHHHHHTSCH---HHHHHHHH
T ss_pred CCCCHHHHHHHHCCcH---HHHHHHHH
Confidence 6899999999999954 67777665
No 195
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=61.77 E-value=11 Score=31.82 Aligned_cols=46 Identities=9% Similarity=0.056 Sum_probs=36.2
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++..|-..+...+...+..+||..+|+++ +.+.+.+..|.+.|+++
T Consensus 4 ~e~~iL~~l~~~~~~~~~~~la~~~g~~~---~~v~~~~~~L~~kg~v~ 49 (492)
T PLN02853 4 AEEALLGALSNNEEISDSGQFAASHGLDH---NEVVGVIKSLHGFRYVD 49 (492)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCH---HHHHHHHHHHHhCCCEE
Confidence 45566677765432389999999999944 89999999999999875
No 196
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=61.59 E-value=14 Score=27.13 Aligned_cols=41 Identities=15% Similarity=0.207 Sum_probs=32.7
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|.+-.+|+-+ +|+|-.||++..|+++ ..+++.|...|++.+
T Consensus 93 LEtLaiIay~-qPiTr~eI~~irGv~~------~~ii~~L~~~gLI~e 133 (188)
T PRK00135 93 LEVLAIIAYK-QPITRIEIDEIRGVNS------DGALQTLLAKGLIKE 133 (188)
T ss_pred HHHHHHHHHc-CCcCHHHHHHHHCCCH------HHHHHHHHHCCCeEE
Confidence 3445667654 7999999999999942 789999999999864
No 197
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=61.57 E-value=11 Score=28.41 Aligned_cols=36 Identities=11% Similarity=0.202 Sum_probs=27.6
Q ss_pred HHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844 53 DIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS 91 (97)
Q Consensus 53 D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~ 91 (97)
+.|.++ ..++|+++||+.+|.++ ..+.|+.+..+..
T Consensus 12 ~~i~~~~~~~~~l~~lA~~~~~S~---~~l~r~F~~~~g~ 48 (289)
T PRK15121 12 IWLEGHLDQPLSLDNVAAKAGYSK---WHLQRMFKDVTGH 48 (289)
T ss_pred HHHHhcccCCCCHHHHHHHHCcCH---HHHHHHHHHHHCc
Confidence 445444 36899999999999955 8899999876543
No 198
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=61.39 E-value=19 Score=24.91 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=28.9
Q ss_pred HHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 32 TFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 32 ~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+..| .-.||+|| ..|+.+ ||.+..+|+..+++ +.-.+||+
T Consensus 54 mTAY-RQ~Al~~A--------~~L~~~-Gp~~~~~l~~~~~~-----~~A~~IL~ 93 (118)
T PF09929_consen 54 MTAY-RQDALRCA--------AALAEH-GPSRPADLRKATGV-----PKATSILR 93 (118)
T ss_pred chhh-HHHHHHHH--------HHHHHc-CCCCHHHHHHhcCC-----ChHHHHHH
Confidence 3344 45688888 567653 79999999999988 34566776
No 199
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=61.33 E-value=13 Score=31.31 Aligned_cols=46 Identities=13% Similarity=0.094 Sum_probs=37.2
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+..|...|..+++..+..+||+.+|++ .+.+.+.+..|.+.|+++
T Consensus 7 ~e~~iL~~l~~~~~~~~~~~la~~~~~~---~~~v~~~~~~L~~kg~v~ 52 (494)
T PTZ00326 7 EENTILSKLESENEIVNSLALAESLNID---HQKVVGAIKSLESANYIT 52 (494)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCC---HHHHHHHHHHHHhCCCEE
Confidence 4555667776545679999999999994 489999999999999875
No 200
>PHA02591 hypothetical protein; Provisional
Probab=61.00 E-value=14 Score=24.14 Aligned_cols=31 Identities=13% Similarity=0.217 Sum_probs=23.6
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
++..|.+ ..+|..+||+.+|+ +...+++.++
T Consensus 51 vA~eL~e--qGlSqeqIA~~LGV---sqetVrKYL~ 81 (83)
T PHA02591 51 VTHELAR--KGFTVEKIASLLGV---SVRKVRRYLE 81 (83)
T ss_pred HHHHHHH--cCCCHHHHHHHhCC---CHHHHHHHHh
Confidence 3455655 68999999999999 4477777766
No 201
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=60.93 E-value=16 Score=25.73 Aligned_cols=30 Identities=10% Similarity=0.151 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhcChhHHHhhCC-CCCCHHHHHHHhCCC
Q 041844 38 SMSLKCVKLIQVGIPDIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 38 s~aL~~a~~veLgI~D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
-..+.+| .+.+.+.| ...|+++||++.|+.
T Consensus 14 ~~Il~AA-------~~lf~e~G~~~~t~~~Ia~~agvs 44 (215)
T PRK10668 14 QHILDAA-------LRLFSQQGVSATSLADIAKAAGVT 44 (215)
T ss_pred HHHHHHH-------HHHHHHcCcccCCHHHHHHHhCCC
Confidence 3455566 34555666 678999999999984
No 202
>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=60.78 E-value=5.4 Score=22.95 Aligned_cols=29 Identities=14% Similarity=0.279 Sum_probs=18.5
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHH-HhcCcc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSL-VRSGFF 94 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~L-aa~gif 94 (97)
.++++.|||..+|+++ ..|++.| ...|+.
T Consensus 2 ~~i~V~elAk~l~v~~------~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 2 EKIRVSELAKELGVPS------KEIIKKLFKELGIM 31 (54)
T ss_dssp -EE-TTHHHHHHSSSH------HHHHHHH-HHHTS-
T ss_pred CceEHHHHHHHHCcCH------HHHHHHHHHhCCcC
Confidence 3678999999999943 4466666 336654
No 203
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=60.56 E-value=26 Score=20.87 Aligned_cols=41 Identities=20% Similarity=0.220 Sum_probs=29.9
Q ss_pred hhHHHhhCCCCCCHHHHHHHh----CCCCCCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGAL----QIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~----g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+...+.++ +..|+.+|.+.+ +.+ +...-.++|+|.+.+.+.
T Consensus 32 i~~~l~~~-~~~tl~~l~~~~d~~~~l~---~g~~L~~l~~LiA~k~i~ 76 (79)
T PF08721_consen 32 ILARLRKN-PTMTLRDLCKELDKDYELE---PGTALPLLRHLIATKRIK 76 (79)
T ss_dssp HHHHHHHT-TTSBHHHHHHHHHHHCT-----TTHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHc-CCCCHHHHHHHHHHhcCCC---cCChHHHHHHHHhCChhc
Confidence 45666555 459999999887 563 377888999999988764
No 204
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=60.37 E-value=5.5 Score=22.32 Aligned_cols=24 Identities=17% Similarity=0.170 Sum_probs=16.6
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
..+|..|+|+.+|+++ ..+.|+++
T Consensus 8 ~gls~~~la~~~gis~---~~i~~~~~ 31 (55)
T PF01381_consen 8 KGLSQKELAEKLGISR---STISRIEN 31 (55)
T ss_dssp TTS-HHHHHHHHTS-H---HHHHHHHT
T ss_pred cCCCHHHHHHHhCCCc---chhHHHhc
Confidence 5688899999999843 66666654
No 205
>PRK13503 transcriptional activator RhaS; Provisional
Probab=60.33 E-value=11 Score=27.63 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=27.3
Q ss_pred hhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 51 IPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 51 I~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
+.+.|.++- .++|++++|+.+++++ ..|.|+.+.-.
T Consensus 176 ~~~~I~~~~~~~~tl~~lA~~~~lS~---~~l~r~Fk~~~ 212 (278)
T PRK13503 176 LLAWLEDHFAEEVNWEALADQFSLSL---RTLHRQLKQQT 212 (278)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCCCH---HHHHHHHHHHh
Confidence 344455443 6999999999999965 88999887544
No 206
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=59.72 E-value=13 Score=21.65 Aligned_cols=27 Identities=15% Similarity=0.202 Sum_probs=18.6
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|+.|+|+.+|+++ . -+|.....|++.
T Consensus 1 ~s~~eva~~~gvs~---~----tlr~~~~~gli~ 27 (70)
T smart00422 1 YTIGEVAKLAGVSV---R----TLRYYERIGLLP 27 (70)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHCCCCC
Confidence 47889999999965 4 444555577654
No 207
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=59.45 E-value=17 Score=26.48 Aligned_cols=31 Identities=10% Similarity=0.265 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhcChhHHHhhCC-CCCCHHHHHHHhCCCC
Q 041844 38 SMSLKCVKLIQVGIPDIIHNHT-KPMTLNQLLGALQIHP 75 (97)
Q Consensus 38 s~aL~~a~~veLgI~D~La~~~-gp~s~~ELA~~~g~~~ 75 (97)
-.++.+| + +++.+.| ...|+.+||+++|+.+
T Consensus 7 e~Il~aA--~-----~l~~e~G~~~lsmr~lA~~lgv~~ 38 (205)
T PRK13756 7 EKVIDSA--L-----ELLNEVGIEGLTTRKLAQKLGVEQ 38 (205)
T ss_pred HHHHHHH--H-----HHHHHcCcccCCHHHHHHHhCCCc
Confidence 4456666 3 4454555 6899999999999853
No 208
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=59.26 E-value=12 Score=24.32 Aligned_cols=25 Identities=8% Similarity=-0.012 Sum_probs=21.4
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHH
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSL 88 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~L 88 (97)
..|..|||+.+|++. ..++|+.|.|
T Consensus 50 G~S~~eIA~~LgISr---sTIyRi~R~~ 74 (88)
T TIGR02531 50 GKTYSDIEAETGAST---ATISRVKRCL 74 (88)
T ss_pred CCCHHHHHHHHCcCH---HHHHHHHHhc
Confidence 479999999999955 8899988853
No 209
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=59.16 E-value=12 Score=27.53 Aligned_cols=34 Identities=9% Similarity=0.139 Sum_probs=29.5
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |-.|||+.+|++. ..++.-|+.|.+.|+++
T Consensus 30 G~~LpsE~eLa~~~gVSR---tpVREAL~~L~~eGlV~ 64 (257)
T PRK10225 30 GERLPPEREIAEMLDVTR---TVVREALIMLEIKGLVE 64 (257)
T ss_pred CCcCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence 4677 6899999999954 78999999999999986
No 210
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=59.01 E-value=67 Score=23.90 Aligned_cols=62 Identities=16% Similarity=0.360 Sum_probs=43.5
Q ss_pred hhHHhHHHHHHHHHHHHHhcCh--hH-----HHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 30 DNTFSFINSMSLKCVKLIQVGI--PD-----IIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 30 ~l~~~~~~s~aL~~a~~veLgI--~D-----~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
...|+.|.-.|+.+| .+.++ +| +|...+.|+++.+|+..++.+ |...+.--+|-|-.-|+++
T Consensus 62 y~Af~rW~vrCmAaa--g~~~ls~~e~l~lH~irhrdR~K~laDic~~ln~e--Dth~itYslrKL~k~gLit 130 (199)
T COG5631 62 YEAFGRWQVRCMAAA--GEFSLSGPENLLLHIIRHRDRPKSLADICQMLNRE--DTHNITYSLRKLLKGGLIT 130 (199)
T ss_pred HHHHHHHHHHHHHHh--cCCCCcchHHHHHHHHhhcCchhhHHHHHHHhccc--cchhHHHHHHHHHhcccee
Confidence 346777877787777 43322 12 344457899999999999883 4466777788888888775
No 211
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=58.77 E-value=3.2 Score=29.79 Aligned_cols=25 Identities=24% Similarity=0.422 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
.|+|..|+|..+|+|+ +.+.|+.+.
T Consensus 48 ~PLt~~~iA~~lgl~~---STVSRav~~ 72 (160)
T PF04552_consen 48 KPLTMKDIADELGLHE---STVSRAVKN 72 (160)
T ss_dssp ----------------------------
T ss_pred cCCCHHHHHHHhCCCH---hHHHHHHcC
Confidence 7999999999999977 889998763
No 212
>COG3703 ChaC Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]
Probab=58.70 E-value=13 Score=27.77 Aligned_cols=36 Identities=11% Similarity=0.135 Sum_probs=28.0
Q ss_pred CCCCHH----HHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLN----QLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~----ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|+.+.. .||.++|-.+++.+.|.+.+.+|.++|+=+
T Consensus 130 g~l~~~~~A~~ia~a~G~sG~n~eYL~~t~~hL~~~gi~d 169 (190)
T COG3703 130 GDLDAEQIAAIIAAAVGLSGPNAEYLFNTLQHLRKLGIRD 169 (190)
T ss_pred CCCcHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHhcCCcc
Confidence 556654 456667777778899999999999999744
No 213
>PF13551 HTH_29: Winged helix-turn helix
Probab=58.42 E-value=16 Score=22.93 Aligned_cols=27 Identities=19% Similarity=0.208 Sum_probs=24.0
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
|..++|..+|+++ ..++|.++-....|
T Consensus 14 ~~~~ia~~lg~s~---~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISR---RTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCH---HHHHHHHHHHHccc
Confidence 7999999999965 89999999887777
No 214
>PRK03837 transcriptional regulator NanR; Provisional
Probab=58.23 E-value=14 Score=26.76 Aligned_cols=34 Identities=12% Similarity=0.231 Sum_probs=29.6
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ +-.|||+.+|++- ..++--|+.|...|+++
T Consensus 34 G~~Lp~E~~Lae~~gVSR---t~VREAL~~L~~eGlv~ 68 (241)
T PRK03837 34 GDQLPSERELMAFFGVGR---PAVREALQALKRKGLVQ 68 (241)
T ss_pred CCCCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence 4567 8999999999944 78999999999999986
No 215
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=58.18 E-value=13 Score=26.93 Aligned_cols=34 Identities=15% Similarity=0.253 Sum_probs=29.5
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |-.|||+.+|++- ..++.-|+.|...|++.
T Consensus 28 G~~LPsE~eLae~~gVSR---t~VReAL~~L~~eGlv~ 62 (239)
T PRK04984 28 GSILPAERELSELIGVTR---TTLREVLQRLARDGWLT 62 (239)
T ss_pred CCcCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 4567 7899999999944 78999999999999886
No 216
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=58.00 E-value=14 Score=21.43 Aligned_cols=33 Identities=3% Similarity=0.095 Sum_probs=21.7
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
++.|.+.+.. |+ +..+||...|+.. ..++.|+.
T Consensus 12 K~~iI~~~e~--g~-s~~~ia~~fgv~~---sTv~~I~K 44 (53)
T PF04218_consen 12 KLEIIKRLEE--GE-SKRDIAREFGVSR---STVSTILK 44 (53)
T ss_dssp HHHHHHHHHC--TT--HHHHHHHHT--C---CHHHHHHH
T ss_pred HHHHHHHHHc--CC-CHHHHHHHhCCCH---HHHHHHHH
Confidence 3445555543 55 9999999999955 78888875
No 217
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=57.98 E-value=14 Score=26.78 Aligned_cols=33 Identities=15% Similarity=0.227 Sum_probs=26.1
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
.|++|.+|||.+.|+.+ .-+.--|-.+++.|-+
T Consensus 4 ~Ga~T~eELA~~FGvtt---RkvaStLa~~ta~Grl 36 (155)
T PF07789_consen 4 EGAKTAEELAGKFGVTT---RKVASTLAMVTATGRL 36 (155)
T ss_pred cCcccHHHHHHHhCcch---hhhHHHHHHHHhccee
Confidence 48999999999999954 6676777777777754
No 218
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=57.54 E-value=14 Score=27.26 Aligned_cols=34 Identities=21% Similarity=0.198 Sum_probs=29.2
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |-.|||+.+|++. ..++.-|+.|.+.|+++
T Consensus 23 G~~LpsE~eLae~~gVSR---tpVREAL~~Le~~GlV~ 57 (253)
T PRK10421 23 GMKLPAERQLAMQLGVSR---NSLREALAKLVSEGVLL 57 (253)
T ss_pred CCcCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence 3567 6899999999954 78999999999999986
No 219
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=57.32 E-value=8.3 Score=30.54 Aligned_cols=43 Identities=14% Similarity=0.155 Sum_probs=31.4
Q ss_pred hhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 51 IPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 51 I~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|.++|.++| ..+...+|-.+++++. ..|.|+|+.|.+.+++++
T Consensus 89 vy~~I~~ag~~GIw~~~i~~~t~l~~---~~~~k~lk~Le~k~lIK~ 132 (327)
T PF05158_consen 89 VYQLIEEAGNKGIWTKDIKKKTNLHQ---TQLTKILKSLESKKLIKS 132 (327)
T ss_dssp HHHHHHHHTTT-EEHHHHHHHCT--H---HHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHhCCCCCcHHHHHHHcCCCH---HHHHHHHHHHHhCCCEEE
Confidence 445555544 6788889999999955 789999999999998764
No 220
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=57.25 E-value=14 Score=26.80 Aligned_cols=34 Identities=15% Similarity=0.253 Sum_probs=29.6
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |-.+||+.+|++. ..++.-|+.|.+.|+++
T Consensus 27 G~~LpsE~~La~~lgVSR---tpVREAL~~Le~eGlV~ 61 (235)
T TIGR02812 27 GSILPAERELSELIGVTR---TTLREVLQRLARDGWLT 61 (235)
T ss_pred CCcCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence 4568 7999999999954 77999999999999986
No 221
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=57.22 E-value=20 Score=23.64 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=35.1
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
++.|--+|... +|=.+.-+|..++++ .+-+.++++-|..+|++++
T Consensus 9 ~~~IL~hl~~~-~~Dy~k~ia~~l~~~---~~~v~~~l~~Le~~GLler 53 (92)
T PF10007_consen 9 DLKILQHLKKA-GPDYAKSIARRLKIP---LEEVREALEKLEEMGLLER 53 (92)
T ss_pred HHHHHHHHHHH-CCCcHHHHHHHHCCC---HHHHHHHHHHHHHCCCeEE
Confidence 34455556543 688888899999994 4889999999999999864
No 222
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=56.94 E-value=14 Score=27.03 Aligned_cols=34 Identities=15% Similarity=0.153 Sum_probs=29.8
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |-.|||+.+|++. ..++--|+.|...|+++
T Consensus 28 G~~LPsE~eLa~~~gVSR---tpVREAL~~L~~eGlV~ 62 (251)
T PRK09990 28 GQALPSERRLCEKLGFSR---SALREGLTVLRGRGIIE 62 (251)
T ss_pred CCcCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 4678 7899999999954 77999999999999885
No 223
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=56.86 E-value=10 Score=25.69 Aligned_cols=32 Identities=13% Similarity=0.076 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
++.+|.+|+++..+.+ +..+..+...|...|+
T Consensus 45 gk~Lt~~e~~~~~~p~---~~~v~~V~~wL~~~G~ 76 (143)
T PF09286_consen 45 GKYLTPEEFAALFAPS---PEDVAAVKSWLKSHGL 76 (143)
T ss_dssp T----HHHHHHHHS-----HHHHHHHHHHHHHCT-
T ss_pred ccCCCHHHHHHHHCCC---HHHHHHHHHHHHHcCC
Confidence 4679999999999874 4789999999999996
No 224
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=56.68 E-value=18 Score=25.77 Aligned_cols=31 Identities=13% Similarity=0.124 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHhcChhHHHhhCC-CCCCHHHHHHHhCCC
Q 041844 37 NSMSLKCVKLIQVGIPDIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 37 ~s~aL~~a~~veLgI~D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
....+.+| .+.+.+.| ...|+++||++.|+.
T Consensus 20 r~~IL~AA-------~~lf~e~Gy~~~s~~dIA~~aGvs 51 (212)
T PRK15008 20 KKAILSAA-------LDTFSQFGFHGTRLEQIAELAGVS 51 (212)
T ss_pred HHHHHHHH-------HHHHHHhCcccCCHHHHHHHhCcC
Confidence 45566677 45566666 678999999999984
No 225
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=56.20 E-value=11 Score=22.10 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+|+.|+|..+|+++ +.+|+....|++.
T Consensus 1 yti~eva~~~gvs~-------~tlr~y~~~gll~ 27 (69)
T PF13411_consen 1 YTIKEVAKLLGVSP-------STLRYYEREGLLP 27 (69)
T ss_dssp EEHHHHHHHTTTTH-------HHHHHHHHTTSST
T ss_pred CcHHHHHHHHCcCH-------HHHHHHHHhcCcc
Confidence 36889999999954 3677777777664
No 226
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=56.13 E-value=15 Score=26.93 Aligned_cols=34 Identities=12% Similarity=0.163 Sum_probs=29.4
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |-.|||+.+|++. ..++--|+.|.+.|+++
T Consensus 31 G~~LpsE~eLa~~lgVSR---tpVREAL~~L~~eGlv~ 65 (254)
T PRK09464 31 GEKLPPERELAKQFDVSR---PSLREAIQRLEAKGLLL 65 (254)
T ss_pred CCcCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence 4567 8999999999954 78999999999999986
No 227
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=56.00 E-value=12 Score=31.06 Aligned_cols=33 Identities=24% Similarity=0.416 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+|++|||+.+.|.+ ...+++|+.|...|.++
T Consensus 22 ~~~~l~~la~~l~cs~---R~~~~~l~~~~~~gwl~ 54 (552)
T PRK13626 22 QETTLNELAELLNCSR---RHMRTLLNTMQQRGWLT 54 (552)
T ss_pred ceeeHHHHHHHhcCCh---hHHHHHHHHHHHCCCee
Confidence 5789999999999965 89999999999998764
No 228
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=55.96 E-value=13 Score=20.69 Aligned_cols=24 Identities=4% Similarity=0.036 Sum_probs=20.1
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
..|..++|..+|+++ ..+.|++..
T Consensus 27 ~~s~~~vA~~~~vs~---~TV~ri~~~ 50 (52)
T PF13542_consen 27 SRSFKDVARELGVSW---STVRRIFDR 50 (52)
T ss_pred cCCHHHHHHHHCCCH---HHHHHHHHh
Confidence 379999999999955 888888864
No 229
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=55.65 E-value=20 Score=24.91 Aligned_cols=49 Identities=16% Similarity=0.330 Sum_probs=36.7
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCC-CcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPT-KTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~-~~~~L~RlLR~Laa~gif~e 96 (97)
.|-.|-++|-.. ||.|+.||-+.++.+.. ....+.-+|+-|+-.|+++.
T Consensus 7 aE~eVM~ilW~~-~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~ 56 (123)
T COG3682 7 AEWEVMEILWSR-GPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTR 56 (123)
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhh
Confidence 344556666554 69999999999987532 34679999999999998763
No 230
>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=55.51 E-value=9.4 Score=22.47 Aligned_cols=38 Identities=24% Similarity=0.302 Sum_probs=26.6
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHH
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSL 88 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~L 88 (97)
-++.|.+.|-. .+.+|+.|||..+|+.. ..+.+-+-.|
T Consensus 6 rq~~Ll~~L~~-~~~~~~~ela~~l~~S~---rti~~~i~~L 43 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLKELAKKLNISE---RTIKNDINEL 43 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHHHHHHHCTS-H---HHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHHHHHHHHCCCH---HHHHHHHHHH
Confidence 35567777766 58999999999999943 5555554444
No 231
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=55.34 E-value=14 Score=25.01 Aligned_cols=32 Identities=13% Similarity=0.053 Sum_probs=25.6
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa 90 (97)
.|+-+|-.|||...|... .+..+.|+|++|..
T Consensus 20 ~GkV~TYGdIA~laG~p~-~ARqVG~il~~l~~ 51 (103)
T COG3695 20 EGKVSTYGDIAKLAGLPR-AARQVGRILKHLPE 51 (103)
T ss_pred CCceeeHHHHHHHhCCCh-hHHHHHHHHhhCCC
Confidence 357899999999999853 45889999997753
No 232
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=55.07 E-value=13 Score=28.10 Aligned_cols=40 Identities=13% Similarity=0.156 Sum_probs=29.5
Q ss_pred ChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 50 GIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 50 gI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
++++.|+..+ .-.|..|||+++|++| ..++|=+-++-..|
T Consensus 20 R~le~l~a~~v~rvsS~els~~~~vds---atIRrDfSYFG~lG 60 (211)
T COG2344 20 RVLERLHASGVERVSSKELSEALGVDS---ATIRRDFSYFGELG 60 (211)
T ss_pred HHHHHHHHcCCceecHHHHHHHhCCCH---HHHhhhhHHHHhcC
Confidence 4566676656 5689999999999955 88888666655444
No 233
>COG4671 Predicted glycosyl transferase [General function prediction only]
Probab=54.54 E-value=19 Score=29.67 Aligned_cols=36 Identities=19% Similarity=0.336 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCC
Q 041844 38 SMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHP 75 (97)
Q Consensus 38 s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~ 75 (97)
-+.+|+.++-+||++|.|.. ..+|.+-||+++...+
T Consensus 328 EQliRA~Rl~~LGL~dvL~p--e~lt~~~La~al~~~l 363 (400)
T COG4671 328 EQLIRAQRLEELGLVDVLLP--ENLTPQNLADALKAAL 363 (400)
T ss_pred HHHHHHHHHHhcCcceeeCc--ccCChHHHHHHHHhcc
Confidence 45677878899999999966 7888999999987643
No 234
>PRK09480 slmA division inhibitor protein; Provisional
Probab=54.45 E-value=23 Score=24.18 Aligned_cols=16 Identities=13% Similarity=0.221 Sum_probs=13.8
Q ss_pred CCCCCHHHHHHHhCCC
Q 041844 59 TKPMTLNQLLGALQIH 74 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~ 74 (97)
|...|+.+||++.|+.
T Consensus 28 G~~~ti~~Ia~~agvs 43 (194)
T PRK09480 28 GERITTAKLAARVGVS 43 (194)
T ss_pred CCccCHHHHHHHhCCC
Confidence 4788999999999984
No 235
>PRK13502 transcriptional activator RhaR; Provisional
Probab=54.43 E-value=16 Score=26.94 Aligned_cols=37 Identities=16% Similarity=0.153 Sum_probs=27.9
Q ss_pred ChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 50 GIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 50 gI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
.+.+.|.++ ..+.++++||+.+|++| ..|.|+.|--+
T Consensus 180 ~~~~~I~~~~~~~~~~~~lA~~~~iS~---~~L~r~fk~~~ 217 (282)
T PRK13502 180 KLITALANSLECPFALDAFCQQEQCSE---RVLRQQFRAQT 217 (282)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCcCH---HHHHHHHHHHH
Confidence 344555544 26899999999999966 89999988544
No 236
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=54.36 E-value=24 Score=25.56 Aligned_cols=43 Identities=9% Similarity=0.068 Sum_probs=33.7
Q ss_pred HhcChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 47 IQVGIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 47 veLgI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
....|.+.|.+.+ ..+|..|||+..|++| ..++|=|+.|...|
T Consensus 17 ~~~~il~~l~~~~~~~vs~~~L~~~~~v~~---~tirrDl~~l~~~G 60 (213)
T PRK05472 17 LYYRYLKELKEEGVERVSSKELAEALGVDS---AQIRKDLSYFGEFG 60 (213)
T ss_pred HHHHHHHHHHHcCCcEEeHHHHHHHhCcCH---HHHHHHHHHHHhcC
Confidence 5556677776643 3899999999999965 78899888887666
No 237
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=53.95 E-value=14 Score=29.25 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.++|=+|||+++|+.. ..+.|++......|+++
T Consensus 25 ~gltQ~eIA~~LgiSR---~~v~rlL~~Ar~~GiV~ 57 (321)
T COG2390 25 EGLTQSEIAERLGISR---ATVSRLLAKAREEGIVK 57 (321)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCeEE
Confidence 6899999999999954 78999999999999875
No 238
>PRK00767 transcriptional regulator BetI; Validated
Probab=53.79 E-value=22 Score=24.35 Aligned_cols=23 Identities=13% Similarity=0.030 Sum_probs=17.7
Q ss_pred hHHHhhCC-CCCCHHHHHHHhCCC
Q 041844 52 PDIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 52 ~D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
.+++.+.| ...|+++||+++|+.
T Consensus 19 ~~lf~~~G~~~~s~~~Ia~~aGvs 42 (197)
T PRK00767 19 LRAIGEVGLLDATIAQIARRAGVS 42 (197)
T ss_pred HHHHHHcCcccCCHHHHHHHhCCC
Confidence 34566666 778999999999984
No 239
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=53.76 E-value=14 Score=26.15 Aligned_cols=26 Identities=12% Similarity=0.184 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSL 88 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~L 88 (97)
+..|..|||+.+|+++ ..++|-++..
T Consensus 150 ~Gls~~EIA~~lgiS~---~tV~r~l~~a 175 (185)
T PF07638_consen 150 EGLSVEEIAERLGISE---RTVRRRLRRA 175 (185)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 5689999999999965 8888887754
No 240
>PF13814 Replic_Relax: Replication-relaxation
Probab=53.35 E-value=21 Score=24.76 Aligned_cols=36 Identities=17% Similarity=0.136 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.+|.+||+.....+...+...+|.|+-|...|++.
T Consensus 8 r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~ 43 (191)
T PF13814_consen 8 RFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVD 43 (191)
T ss_pred cCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEE
Confidence 689999999998875522347999999999999875
No 241
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=53.11 E-value=20 Score=27.98 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=32.5
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
.|..+|..+.. +|+.+||+.++++. ..++|=++.|...|+
T Consensus 12 ~ii~~L~~~~~-vta~~lA~~~~VS~---RTi~RDi~~L~~~gv 51 (311)
T COG2378 12 QIIQILRAKET-VTAAELADEFEVSV---RTIYRDIATLRAAGV 51 (311)
T ss_pred HHHHHHHhCcc-chHHHHHHhcCCCH---HHHHHHHHHHHHCCC
Confidence 45556665545 99999999999954 899999999998885
No 242
>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=53.06 E-value=26 Score=21.99 Aligned_cols=34 Identities=24% Similarity=0.332 Sum_probs=26.0
Q ss_pred hHHHhhCC-CCCCHHHHHHHhC-CCCCCcccHHHHHHH
Q 041844 52 PDIIHNHT-KPMTLNQLLGALQ-IHPTKTRCLHFLVCS 87 (97)
Q Consensus 52 ~D~La~~~-gp~s~~ELA~~~g-~~~~~~~~L~RlLR~ 87 (97)
.|.|...+ .|+|++||.+.++ .+. . ..+.++|+.
T Consensus 15 V~ymK~r~~~Plt~~EIl~~ls~~d~-~-~~~~~~L~~ 50 (75)
T cd07977 15 VDYMKKRHQHPLTLDEILDYLSLLDI-G-PKLKEWLKS 50 (75)
T ss_pred HHHHHhcCCCCccHHHHHHHHhccCc-c-HHHHHHHHh
Confidence 38888888 9999999999999 654 1 455666663
No 243
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=53.04 E-value=12 Score=28.26 Aligned_cols=29 Identities=14% Similarity=0.419 Sum_probs=23.4
Q ss_pred HhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 55 IHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 55 La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
|+... ...|+..||+..++.| +.++|||+
T Consensus 22 L~~~~p~~~t~~~Lae~F~vsp---e~irrILk 51 (225)
T PF06413_consen 22 LHKEDPEEWTVERLAESFKVSP---EAIRRILK 51 (225)
T ss_pred HHHhCccccCHHHHHhhCCCCH---HHHHHHHh
Confidence 44433 4579999999999965 99999998
No 244
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=52.44 E-value=30 Score=26.82 Aligned_cols=45 Identities=11% Similarity=0.143 Sum_probs=36.0
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccccC
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR 97 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e~ 97 (97)
-||+-|....|-+.++-||.++|+-. +.+---||-|.+.|+++.|
T Consensus 193 ~I~eELdG~EG~lvASkiADrvGITR---SVIVNALRKlESAGvIeSR 237 (261)
T COG4465 193 HIFEELDGNEGLLVASKIADRVGITR---SVIVNALRKLESAGVIESR 237 (261)
T ss_pred HHHHhcCCccceeeehhhhhhhCchH---HHHHHHHHHhhhcCceeec
Confidence 35666644458899999999999943 6788899999999998754
No 245
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=52.13 E-value=23 Score=24.53 Aligned_cols=22 Identities=14% Similarity=0.232 Sum_probs=16.2
Q ss_pred HHHhhCC-CCCCHHHHHHHhCCC
Q 041844 53 DIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 53 D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
+.+.++| ...|+++||++.|+.
T Consensus 19 ~lf~e~G~~~tSi~~Ia~~aGvs 41 (192)
T PRK14996 19 RVALAEGFAAMTVRRIASEAQVA 41 (192)
T ss_pred HHHHhcChhhccHHHHHHHhCCC
Confidence 3445555 668999999999974
No 246
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=51.77 E-value=20 Score=26.39 Aligned_cols=36 Identities=14% Similarity=0.134 Sum_probs=27.7
Q ss_pred HHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844 53 DIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS 91 (97)
Q Consensus 53 D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~ 91 (97)
+.|.++ ..++|++++|+.+++++ ..|.|+.|-.+.+
T Consensus 193 ~~I~~~~~~~~sl~~lA~~~~~S~---~~l~r~Fk~~~G~ 229 (287)
T TIGR02297 193 FLIEENYKQHLRLPEYADRLGISE---SRLNDICRRFSAL 229 (287)
T ss_pred HHHHHhhccCCCHHHHHHHHCCCH---HHHHHHHHHHhCC
Confidence 345444 37899999999999965 8999999876544
No 247
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=51.66 E-value=49 Score=23.68 Aligned_cols=51 Identities=10% Similarity=0.037 Sum_probs=36.7
Q ss_pred HhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHh--CCCCCCcccHHHHHHHHHhcCcccc
Q 041844 33 FSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL--QIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 33 ~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~--g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+..|...+++.. +++. ++.-+..+||.++ ++.. +-++.-|..|...|+++.
T Consensus 21 ~~~W~~~~ir~l--~~l~--------~~~~d~~~iak~l~p~is~---~ev~~sL~~L~~~gli~k 73 (171)
T PF14394_consen 21 YSSWYHPAIREL--LPLM--------PFAPDPEWIAKRLRPKISA---EEVRDSLEFLEKLGLIKK 73 (171)
T ss_pred HhhhHHHHHHHH--hhcC--------CCCCCHHHHHHHhcCCCCH---HHHHHHHHHHHHCCCeEE
Confidence 344555566666 4432 2344899999999 7744 789999999999998864
No 248
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=51.30 E-value=26 Score=21.89 Aligned_cols=35 Identities=20% Similarity=0.169 Sum_probs=26.7
Q ss_pred CCCCCCHHHHHHHhC-CCCCCcccHHHHHHHHHhcCccc
Q 041844 58 HTKPMTLNQLLGALQ-IHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g-~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.++.+|.++--+.+. . |...+.|+-.+|...|+++
T Consensus 50 ~~~~lt~~~~~~~i~~~---d~~~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 50 PNKYLTKTDARKLIKGI---DVNKIRRIYDFLERWGLIN 85 (86)
T ss_dssp TTS---HHHHHHHTTSS---SHHHHHHHHHHHHHTTSSS
T ss_pred CCCcccHHHHHHHcccc---CHHHHHHHHHHHHHcCccC
Confidence 358899999877777 4 6699999999999999874
No 249
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. 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 sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=51.11 E-value=12 Score=30.71 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|+|..|+|+.+|+|+ +.+.|+.+
T Consensus 317 kPLtlkdiA~~lglhe---STVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHE---STISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCc---cchhhhhc
Confidence 7999999999999987 88999865
No 250
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=51.06 E-value=19 Score=27.88 Aligned_cols=34 Identities=18% Similarity=0.180 Sum_probs=26.2
Q ss_pred hhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 51 IPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 51 I~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
|.+.|..+- .+.|+++||+.+|.++ ..+.|.++.
T Consensus 186 i~~~I~~~~~~~~sl~~lA~~~gmS~---stl~R~Fk~ 220 (291)
T PRK15186 186 IYNIIISDISRKWALKDISDSLYMSC---STLKRKLKQ 220 (291)
T ss_pred HHHHHHhCccCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 345555443 7899999999999954 889998885
No 251
>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=50.81 E-value=17 Score=21.80 Aligned_cols=30 Identities=13% Similarity=0.012 Sum_probs=21.5
Q ss_pred hCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 57 NHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 57 ~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
+.|.+-|..|||+.+|+++ .-++.+|+...
T Consensus 16 ~lgr~Pt~eEiA~~lgis~---~~v~~~l~~~~ 45 (78)
T PF04539_consen 16 ELGREPTDEEIAEELGISV---EEVRELLQASR 45 (78)
T ss_dssp HHSS--BHHHHHHHHTS-H---HHHHHHHHHHS
T ss_pred HhCCCCCHHHHHHHHcccH---HHHHHHHHhCC
Confidence 3457889999999999944 78888888543
No 252
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=50.63 E-value=22 Score=24.97 Aligned_cols=32 Identities=6% Similarity=0.239 Sum_probs=22.9
Q ss_pred hHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 52 PDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 52 ~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
-+.|.++. ...|+.|+++.||+++ ..+.+++|
T Consensus 36 ~~yLr~~p~~~ati~eV~e~tgVs~---~~I~~~Ir 68 (137)
T TIGR03826 36 YKFLRKHENRQATVSEIVEETGVSE---KLILKFIR 68 (137)
T ss_pred HHHHHHCCCCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 34555554 3589999999999944 66766665
No 253
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=50.56 E-value=49 Score=20.95 Aligned_cols=23 Identities=13% Similarity=0.105 Sum_probs=17.5
Q ss_pred CC-CCCCHHHHHHHhCCCCCCcccHHH
Q 041844 58 HT-KPMTLNQLLGALQIHPTKTRCLHF 83 (97)
Q Consensus 58 ~~-gp~s~~ELA~~~g~~~~~~~~L~R 83 (97)
.| ..+|+.+||+++|+++ ..++|
T Consensus 28 ~G~~~~t~~~Ia~~agvs~---~~~Y~ 51 (201)
T COG1309 28 KGYAATTVDEIAKAAGVSK---GTLYR 51 (201)
T ss_pred cCcCCCCHHHHHHHhCCCc---chhHH
Confidence 44 6789999999999854 55554
No 254
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=50.53 E-value=23 Score=24.16 Aligned_cols=32 Identities=19% Similarity=0.468 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
+|.|+.|||+.++.+- ..++=++--|...|.+
T Consensus 54 ~~~SVAEiAA~L~lPl---gVvrVLvsDL~~~G~v 85 (114)
T PF05331_consen 54 RPLSVAEIAARLGLPL---GVVRVLVSDLADAGLV 85 (114)
T ss_pred CCccHHHHHHhhCCCc---hhhhhhHHHHHhCCCE
Confidence 4777777777777632 3333344444444443
No 255
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=50.36 E-value=18 Score=27.59 Aligned_cols=35 Identities=9% Similarity=0.203 Sum_probs=26.6
Q ss_pred hHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 52 PDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 52 ~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
.+.|.++ ..++|+++||+.+|+++ ..+.|+.+.-+
T Consensus 197 ~~~i~~~~~~~~tl~~lA~~~~~S~---~~l~r~Fk~~~ 232 (302)
T PRK10371 197 LGFIAENYDQALTINDVAEHVKLNA---NYAMGIFQRVM 232 (302)
T ss_pred HHHHHHhhcCCCCHHHHHHHHCcCH---HHHHHHHHHHh
Confidence 3445443 36899999999999955 88999888654
No 256
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=50.25 E-value=18 Score=27.72 Aligned_cols=34 Identities=18% Similarity=0.285 Sum_probs=26.0
Q ss_pred hhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 51 IPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 51 I~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
+.+.++.+ .+++|+++||+.+|.++ ..+.|..+.
T Consensus 139 v~~~I~~~~~~~~tl~~LA~~~gmS~---s~l~R~FK~ 173 (253)
T PRK09940 139 VRNIVNMKLAHPWKLKDICDCLYISE---SLLKKKLKQ 173 (253)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 33455443 37899999999999965 889998875
No 257
>PHA00542 putative Cro-like protein
Probab=50.24 E-value=20 Score=22.52 Aligned_cols=23 Identities=9% Similarity=0.082 Sum_probs=15.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLV 85 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlL 85 (97)
..+|..|||+.+|+.+ ..+.|+.
T Consensus 30 ~glTq~elA~~lgIs~---~tIsr~e 52 (82)
T PHA00542 30 AGWSQEQIADATDVSQ---PTICRIY 52 (82)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHH
Confidence 4688888888888743 4555544
No 258
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=50.18 E-value=22 Score=26.19 Aligned_cols=34 Identities=6% Similarity=0.101 Sum_probs=29.2
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |-.|||+.+|++. ..++--|+.|...|+++
T Consensus 29 G~~LpsE~eLae~~gVSR---tpVREAL~~L~~eGlV~ 63 (253)
T PRK11523 29 GDKLPAERFIADEKNVSR---TVVREAIIMLEVEGYVE 63 (253)
T ss_pred CCCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 4677 5789999999954 77999999999999985
No 259
>PRK15340 transcriptional regulator InvF; Provisional
Probab=50.06 E-value=20 Score=27.00 Aligned_cols=40 Identities=10% Similarity=-0.001 Sum_probs=29.7
Q ss_pred ChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 50 GIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 50 gI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
+|...|..+ ..+.|++|||+.+|+++ ..+.|+.|.-+.++
T Consensus 113 ~l~~~Ll~~~~~~~sleeLA~~~gvS~---r~f~RlFk~~~G~t 153 (216)
T PRK15340 113 WLVGYLLAQSTSGNTMRMLGEDYGVSY---THFRRLCSRALGGK 153 (216)
T ss_pred HHHHHHHhCccCCCCHHHHHHHHCcCH---HHHHHHHHHHHCcC
Confidence 444444333 37899999999999955 89999998766554
No 260
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=49.97 E-value=12 Score=22.56 Aligned_cols=16 Identities=6% Similarity=0.227 Sum_probs=10.5
Q ss_pred cccHHHHHHHHHhcCc
Q 041844 78 TRCLHFLVCSLVRSGF 93 (97)
Q Consensus 78 ~~~L~RlLR~Laa~gi 93 (97)
++.-.|+.+.+..+|+
T Consensus 29 ~~t~~~i~~~~~~~gy 44 (70)
T smart00354 29 EETREKVLAAMEELGY 44 (70)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 3556677777777665
No 261
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=49.27 E-value=34 Score=27.07 Aligned_cols=32 Identities=16% Similarity=0.133 Sum_probs=24.7
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.++.+|+.+|+..+|+.+ .-|+..|..+|++.
T Consensus 220 ~~~~isi~~is~~T~i~~------~Dii~tL~~l~~l~ 251 (290)
T PLN03238 220 VKGDVSIKDLSLATGIRG------EDIVSTLQSLNLIK 251 (290)
T ss_pred cCCCccHHHHHHHhCCCH------HHHHHHHHHCCcEE
Confidence 347899999999999954 23777777887664
No 262
>PRK13501 transcriptional activator RhaR; Provisional
Probab=48.85 E-value=19 Score=26.77 Aligned_cols=36 Identities=11% Similarity=0.069 Sum_probs=27.3
Q ss_pred hHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844 52 PDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 52 ~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa 90 (97)
.+.|.++ ..++|++|+|+++++++ ..|.|+.+--+.
T Consensus 182 ~~~I~~~~~e~~sl~~lA~~~~lS~---~~l~r~Fk~~~G 218 (290)
T PRK13501 182 MSALQQSLGAYFDMADFCHKNQLVE---RSLKQLFRQQTG 218 (290)
T ss_pred HHHHHHhhccCCCHHHHHHHHCcCH---HHHHHHHHHHHC
Confidence 4445443 36899999999999965 899999986543
No 263
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=48.62 E-value=20 Score=23.89 Aligned_cols=25 Identities=20% Similarity=0.239 Sum_probs=19.4
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
...+|+.|||+.+|+++ ..+.|.|.
T Consensus 69 ~pd~tl~Ela~~l~Vs~---~ti~~~Lk 93 (119)
T PF01710_consen 69 NPDATLRELAERLGVSP---STIWRALK 93 (119)
T ss_pred CCCcCHHHHHHHcCCCH---HHHHHHHH
Confidence 35799999999999954 66666655
No 264
>PRK15185 transcriptional regulator HilD; Provisional
Probab=48.60 E-value=22 Score=28.24 Aligned_cols=35 Identities=11% Similarity=0.196 Sum_probs=27.4
Q ss_pred ChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 50 GIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 50 gI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
.+.+.|..+- .+.|++++|+.++.++ ..|.|.++.
T Consensus 210 rV~~~I~~n~~~~~SledLA~~lgmS~---~tL~R~FK~ 245 (309)
T PRK15185 210 RVYNIISSSPSRQWKLTDVADHIFMST---STLKRKLAE 245 (309)
T ss_pred HHHHHHHhCccCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 3556666554 7899999999999965 889888874
No 265
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=48.47 E-value=34 Score=28.61 Aligned_cols=33 Identities=15% Similarity=0.273 Sum_probs=25.9
Q ss_pred hCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 57 NHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 57 ~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
++.+.+|+.+|+..+++.+ .-|+..|..+|++.
T Consensus 370 ~~~~~~si~~is~~T~i~~------~Dii~tL~~l~~l~ 402 (450)
T PLN00104 370 KHKGNISIKELSDMTAIKA------EDIVSTLQSLNLIQ 402 (450)
T ss_pred hcCCCccHHHHHHHhCCCH------HHHHHHHHHCCCEE
Confidence 4457899999999999943 34788888888764
No 266
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=48.03 E-value=22 Score=27.54 Aligned_cols=34 Identities=21% Similarity=0.318 Sum_probs=26.4
Q ss_pred hhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 51 IPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 51 I~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
+.+.|.++ ..++|+++||+.+|+++ ..|.|+.+.
T Consensus 147 v~~yI~~~~~~~lsl~~lA~~~g~S~---~~L~R~Fk~ 181 (274)
T PRK09978 147 VCTVINNNIAHEWTLARIASELLMSP---SLLKKKLRE 181 (274)
T ss_pred HHHHHHhcccCCCCHHHHHHHHCcCH---HHHHHHHHh
Confidence 44555554 37899999999999965 889998874
No 267
>PRK10736 hypothetical protein; Provisional
Probab=47.62 E-value=22 Score=28.87 Aligned_cols=42 Identities=5% Similarity=-0.035 Sum_probs=32.0
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|.+.+. ..|++++||+.++|.++ ..+..+|-.|.-.|++.+
T Consensus 312 ~v~~~l~--~~~~~iD~L~~~~~l~~---~~v~~~L~~LEl~G~v~~ 353 (374)
T PRK10736 312 ELLANVG--DEVTPVDVVAERAGQPV---PEVVTQLLELELAGWIAA 353 (374)
T ss_pred HHHHhcC--CCCCCHHHHHHHHCcCH---HHHHHHHHHHHhCCcEEE
Confidence 3444442 27899999999999954 778888888888887753
No 268
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=47.43 E-value=15 Score=20.20 Aligned_cols=15 Identities=13% Similarity=0.042 Sum_probs=11.4
Q ss_pred CCCCHHHHHHHhCCC
Q 041844 60 KPMTLNQLLGALQIH 74 (97)
Q Consensus 60 gp~s~~ELA~~~g~~ 74 (97)
..+|..|+|..+|++
T Consensus 14 ~gltq~~lA~~~gvs 28 (58)
T TIGR03070 14 LGLTQADLADLAGVG 28 (58)
T ss_pred cCCCHHHHHHHhCCC
Confidence 467788888888874
No 269
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=46.99 E-value=26 Score=18.76 Aligned_cols=24 Identities=13% Similarity=0.187 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
..+|..|||..+|+++ ..+++.++
T Consensus 17 ~g~s~~eia~~l~is~---~tv~~~~~ 40 (58)
T smart00421 17 EGLTNKEIAERLGISE---KTVKTHLS 40 (58)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 3579999999999954 55555444
No 270
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=46.86 E-value=37 Score=24.71 Aligned_cols=42 Identities=14% Similarity=0.066 Sum_probs=34.3
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.--.|||.|.+ +-+|..||.+..|- +. .+-+..|-..|++++
T Consensus 18 ~~kkV~~~Ls~--~W~T~~El~e~~G~-----d~-~~~L~~LkK~gLiE~ 59 (160)
T PF09824_consen 18 VYKKVYDELSK--GWMTEEELEEKYGK-----DV-RESLLILKKGGLIES 59 (160)
T ss_pred HHHHHHHHHHh--ccCCHHHHHHHHCc-----CH-HHHHHHHHHcCchhh
Confidence 55577999976 89999999999997 33 778888888888764
No 271
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=46.52 E-value=58 Score=18.94 Aligned_cols=45 Identities=16% Similarity=0.267 Sum_probs=35.1
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+.|...+... .+.++.+|+..++.+. ..+.+-|+.|...|++.
T Consensus 26 ~r~~il~~l~~~-~~~~~~~l~~~~~~~~---~~v~~hL~~L~~~glv~ 70 (110)
T COG0640 26 TRLEILSLLAEG-GELTVGELAEALGLSQ---STVSHHLKVLREAGLVE 70 (110)
T ss_pred HHHHHHHHHHhc-CCccHHHHHHHHCCCh---hHHHHHHHHHHHCCCeE
Confidence 455666667553 5888999999998744 78999999999988875
No 272
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=46.00 E-value=41 Score=24.40 Aligned_cols=30 Identities=3% Similarity=-0.054 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHhcChhHHHhhCC-CCCCHHHHHHHhCCC
Q 041844 37 NSMSLKCVKLIQVGIPDIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 37 ~s~aL~~a~~veLgI~D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
.-..+.+| .+.+++.| . .|+++||++.|++
T Consensus 15 r~~Il~aA-------~~lF~~~Gy~-~s~~~IA~~AGvs 45 (225)
T PRK11552 15 KQQLIAAA-------LAQFGEYGLH-ATTRDIAAQAGQN 45 (225)
T ss_pred HHHHHHHH-------HHHHHHhCcc-CCHHHHHHHhCCC
Confidence 34456666 34556666 7 9999999999984
No 273
>smart00351 PAX Paired Box domain.
Probab=45.83 E-value=33 Score=23.12 Aligned_cols=33 Identities=9% Similarity=0.178 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+..|..+||..+|+++ ..++|+++-....|.+.
T Consensus 32 ~G~s~~~iA~~~gvs~---~tV~kwi~r~~~~G~~~ 64 (125)
T smart00351 32 NGVRPCDISRQLCVSH---GCVSKILGRYYETGSIR 64 (125)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHHHHHHcCCcC
Confidence 4578999999999955 89999998777777654
No 274
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=45.62 E-value=15 Score=31.16 Aligned_cols=42 Identities=14% Similarity=0.139 Sum_probs=30.9
Q ss_pred hcChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 48 QVGIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 48 eLgI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
|-.|+|.|-++. .-+|+.|||+++++++ ..+.|+.|-|--.|
T Consensus 358 E~~IA~yIl~n~~~v~~~si~eLA~~~~vS~---aTV~Rf~kkLGf~G 402 (638)
T PRK14101 358 ERRVADLALNHPRSIINDPIVDIARKADVSQ---PTVIRFCRSLGCQG 402 (638)
T ss_pred HHHHHHHHHhCHHHHHhccHHHHHHHhCCCH---HHHHHHHHHhCCCC
Confidence 345566665543 4689999999999965 78888888776555
No 275
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=45.54 E-value=25 Score=26.12 Aligned_cols=34 Identities=21% Similarity=0.289 Sum_probs=24.6
Q ss_pred hhHHHhhC-CCC-CCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 51 IPDIIHNH-TKP-MTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 51 I~D~La~~-~gp-~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
+-+.|.++ ..| +|+++||+++|+++ ..|.|+.+-
T Consensus 202 ~~~~I~~~l~~~~ls~~~lA~~~giS~---r~L~r~Fk~ 237 (302)
T PRK09685 202 VVALIDQSIQEEILRPEWIAGELGISV---RSLYRLFAE 237 (302)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence 33445444 245 99999999999955 788888763
No 276
>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=45.48 E-value=26 Score=21.62 Aligned_cols=38 Identities=11% Similarity=0.169 Sum_probs=25.9
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS 91 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~ 91 (97)
.|.+.|.. .+++|++||+..++.+. .-+..-+--|+.-
T Consensus 12 ~Vw~~L~~-~~~~s~~el~k~~~l~~---~~~~~AiGWLarE 49 (65)
T PF10771_consen 12 KVWQLLNE-NGEWSVSELKKATGLSD---KEVYLAIGWLARE 49 (65)
T ss_dssp HHHHHHCC-SSSEEHHHHHHHCT-SC---HHHHHHHHHHHCT
T ss_pred HHHHHHhh-CCCcCHHHHHHHhCcCH---HHHHHHHHHHhcc
Confidence 46777865 48999999999999943 4555555555443
No 277
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=45.45 E-value=16 Score=30.18 Aligned_cols=24 Identities=21% Similarity=0.391 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|+|..|+|+.+|+|+ +.+.|..+
T Consensus 342 kPLtlkdvAe~lglhe---STVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGMHE---STISRATT 365 (455)
T ss_pred cCccHHHHHHHhCCCc---cchhhhhc
Confidence 7999999999999987 88988865
No 278
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=45.32 E-value=31 Score=26.25 Aligned_cols=35 Identities=20% Similarity=0.288 Sum_probs=26.8
Q ss_pred HHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844 53 DIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 53 D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa 90 (97)
+.|.++ ..++|+++||+.+|+++ ..|.|+.+....
T Consensus 225 ~~i~~~~~~~~sl~~lA~~~~~S~---~~l~r~fk~~~g 260 (322)
T PRK09393 225 DWMRAHLAEPHTVASLAARAAMSP---RTFLRRFEAATG 260 (322)
T ss_pred HHHHhccCCCCCHHHHHHHHCcCH---HHHHHHHHHHHC
Confidence 445444 36899999999999955 889999886553
No 279
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=45.16 E-value=20 Score=28.60 Aligned_cols=27 Identities=22% Similarity=0.335 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
.|+|+.|||..+++.+ ..|.|+.|.-.
T Consensus 235 ~plsl~~LA~~~~~S~---R~leRlF~~~l 261 (328)
T COG4977 235 EPLSLEELADRAGLSR---RQLERLFRAEL 261 (328)
T ss_pred CCcCHHHHHHHhCCCH---HHHHHHHHHHh
Confidence 7999999999999955 88988887543
No 280
>PRK15044 transcriptional regulator SirC; Provisional
Probab=45.06 E-value=27 Score=27.62 Aligned_cols=35 Identities=17% Similarity=0.234 Sum_probs=27.2
Q ss_pred ChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 50 GIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 50 gI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
.+-+.|..+ +.+.|++|||+.+|.++ ..|.|.++.
T Consensus 196 kV~~~I~~nl~~~~SLeeLA~~lgmS~---~tL~R~Fk~ 231 (295)
T PRK15044 196 KVYNIIISDLTRKWSQAEVAGKLFMSV---SSLKRKLAA 231 (295)
T ss_pred HHHHHHHhCcccCCCHHHHHHHhCCCH---HHHHHHHHH
Confidence 345556554 37999999999999965 889998875
No 281
>PRK13500 transcriptional activator RhaR; Provisional
Probab=43.91 E-value=28 Score=26.51 Aligned_cols=37 Identities=11% Similarity=0.141 Sum_probs=28.5
Q ss_pred hhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844 51 IPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 51 I~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa 90 (97)
+.+.|.++ ..++|+++||+.+++++ ..|.|+.+--+.
T Consensus 211 i~~yI~~~~~e~isl~~lA~~~~iS~---~~L~r~FK~~tG 248 (312)
T PRK13500 211 LITRLAASLKSPFALDKFCDEASCSE---RVLRQQFRQQTG 248 (312)
T ss_pred HHHHHHHcccCCCCHHHHHHHHCcCH---HHHHHHHHHHHC
Confidence 44556554 36899999999999965 889999886543
No 282
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=43.81 E-value=33 Score=25.47 Aligned_cols=34 Identities=24% Similarity=0.380 Sum_probs=26.7
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
..|..+..+.++++||.++|.+| ..++|+.+.-.
T Consensus 89 ~~ie~~~~~~~le~la~~lg~sp---~~~~R~FK~~~ 122 (187)
T COG2169 89 RLIEQNPEKRWLEELADELGVSP---STLHRLFKAIT 122 (187)
T ss_pred HHHHcCCCcccHHHHHHHhCCCh---HHHHHHHHHHh
Confidence 34555568899999999999965 89999987543
No 283
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=43.64 E-value=30 Score=21.37 Aligned_cols=32 Identities=19% Similarity=0.284 Sum_probs=23.0
Q ss_pred HHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 64 LNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 64 ~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-.+|++..|++|-....+..+++-|...|+++
T Consensus 25 Y~~lc~~~~~~pls~~r~~~~l~eL~~~gli~ 56 (85)
T PF09079_consen 25 YEELCESLGVDPLSYRRFSDYLSELEMLGLIE 56 (85)
T ss_dssp HHHHHHHTTS----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHHhCCCeE
Confidence 45788888997766677888889999999875
No 284
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=43.53 E-value=17 Score=21.27 Aligned_cols=41 Identities=20% Similarity=0.412 Sum_probs=21.4
Q ss_pred hhHHHhhCCCCCCHHHHHHHhC----CCCCC-cccHHHHHHHHHhcCcc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQ----IHPTK-TRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g----~~~~~-~~~L~RlLR~Laa~gif 94 (97)
|++.+ .|+.|+.||++.+- +++.+ ..-+..++..|...|++
T Consensus 22 Iw~~~---~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 22 IWELL---DGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp HHHH-----SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT--
T ss_pred HHHHc---cCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCc
Confidence 34555 26888888877643 43310 12367777778888875
No 285
>PRK13824 replication initiation protein RepC; Provisional
Probab=43.51 E-value=24 Score=28.83 Aligned_cols=32 Identities=19% Similarity=0.092 Sum_probs=27.6
Q ss_pred CCHHHHHHHh-CCCCCCcccHHHHHHHHHhcCcccc
Q 041844 62 MTLNQLLGAL-QIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 62 ~s~~ELA~~~-g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|-.+|+.++ |..+ ..|+|.++.|+..|++..
T Consensus 83 pSN~~La~r~~Gms~---~tlrRhla~LveaGLI~r 115 (404)
T PRK13824 83 PSNAQLSLRAHGMAG---ATLRRHLAALVEAGLIIR 115 (404)
T ss_pred hhHHHHHHHHcCCCH---HHHHHHHHHHHHCCCeEe
Confidence 4889999985 8855 899999999999998753
No 286
>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=43.14 E-value=28 Score=18.17 Aligned_cols=25 Identities=8% Similarity=0.130 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
..+|..++|+.+|+.. ..++|.++.
T Consensus 25 ~~~~~~~ia~~~~~s~---~~i~~~~~~ 49 (55)
T cd06171 25 EGLSYEEIAEILGISR---STVRQRLHR 49 (55)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 5689999999999954 677766653
No 287
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=42.90 E-value=16 Score=22.12 Aligned_cols=37 Identities=16% Similarity=0.133 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHhCCC-----CCCcccHHHHHHHHHhcCcccc
Q 041844 60 KPMTLNQLLGALQIH-----PTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 60 gp~s~~ELA~~~g~~-----~~~~~~L~RlLR~Laa~gif~e 96 (97)
+|++--||.+.+.-. ..++..|++.|+.|...|+++.
T Consensus 8 ~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~ 49 (75)
T PF03551_consen 8 GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIES 49 (75)
T ss_dssp S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEE
T ss_pred CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEE
Confidence 688888887776531 1256889999999999998864
No 288
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=42.79 E-value=35 Score=20.97 Aligned_cols=31 Identities=10% Similarity=0.173 Sum_probs=25.0
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-+..+...++.+ +++.+.|+.|.|-.+|+.+
T Consensus 17 ~ier~~~~~~~~--~~e~~~~f~~~L~~~Gv~~ 47 (69)
T TIGR03595 17 KIERWVAKTPFN--NDENLRRFARKLKKLGVED 47 (69)
T ss_pred HHHHHHHHcCCC--CHHHHHHHHHHHHHCCHHH
Confidence 467788888874 5589999999999999754
No 289
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=42.42 E-value=36 Score=29.40 Aligned_cols=45 Identities=20% Similarity=0.414 Sum_probs=34.9
Q ss_pred hhHHHhh-CCCCCCHHHHHHHhCCCC-CCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHN-HTKPMTLNQLLGALQIHP-TKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~-~~gp~s~~ELA~~~g~~~-~~~~~L~RlLR~Laa~gif~ 95 (97)
|.+.|.. .+.|++..||+..++.+. .+...|.++|+.|...|.+.
T Consensus 7 il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~ 53 (709)
T TIGR02063 7 ILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVK 53 (709)
T ss_pred HHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEE
Confidence 4455544 348999999999999854 24567999999999999764
No 290
>PF02387 IncFII_repA: IncFII RepA protein family; InterPro: IPR003446 These proteins are plasmid encoded and essential for plasmid replication, they are also involved in copy control functions [].; GO: 0006276 plasmid maintenance
Probab=42.40 E-value=34 Score=26.75 Aligned_cols=37 Identities=11% Similarity=0.085 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCCCCcc---cHHHHHHH----HHhcCcccc
Q 041844 60 KPMTLNQLLGALQIHPTKTR---CLHFLVCS----LVRSGFFNL 96 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~---~L~RlLR~----Laa~gif~e 96 (97)
-.+|+++||..+|..+.+.. .+.|+-|. |..+|++++
T Consensus 94 V~~sie~LA~ecGLst~s~~Gn~sitRasR~i~e~le~~Gli~~ 137 (281)
T PF02387_consen 94 VQASIEQLADECGLSTKSAAGNKSITRASRLISEFLEPLGLITC 137 (281)
T ss_pred eeecHHHHHHHhCCcccCCCCCeeHHHHHHHHHHHHHhcCCeee
Confidence 56899999999997432222 24444444 567898764
No 291
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=42.35 E-value=36 Score=21.18 Aligned_cols=28 Identities=29% Similarity=0.334 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa 90 (97)
.+.++.++|+.+|+++ ..|.|..+....
T Consensus 35 ~~~~l~~la~~~g~S~---~~l~r~f~~~~g 62 (127)
T COG2207 35 EPLTLEDLARRLGMSR---RTLSRLFKKETG 62 (127)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHHHHHC
Confidence 5699999999999965 888888885443
No 292
>PRK00118 putative DNA-binding protein; Validated
Probab=41.79 E-value=25 Score=23.55 Aligned_cols=24 Identities=4% Similarity=0.101 Sum_probs=18.6
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+.+|..|||+.+|+++ ..+++.++
T Consensus 32 eg~S~~EIAe~lGIS~---~TV~r~L~ 55 (104)
T PRK00118 32 DDYSLGEIAEEFNVSR---QAVYDNIK 55 (104)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 6899999999999965 55555543
No 293
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=41.47 E-value=45 Score=20.62 Aligned_cols=28 Identities=11% Similarity=0.003 Sum_probs=19.7
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|.-.|..+||+.+|.+. .+..+.+.|+
T Consensus 14 ~G~v~TYg~iA~~~g~p~-~~R~Vg~al~ 41 (79)
T cd06445 14 YGEVTTYGQIAKLAGTPK-AARAVGSALA 41 (79)
T ss_pred CCCcCcHHHHHHHHCCCC-cHHHHHHHHH
Confidence 467899999999999842 2345555554
No 294
>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=41.29 E-value=28 Score=24.88 Aligned_cols=33 Identities=12% Similarity=0.078 Sum_probs=28.4
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
-.|..+||+.+|+.. +.+.|.+..|...+++..
T Consensus 75 ~~t~~~ia~~l~iS~---~Tv~r~ik~L~e~~iI~k 107 (165)
T PF05732_consen 75 VATQKEIAEKLGISK---PTVSRAIKELEEKNIIKK 107 (165)
T ss_pred EeeHHHHHHHhCCCH---HHHHHHHHHHHhCCcEEE
Confidence 368999999999954 789999999999998753
No 295
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=40.84 E-value=17 Score=21.20 Aligned_cols=23 Identities=13% Similarity=0.143 Sum_probs=14.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLV 85 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlL 85 (97)
..+|..|+|..+|+++ ..+.|+.
T Consensus 13 ~gls~~~lA~~~g~s~---s~v~~iE 35 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQ---STVSRIE 35 (64)
T ss_dssp HTS-HHHHHHHHTS-H---HHHHHHH
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHH
Confidence 3588999999999743 4555544
No 296
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=40.77 E-value=43 Score=22.64 Aligned_cols=33 Identities=18% Similarity=0.316 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-++|-.+||..+|... ..+.|++..|...|++.
T Consensus 170 ~~~~~~~ia~~~g~~~---~~vsr~l~~l~~~g~i~ 202 (214)
T COG0664 170 LPLTHKDLAEYLGLSR---ETVSRILKELRKDGLIS 202 (214)
T ss_pred ccCCHHHHHHHhCCch---hhHHHHHHHHHhCCcEe
Confidence 3799999999999854 88999999999999875
No 297
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=40.71 E-value=37 Score=19.83 Aligned_cols=14 Identities=14% Similarity=0.449 Sum_probs=11.1
Q ss_pred CCHHHHHHHhCCCC
Q 041844 62 MTLNQLLGALQIHP 75 (97)
Q Consensus 62 ~s~~ELA~~~g~~~ 75 (97)
.|+.|+|+.+|+++
T Consensus 1 ~~i~evA~~~gvs~ 14 (67)
T cd04764 1 YTIKEVSEIIGVKP 14 (67)
T ss_pred CCHHHHHHHHCcCH
Confidence 36789999999855
No 298
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=40.69 E-value=34 Score=24.27 Aligned_cols=39 Identities=13% Similarity=0.198 Sum_probs=29.0
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
.-+|.+.+..|-++..|+|..+++-+ ..|.+.|| .+|++
T Consensus 36 ~f~D~v~~~~gli~~re~AK~lkige---~~l~~~L~---e~~~l 74 (135)
T COG3645 36 EFADAVVEASGLILFRELAKLLKIGE---NRLFAWLR---ENKYL 74 (135)
T ss_pred HHHHHHhcCccceeHHHHHHHHccCH---HHHHHHHH---HCCEE
Confidence 44688877778999999999999843 55666666 55543
No 299
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=40.34 E-value=34 Score=25.44 Aligned_cols=32 Identities=9% Similarity=0.133 Sum_probs=27.6
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
=|=.||++.+|+.- ..|+--|+.|.+.|+++-
T Consensus 35 P~EreLae~fgVSR---~~vREAl~~L~a~Glve~ 66 (241)
T COG2186 35 PSERELAERFGVSR---TVVREALKRLEAKGLVEI 66 (241)
T ss_pred CCHHHHHHHHCCCc---HHHHHHHHHHHHCCCeee
Confidence 35789999999954 789999999999999864
No 300
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=40.32 E-value=38 Score=23.94 Aligned_cols=21 Identities=14% Similarity=0.309 Sum_probs=16.3
Q ss_pred HhhCC-CCCCHHHHHHHhCCCC
Q 041844 55 IHNHT-KPMTLNQLLGALQIHP 75 (97)
Q Consensus 55 La~~~-gp~s~~ELA~~~g~~~ 75 (97)
+.+.| ...|+.+||++.|+.+
T Consensus 25 ~~~~G~~~~si~~IA~~Agvs~ 46 (203)
T PRK11202 25 SAERSFSSLSLREVAREAGIAP 46 (203)
T ss_pred HhcCCcccCCHHHHHHHhCCCc
Confidence 44555 6789999999999843
No 301
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=40.10 E-value=40 Score=19.80 Aligned_cols=25 Identities=20% Similarity=0.379 Sum_probs=16.7
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhc-Ccc
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRS-GFF 94 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~-gif 94 (97)
|+.|+|+.+|+++ . -+|+.... |++
T Consensus 2 ~i~e~A~~~gVs~---~----tlr~ye~~~gl~ 27 (68)
T cd04763 2 TIGEVALLTGIKP---H----VLRAWEREFGLL 27 (68)
T ss_pred CHHHHHHHHCcCH---H----HHHHHHHhcCCC
Confidence 6789999999955 4 44555443 555
No 302
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=39.98 E-value=32 Score=21.67 Aligned_cols=27 Identities=26% Similarity=0.530 Sum_probs=19.7
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+|+.|++..+|+++ . .++.|+..|++.
T Consensus 1 is~~e~~~~~~i~~---~----~l~~lve~Gli~ 27 (84)
T PF13591_consen 1 ISLEEFCEACGIEP---E----FLRELVEEGLIE 27 (84)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHCCCee
Confidence 47888999988855 4 566677777764
No 303
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=39.93 E-value=61 Score=18.54 Aligned_cols=28 Identities=18% Similarity=0.018 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
+|.+||.+.+|.. .=.+-.+.|..+|+.
T Consensus 3 LT~~El~elTG~k-----~~~~Q~~~L~~~Gi~ 30 (47)
T PF13986_consen 3 LTDEELQELTGYK-----RPSKQIRWLRRNGIP 30 (47)
T ss_pred CCHHHHHHHHCCC-----CHHHHHHHHHHCCCe
Confidence 6889999999972 334556666677864
No 304
>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=39.68 E-value=25 Score=20.11 Aligned_cols=26 Identities=12% Similarity=0.221 Sum_probs=18.7
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCC
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHP 75 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~ 75 (97)
.|..|...+.. ..|..|||..+++.+
T Consensus 7 ~E~~vl~~l~~---G~~~~eIA~~l~is~ 32 (58)
T PF00196_consen 7 RELEVLRLLAQ---GMSNKEIAEELGISE 32 (58)
T ss_dssp HHHHHHHHHHT---TS-HHHHHHHHTSHH
T ss_pred HHHHHHHHHHh---cCCcchhHHhcCcch
Confidence 45556666654 789999999999954
No 305
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=39.61 E-value=25 Score=29.50 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|+++.++|+.+|+|+ +.+.|+..
T Consensus 368 kPLtlkdVAe~lglHe---STVSRa~~ 391 (481)
T PRK12469 368 KPLVLRDVAEELGLHE---STISRATG 391 (481)
T ss_pred cCCcHHHHHHHhCCCc---chhhHHhc
Confidence 7999999999999987 88999864
No 306
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=39.57 E-value=21 Score=26.30 Aligned_cols=31 Identities=19% Similarity=0.119 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCCCC-------------cccHHHHHHHHHh
Q 041844 60 KPMTLNQLLGALQIHPTK-------------TRCLHFLVCSLVR 90 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~-------------~~~L~RlLR~Laa 90 (97)
.-.|-.|||-.+|+.|++ ...|.|-||.+.-
T Consensus 69 eikTW~~La~~LGVepp~~ek~qStQKvqQYaVRLKRWM~aMHV 112 (175)
T PF09441_consen 69 EIKTWAQLALELGVEPPDPEKGQSTQKVQQYAVRLKRWMRAMHV 112 (175)
T ss_pred hHhHHHHHHHHhCCCCCCcccccchHHHHHHHHHHHHHHHHhhH
Confidence 457889999999997655 2346777776543
No 307
>PRK11640 putative transcriptional regulator; Provisional
Probab=39.45 E-value=47 Score=23.48 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=16.4
Q ss_pred HHHhhCC-CCCCHHHHHHHhCCC
Q 041844 53 DIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 53 D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
+.+.++| ...|+++|++++|+.
T Consensus 12 ~lf~~~Gy~~tsi~~I~~~aGv~ 34 (191)
T PRK11640 12 KLLEQQGLANTTLEMLAERVDYP 34 (191)
T ss_pred HHHHHhCcccCCHHHHHHHhCcC
Confidence 4455566 778899999999874
No 308
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=39.30 E-value=52 Score=22.27 Aligned_cols=34 Identities=24% Similarity=0.367 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHhC-CCCCCcccHHHHHHHHHhcCcccc
Q 041844 60 KPMTLNQLLGALQ-IHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 60 gp~s~~ELA~~~g-~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|++.-+||-..++ +++ ..|.+-||.|...|++..
T Consensus 35 g~~RF~eL~r~i~~Is~---k~Ls~~Lk~Le~~Glv~R 69 (120)
T COG1733 35 GPKRFNELRRSIGGISP---KMLSRRLKELEEDGLVER 69 (120)
T ss_pred CCCcHHHHHHHccccCH---HHHHHHHHHHHHCCCEEe
Confidence 7999999999998 755 899999999999998863
No 309
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=38.84 E-value=41 Score=21.18 Aligned_cols=27 Identities=7% Similarity=0.164 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.|+.|+|+.+|+.+ +-+|+....|++.
T Consensus 2 ~ti~evA~~~gvs~-------~tLR~ye~~Gll~ 28 (88)
T cd01105 2 IGIGEVSKLTGVSP-------RQLRYWEEKGLIK 28 (88)
T ss_pred cCHHHHHHHHCcCH-------HHHHHHHHCCCCC
Confidence 47889999999854 3677777778763
No 310
>PRK04217 hypothetical protein; Provisional
Probab=38.67 E-value=30 Score=23.43 Aligned_cols=25 Identities=8% Similarity=0.016 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
..+|..|||+.+|++. ..+++.++.
T Consensus 57 eGlS~~EIAk~LGIS~---sTV~r~L~R 81 (110)
T PRK04217 57 EGLTQEEAGKRMGVSR---GTVWRALTS 81 (110)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 5789999999999954 677766653
No 311
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=38.46 E-value=27 Score=25.83 Aligned_cols=32 Identities=13% Similarity=0.115 Sum_probs=27.7
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
=|=.|||+..|++. ..++|-|+.|+..|++..
T Consensus 32 PsE~eLa~~f~VSR---~TvRkAL~~L~~eGli~r 63 (236)
T COG2188 32 PSERELAEQFGVSR---MTVRKALDELVEEGLIVR 63 (236)
T ss_pred CCHHHHHHHHCCcH---HHHHHHHHHHHHCCcEEE
Confidence 36789999999954 889999999999998753
No 312
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=38.25 E-value=36 Score=24.22 Aligned_cols=27 Identities=19% Similarity=0.068 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
..+|..|||+.+|.++ ..+.|.|+.+.
T Consensus 119 ~g~s~~~iA~~lg~s~---~~V~r~l~l~~ 145 (187)
T TIGR00180 119 FSMTQEDLAKKIGKSR---AHITNLLRLLK 145 (187)
T ss_pred hCCCHHHHHHHHCcCH---HHHHHHHHHHc
Confidence 4678999999999954 88999988753
No 313
>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=38.04 E-value=26 Score=19.58 Aligned_cols=22 Identities=14% Similarity=0.149 Sum_probs=13.6
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
..+|..|||+.+|+++ ..+.+.
T Consensus 25 ~g~s~~eIa~~l~~s~---~~v~~~ 46 (54)
T PF08281_consen 25 QGMSYAEIAEILGISE---STVKRR 46 (54)
T ss_dssp S---HHHHHHHCTS-H---HHHHHH
T ss_pred HCcCHHHHHHHHCcCH---HHHHHH
Confidence 6789999999999954 554443
No 314
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=37.93 E-value=41 Score=26.30 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+|=+|||+++|++- ..+.|+|..--..|+++
T Consensus 28 ~g~tQ~eIA~~lgiSR---~~VsRlL~~Ar~~GiV~ 60 (318)
T PRK15418 28 DGLTQSEIGERLGLTR---LKVSRLLEKGRQSGIIR 60 (318)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHHHHHHHcCcEE
Confidence 6789999999999954 78999999998999875
No 315
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=37.86 E-value=48 Score=20.15 Aligned_cols=32 Identities=19% Similarity=0.340 Sum_probs=24.9
Q ss_pred HHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 64 LNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 64 ~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..++++..+++|-.......++..|...|++.
T Consensus 32 Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~ 63 (87)
T cd08768 32 YEELCEEIGVDPLTQRRISDLLSELEMLGLLE 63 (87)
T ss_pred HHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeE
Confidence 45677777777756677888889999999876
No 316
>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=37.84 E-value=45 Score=17.96 Aligned_cols=24 Identities=13% Similarity=0.106 Sum_probs=17.0
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+.+|..|+|+.+++.+ ..+++.++
T Consensus 14 ~~~s~~eia~~l~~s~---~tv~~~~~ 37 (57)
T cd06170 14 EGKTNKEIADILGISE---KTVKTHLR 37 (57)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 4689999999999954 44444433
No 317
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=37.77 E-value=29 Score=22.74 Aligned_cols=28 Identities=11% Similarity=0.170 Sum_probs=21.1
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..|..|++..+|+++ . .+.-|+..|++.
T Consensus 7 ~lt~~Elc~~~gi~~---~----~l~eLve~GlIe 34 (101)
T PRK10265 7 TFTITEFCLHTGVSE---E----ELNEIVGLGVIE 34 (101)
T ss_pred EeeHHHHHHHHCcCH---H----HHHHHHHCCCee
Confidence 578999999999965 5 556667777765
No 318
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=37.65 E-value=41 Score=27.73 Aligned_cols=46 Identities=11% Similarity=0.268 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 34 ~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+||....+... .+++ +..+|+.||+..+|+.+.| |+-.|-+++++.
T Consensus 312 sYW~~~ll~~L--~~~~--------~~~isI~~iS~~Tgi~~~D------IisTL~~L~m~~ 357 (396)
T KOG2747|consen 312 SYWRCVLLELL--RKHR--------GEHISIKEISKETGIRPDD------IISTLQSLNMIK 357 (396)
T ss_pred HHHHHHHHHHH--HhcC--------CCcccHHHHHHhhCCCHHH------HHHHHHhhCCcc
Confidence 67776666655 3322 2339999999999996533 555555666554
No 319
>PF14502 HTH_41: Helix-turn-helix domain
Probab=37.54 E-value=59 Score=19.11 Aligned_cols=33 Identities=9% Similarity=0.095 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.-.|++|++++.++.- ..+..-+++|...|.+.
T Consensus 5 Ri~tI~e~~~~~~vs~---GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 5 RIPTISEYSEKFGVSR---GTIQNALKFLEENGAIK 37 (48)
T ss_pred ccCCHHHHHHHhCcch---hHHHHHHHHHHHCCcEE
Confidence 3468999999999943 78999999999988764
No 320
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=37.34 E-value=73 Score=25.29 Aligned_cols=41 Identities=15% Similarity=0.257 Sum_probs=34.1
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.-.+..+++--.|+|+.++-+| ..++-.|..|-++|+++.
T Consensus 17 ~LY~~~~r~IKgeeIA~~l~rnp---GTVRNqmq~LkaLgLVeg 57 (294)
T COG2524 17 NLYRRKKRPIKGEEIAEVLNRNP---GTVRNQMQSLKALGLVEG 57 (294)
T ss_pred HHHHhcCCCcchHHHHHHHccCc---chHHHHHHHHHhcCcccc
Confidence 33344568999999999999966 999999999999998763
No 321
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=37.00 E-value=20 Score=22.78 Aligned_cols=25 Identities=12% Similarity=0.005 Sum_probs=15.5
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHH
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSL 88 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~L 88 (97)
.+|-.|||.++|-++ ..+.+.++.+
T Consensus 3 G~tq~eIA~~lGks~---s~Vs~~l~Ll 27 (93)
T PF08535_consen 3 GWTQEEIAKRLGKSR---SWVSNHLALL 27 (93)
T ss_dssp T--HHHHHHHTT--H---HHHHHHHGGG
T ss_pred CCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 467888999988743 6777777644
No 322
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=36.66 E-value=49 Score=26.33 Aligned_cols=33 Identities=24% Similarity=0.409 Sum_probs=25.4
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
+.|.+ +.+.|+++||+.+|.++ ..|.|+.+...
T Consensus 92 ~~I~~-~~~lsl~eLA~~lG~S~---~~L~R~Fkk~~ 124 (353)
T PRK15435 92 RLLEQ-ETPVTLEALADQVAMSP---FHLHRLFKATT 124 (353)
T ss_pred HHHHh-CCCCCHHHHHHHHCCCH---HHHHHHHHHHH
Confidence 44544 46899999999999954 88888887654
No 323
>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=36.59 E-value=37 Score=24.55 Aligned_cols=31 Identities=10% Similarity=0.194 Sum_probs=27.4
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|=.|||+..|++- ..++|-|+.|+..|++..
T Consensus 26 sE~eLa~~~gVSR---~TVR~Al~~L~~eGli~r 56 (233)
T TIGR02404 26 SEHELMDQYGASR---ETVRKALNLLTEAGYIQK 56 (233)
T ss_pred CHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEE
Confidence 7899999999944 789999999999998753
No 324
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 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. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=36.56 E-value=19 Score=21.73 Aligned_cols=21 Identities=19% Similarity=0.529 Sum_probs=15.1
Q ss_pred hHHHhhCCCCCCHHHHHHHhC
Q 041844 52 PDIIHNHTKPMTLNQLLGALQ 72 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g 72 (97)
.++|.+.++|+|..||.+...
T Consensus 8 ~~vL~~~~~pm~~~eI~~~i~ 28 (72)
T PF05066_consen 8 YEVLEEAGRPMTFKEIWEEIQ 28 (72)
T ss_dssp HHHHHHH-S-EEHHHHHHHHH
T ss_pred HHHHHhcCCCcCHHHHHHHHH
Confidence 466777789999999998754
No 325
>PRK10130 transcriptional regulator EutR; Provisional
Probab=36.36 E-value=38 Score=26.85 Aligned_cols=34 Identities=18% Similarity=0.383 Sum_probs=25.5
Q ss_pred HHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 53 DIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 53 D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
+.|.++ ..|+|+.|||+.+++++ ..|.|..+--.
T Consensus 247 ~~i~~~~~~~ltv~~lA~~~gvS~---r~L~r~Fk~~~ 281 (350)
T PRK10130 247 EYVLENMSEPVTVLDLCNQLHVSR---RTLQNAFHAIL 281 (350)
T ss_pred HHHHhhhcCCCCHHHHHHHHCCCH---HHHHHHHHHHH
Confidence 444433 37899999999999955 88888887544
No 326
>cd00131 PAX Paired Box domain
Probab=36.18 E-value=28 Score=23.64 Aligned_cols=41 Identities=10% Similarity=0.233 Sum_probs=29.4
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
...|.+..+ +..|..+||..+++.+ ..+.|+++-....|=+
T Consensus 23 R~rIv~~~~---~G~s~~~iA~~~~Vs~---~tV~r~i~r~~e~G~v 63 (128)
T cd00131 23 RQRIVELAQ---SGIRPCDISRQLRVSH---GCVSKILNRYYETGSI 63 (128)
T ss_pred HHHHHHHHH---cCCCHHHHHHHHCcCH---HHHHHHHHHHHHcCCc
Confidence 334455442 4689999999999955 8899998877666643
No 327
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=36.13 E-value=52 Score=25.42 Aligned_cols=38 Identities=24% Similarity=0.246 Sum_probs=28.5
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS 91 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~ 91 (97)
|-|-|..+||.+++.||+..+++| ..-+.|..+.++..
T Consensus 60 I~~el~~~gGRv~~~dL~~~LnVd---~~~ie~~~~~i~~~ 97 (272)
T PF09743_consen 60 IKDELYVHGGRVNLVDLAQALNVD---LDHIERRAQEIVKS 97 (272)
T ss_pred HHHHHHHcCCceEHHHHHHhcCcC---HHHHHHHHHHHHhC
Confidence 334555578999999999999994 47788877776643
No 328
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=36.02 E-value=20 Score=23.82 Aligned_cols=41 Identities=15% Similarity=0.241 Sum_probs=32.0
Q ss_pred hhHHHh-hCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 51 IPDIIH-NHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 51 I~D~La-~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
|+|+|. .+++.+...-|.-.++. +-....+++..|+..|++
T Consensus 20 i~dIL~~~~~~~~~~Tri~y~aNl---ny~~~~~yi~~L~~~Gli 61 (95)
T COG3432 20 IFDILKAISEGGIGITRIIYGANL---NYKRAQKYIEMLVEKGLI 61 (95)
T ss_pred HHHHHHHhcCCCCCceeeeeecCc---CHHHHHHHHHHHHhCCCE
Confidence 467776 45577888888888887 348899999999999954
No 329
>PHA01976 helix-turn-helix protein
Probab=36.01 E-value=29 Score=20.08 Aligned_cols=15 Identities=7% Similarity=0.111 Sum_probs=11.9
Q ss_pred CCCCHHHHHHHhCCC
Q 041844 60 KPMTLNQLLGALQIH 74 (97)
Q Consensus 60 gp~s~~ELA~~~g~~ 74 (97)
..+|..|+|+.+|++
T Consensus 14 ~glt~~~lA~~~gvs 28 (67)
T PHA01976 14 RAWSAPELSRRAGVR 28 (67)
T ss_pred cCCCHHHHHHHhCCC
Confidence 468888888888874
No 330
>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=35.79 E-value=43 Score=24.88 Aligned_cols=29 Identities=14% Similarity=0.401 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.+|+.||+.++|+.+ .-|+..|..+|++.
T Consensus 150 ~isi~~is~~Tgi~~------~DIi~tL~~l~~l~ 178 (188)
T PF01853_consen 150 SISIKDISQETGIRP------EDIISTLQQLGMLK 178 (188)
T ss_dssp -EEHHHHHHHH-BTH------HHHHHHHHHTT-EE
T ss_pred eEEHHHHHHHHCCCH------HHHHHHHHHCCCEE
Confidence 799999999999954 34777777877765
No 331
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=35.75 E-value=77 Score=24.62 Aligned_cols=45 Identities=11% Similarity=0.200 Sum_probs=31.9
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.+.+|.=.|.+ ||+|.+||-..+++.+ ..+..=++-|...|++.+
T Consensus 14 kRk~lLllL~e--gPkti~EI~~~l~vs~---~ai~pqiKkL~~~~LV~~ 58 (260)
T COG4742 14 KRKDLLLLLKE--GPKTIEEIKNELNVSS---SAILPQIKKLKDKGLVVQ 58 (260)
T ss_pred HHHHHHHHHHh--CCCCHHHHHHHhCCCc---HHHHHHHHHHhhCCCEEe
Confidence 44555656765 9999999999999965 555555555777776643
No 332
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=35.70 E-value=40 Score=21.31 Aligned_cols=24 Identities=8% Similarity=0.084 Sum_probs=18.4
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
...|..|||+.+|+++ ..+++.++
T Consensus 125 ~g~s~~eIA~~l~~s~---~~v~~~~~ 148 (158)
T TIGR02937 125 EGLSYKEIAEILGISV---GTVKRRLK 148 (158)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 5789999999999955 55555544
No 333
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=35.59 E-value=45 Score=22.60 Aligned_cols=23 Identities=13% Similarity=0.424 Sum_probs=18.7
Q ss_pred hHHHhhCC-CCCCHHHHHHHhCCC
Q 041844 52 PDIIHNHT-KPMTLNQLLGALQIH 74 (97)
Q Consensus 52 ~D~La~~~-gp~s~~ELA~~~g~~ 74 (97)
.+.+.+.+ ..+|+.||+++.|++
T Consensus 13 ~~Ll~~k~~~~ITV~~I~~~Agvs 36 (176)
T TIGR02366 13 KDLMEVQAFSKISVSDIMSTAQIR 36 (176)
T ss_pred HHHHHHCCCccCCHHHHHHHhCCC
Confidence 45666666 789999999999984
No 334
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=35.16 E-value=56 Score=21.22 Aligned_cols=38 Identities=3% Similarity=0.036 Sum_probs=29.3
Q ss_pred HhcChhH-HHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844 47 IQVGIPD-IIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 47 veLgI~D-~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa 90 (97)
-.+.|+. .|. +.+|-.||++.+|+.. ..+.|+=|.|-.
T Consensus 37 ~R~~va~~lL~---~g~syreIa~~tgvS~---aTItRvsr~Lk~ 75 (87)
T PF01371_consen 37 QRWQVAKELLD---EGKSYREIAEETGVSI---ATITRVSRCLKY 75 (87)
T ss_dssp HHHHHHHHHHH---TTSSHHHHHHHHTSTH---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHH---CCCCHHHHHHHhCCCH---HHHHHHHHHHHc
Confidence 5566777 553 5799999999999943 778888887763
No 335
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=35.07 E-value=57 Score=16.43 Aligned_cols=13 Identities=23% Similarity=0.319 Sum_probs=7.9
Q ss_pred CCCHHHHHHHhCC
Q 041844 61 PMTLNQLLGALQI 73 (97)
Q Consensus 61 p~s~~ELA~~~g~ 73 (97)
.+|..++|+.+|+
T Consensus 10 ~~s~~~la~~~~i 22 (56)
T smart00530 10 GLTQEELAEKLGV 22 (56)
T ss_pred CCCHHHHHHHhCC
Confidence 4566666666665
No 336
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=35.00 E-value=34 Score=22.48 Aligned_cols=23 Identities=22% Similarity=0.385 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLV 85 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlL 85 (97)
..+|.+++|+.+++++ .-|.++|
T Consensus 22 ~~ls~~~ia~dL~~s~---~~le~vL 44 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSP---EHLEQVL 44 (89)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHH
Confidence 5678888888888844 6666665
No 337
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=34.90 E-value=52 Score=20.50 Aligned_cols=26 Identities=15% Similarity=0.198 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
+.++|+.|.|..+|+++ ..+.+-+|.
T Consensus 11 s~~~s~~~Aa~~lG~~~---~~v~~wv~~ 36 (65)
T PF05344_consen 11 SQQISVAQAADRLGTDP---GTVRRWVRM 36 (65)
T ss_pred cccccHHHHHHHHCcCH---HHHHHHHHH
Confidence 47999999999999955 777666654
No 338
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=34.77 E-value=20 Score=22.29 Aligned_cols=24 Identities=13% Similarity=0.188 Sum_probs=17.9
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHH
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
..|++||+..+|+...+.++|.++
T Consensus 44 Ga~~~el~~~CgL~~aEAeLl~~L 67 (70)
T PF10975_consen 44 GASVEELMEECGLSRAEAELLLSL 67 (70)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHH
Confidence 467999999999965455666554
No 339
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=34.62 E-value=1.2e+02 Score=19.17 Aligned_cols=35 Identities=14% Similarity=0.047 Sum_probs=24.1
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
.+.+.+..+|...++.+. +......+.|.+...|+
T Consensus 24 ~g~~~~~~~l~~~~~~~~-~~~~~~~l~~~a~~~Gl 58 (125)
T cd02420 24 YGRYVPLSELRIACGVSR-DGSNASNLLKAAREYGL 58 (125)
T ss_pred cCCCCCHHHHHHHcCCCC-CCCCHHHHHHHHHHcCc
Confidence 567889999998877643 22456667777667774
No 340
>PRK01905 DNA-binding protein Fis; Provisional
Probab=34.52 E-value=97 Score=19.07 Aligned_cols=32 Identities=9% Similarity=-0.004 Sum_probs=22.5
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
|-..+...+ -+..+.|..+|+++ ..|+|.||-
T Consensus 42 i~~aL~~~~--gn~s~aAr~LGIsr---stL~rklkk 73 (77)
T PRK01905 42 LEVVMEQAG--GNQSLAAEYLGINR---NTLRKKLQQ 73 (77)
T ss_pred HHHHHHHcC--CCHHHHHHHHCCCH---HHHHHHHHH
Confidence 335565533 44778899999955 789988884
No 341
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=34.26 E-value=1.3e+02 Score=19.45 Aligned_cols=35 Identities=17% Similarity=0.065 Sum_probs=24.8
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
++.+.++++|...++.++ +...+..+.|.+...|+
T Consensus 25 ~g~~~~~~~l~~~~~~~~-~g~s~~~l~~~a~~~Gl 59 (129)
T cd02424 25 YKKKYDLNELKIKANLKK-NGLSIYDLENLAKKFGL 59 (129)
T ss_pred cCCCccHHHHHHHhCCCC-CCccHHHHHHHHHHcCC
Confidence 456788888888877654 33567777777777774
No 342
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=34.12 E-value=1.2e+02 Score=23.64 Aligned_cols=49 Identities=16% Similarity=0.309 Sum_probs=36.8
Q ss_pred HHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 40 SLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 40 aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
.|++. |+ +-+. .+.|+....|++..+.+- .+..++-.|-.|...|++..
T Consensus 8 IL~~i--V~----~Yi~-t~~PVGSk~L~~~~~l~~-SsATIRn~m~~LE~~G~L~q 56 (260)
T PRK03911 8 LLDSI--IQ----TYLQ-DNEPIGSNELKSLMNLKI-SAATIRNYFKKLSDEGLLTQ 56 (260)
T ss_pred HHHHH--HH----HHhc-cCCccCHHHHHHHcCCCC-CcHHHHHHHHHHHHCcCccC
Confidence 45555 54 4454 368999999999987532 34889999999999998864
No 343
>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=34.11 E-value=81 Score=20.19 Aligned_cols=41 Identities=15% Similarity=0.148 Sum_probs=30.0
Q ss_pred HHHhhCCCCCCHHHHHHHhCC-----CCCCcccHHHHHHHHHhcCccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQI-----HPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~-----~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-.|.. +|++--||.+.+.- -+.++..++++|+-|...|+++
T Consensus 11 ~~L~~--~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~ 56 (100)
T TIGR03433 11 KTLSL--GPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIA 56 (100)
T ss_pred HHHhc--CCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeE
Confidence 34543 78888888888631 0125588999999999999876
No 344
>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=33.92 E-value=37 Score=25.46 Aligned_cols=24 Identities=13% Similarity=0.199 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.++|..|||+.+|+++ ..++++++
T Consensus 235 ~~~t~~eIA~~lgvS~---~~V~q~~~ 258 (270)
T TIGR02392 235 DKLTLQELAAEYGVSA---ERIRQIEK 258 (270)
T ss_pred CCcCHHHHHHHHCCCH---HHHHHHHH
Confidence 5899999999999955 67776654
No 345
>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=33.90 E-value=44 Score=24.04 Aligned_cols=31 Identities=16% Similarity=0.262 Sum_probs=27.3
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|=.|||+..|++- ..++|-|..|+..|++..
T Consensus 34 sE~eLa~~~~VSR---~TvR~Al~~L~~eGli~r 64 (238)
T TIGR02325 34 AEMQLAERFGVNR---HTVRRAIAALVERGLLRA 64 (238)
T ss_pred CHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEE
Confidence 7889999999944 789999999999998753
No 346
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=33.84 E-value=36 Score=25.58 Aligned_cols=36 Identities=17% Similarity=0.213 Sum_probs=24.0
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHH
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLV 85 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlL 85 (97)
.+|...+.|..--.-.|..||++.+|+++ ..|.|=.
T Consensus 9 ~~~~~v~~lr~lk~~~ty~el~~~~g~p~---~~l~RYv 44 (238)
T PRK08558 9 LQLRAVRVLRSLKKTYTYEELSSITGLPE---SVLNRYV 44 (238)
T ss_pred HHHHHHHHHHHHhcccCHHHHHHHHCCCH---HHHHHHH
Confidence 44555666644335679999999999854 5666543
No 347
>PRK09492 treR trehalose repressor; Provisional
Probab=33.78 E-value=31 Score=25.34 Aligned_cols=23 Identities=4% Similarity=0.091 Sum_probs=16.7
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
..|+.|||+..|++. ..+.|+|+
T Consensus 4 ~~ti~dIA~~agVS~---~TVSrvLn 26 (315)
T PRK09492 4 KLTIKDIARLSGVGK---STVSRVLN 26 (315)
T ss_pred CCcHHHHHHHhCCCH---HHHhHHhC
Confidence 468999999999843 55666554
No 348
>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=33.73 E-value=15 Score=30.00 Aligned_cols=34 Identities=21% Similarity=0.219 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
...+|++||++.+|++ ...|.|.|..|+..|++.
T Consensus 532 ~~~~t~~ei~~~~~~~---~~~l~~~L~~l~~~~~l~ 565 (588)
T PF00888_consen 532 NDSLTVEEISEKTGIS---EEELKRALKSLVKSKILI 565 (588)
T ss_dssp SSEEEHHHHHHHC------HHHHHHHHHCCCTTTTCS
T ss_pred CCCccHHHHHHHHCcC---HHHHHHHHHHHHhCCcce
Confidence 4689999999999994 489999999999998874
No 349
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=33.56 E-value=43 Score=23.96 Aligned_cols=31 Identities=10% Similarity=0.025 Sum_probs=27.2
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|-.|||+..|++. ..+++-|+.|...|++..
T Consensus 27 sE~eLa~~~~Vsr---~Tvr~Al~~L~~eGli~~ 57 (231)
T TIGR03337 27 SERDLGERFNTTR---VTIREALQQLEAEGLIYR 57 (231)
T ss_pred CHHHHHHHHCCCH---HHHHHHHHHHHHCCeEEE
Confidence 7899999999953 789999999999998754
No 350
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=33.37 E-value=29 Score=25.66 Aligned_cols=32 Identities=6% Similarity=0.222 Sum_probs=18.2
Q ss_pred CCHHHHHHHhCCCC---------------CCcccHHHHHHHHHhcCc
Q 041844 62 MTLNQLLGALQIHP---------------TKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 62 ~s~~ELA~~~g~~~---------------~~~~~L~RlLR~Laa~gi 93 (97)
+|+.|||+..|++. ..+..-.|+++.....|+
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~~~~~~Vs~~tr~rV~~~a~elgY 47 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNY 47 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHhCC
Confidence 35666666666521 234455666666666664
No 351
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=33.26 E-value=55 Score=25.16 Aligned_cols=43 Identities=23% Similarity=0.272 Sum_probs=31.6
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|.+...|+.+++..|.+.++.-..++..++-.|.-|+..|.++
T Consensus 9 d~~~~~gg~i~~~~Li~l~~~~gi~~~~vr~al~RL~~~G~l~ 51 (280)
T TIGR02277 9 DAIRPRGGAIWLGSLIEFLAGLGINERLVRTAVSRLVAQGWLQ 51 (280)
T ss_pred hhccCCCCceeHHHHHHHHHhcCCCcchHHHHHHHHHHCCCEE
Confidence 6677777888877776664431114489999999999999885
No 352
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=33.25 E-value=36 Score=25.04 Aligned_cols=40 Identities=15% Similarity=0.140 Sum_probs=30.6
Q ss_pred hHHH-hhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 52 PDII-HNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 52 ~D~L-a~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
.+.+ ....|.+|..+|+..+|.++ ....-.|..+...|++
T Consensus 180 l~~~~~~~~g~vt~~~l~~~~~ws~---~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 180 LELAEEENGGGVTASELAEKLGWSV---ERAKEALEELEREGLL 220 (223)
T ss_dssp HHHH--TTTSEEEHHHHHHHHTB-H---HHHHHHHHHHHHTTSE
T ss_pred HHHHHhhcCCCCCHHHHHHHhCCCH---HHHHHHHHHHHhCCCE
Confidence 3444 34568999999999999944 7788888889888875
No 353
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=33.03 E-value=79 Score=19.17 Aligned_cols=33 Identities=21% Similarity=0.293 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.++.++|++.++++. +-+.+++.-+...|.+.
T Consensus 23 ~~i~~~~i~~~~~l~~---~~vE~~i~~~i~~~~l~ 55 (88)
T smart00088 23 SSISLSDLAKLLGLSV---PEVEKLVSKAIRDGEIS 55 (88)
T ss_pred ceeeHHHHHHHhCcCH---HHHHHHHHHHHHCCCeE
Confidence 6899999999999954 46888888888888664
No 354
>smart00753 PAM PCI/PINT associated module.
Probab=33.03 E-value=79 Score=19.17 Aligned_cols=33 Identities=21% Similarity=0.293 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.++.++|++.++++. +-+.+++.-+...|.+.
T Consensus 23 ~~i~~~~i~~~~~l~~---~~vE~~i~~~i~~~~l~ 55 (88)
T smart00753 23 SSISLSDLAKLLGLSV---PEVEKLVSKAIRDGEIS 55 (88)
T ss_pred ceeeHHHHHHHhCcCH---HHHHHHHHHHHHCCCeE
Confidence 6899999999999954 46888888888888664
No 355
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=32.96 E-value=51 Score=19.51 Aligned_cols=13 Identities=23% Similarity=0.406 Sum_probs=7.2
Q ss_pred CCCHHHHHHHhCC
Q 041844 61 PMTLNQLLGALQI 73 (97)
Q Consensus 61 p~s~~ELA~~~g~ 73 (97)
.+|..|+|+.+|+
T Consensus 18 ~~t~~~lA~~~gi 30 (78)
T TIGR02607 18 GLSIRALAKALGV 30 (78)
T ss_pred CCCHHHHHHHhCC
Confidence 4555555555555
No 356
>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=32.87 E-value=40 Score=24.01 Aligned_cols=28 Identities=14% Similarity=0.178 Sum_probs=19.3
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
++.|+|+.+||+.++ ++ ..+..+|..|.
T Consensus 10 s~~pvs~~~La~~l~-~~---~~v~~~l~~L~ 37 (159)
T PF04079_consen 10 SGEPVSIEELAEILG-SE---DEVEEALEELQ 37 (159)
T ss_dssp -SS-B-HHHHHHHCT--H---HHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHhC-CH---HHHHHHHHHHH
Confidence 467999999999999 54 66777776665
No 357
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=32.52 E-value=82 Score=23.36 Aligned_cols=40 Identities=18% Similarity=0.249 Sum_probs=27.7
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCc-ccHHHHHH
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKT-RCLHFLVC 86 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~-~~L~RlLR 86 (97)
.+..|.|.|.++|...|+-+||.++|+.-++. ..|++|.|
T Consensus 5 ~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~ 45 (183)
T PHA02701 5 CASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLE 45 (183)
T ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhh
Confidence 34568899988875699999999999943211 23555544
No 358
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=32.51 E-value=68 Score=19.25 Aligned_cols=34 Identities=18% Similarity=0.393 Sum_probs=24.7
Q ss_pred hhHHHhhCCCC-CCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 51 IPDIIHNHTKP-MTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 51 I~D~La~~~gp-~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
+.|.+-. .| .|+.-+++.+++.+ ....|+++-|.
T Consensus 4 Lidll~~--~P~Vsa~mva~~L~vT~---~~A~~li~eLg 38 (54)
T PF11972_consen 4 LIDLLLS--RPLVSAPMVAKELGVTP---QAAQRLIAELG 38 (54)
T ss_pred HHHHHHh--CccccHHHHHHHhCCCH---HHHHHHHHHhh
Confidence 4565544 35 69999999999965 77888876554
No 359
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=32.04 E-value=33 Score=25.54 Aligned_cols=24 Identities=13% Similarity=0.232 Sum_probs=17.9
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+..|+.|||+..|++. ..+.|+|+
T Consensus 5 ~~~Ti~dIA~~agVS~---~TVSr~Ln 28 (342)
T PRK10014 5 KKITIHDVALAAGVSV---STVSLVLS 28 (342)
T ss_pred CCCcHHHHHHHhCCCH---HHHHHHHC
Confidence 4579999999999844 56666664
No 360
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=32.03 E-value=41 Score=21.55 Aligned_cols=20 Identities=30% Similarity=0.428 Sum_probs=16.3
Q ss_pred CCCCcccHHHHHHHHHhcCc
Q 041844 74 HPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 74 ~~~~~~~L~RlLR~Laa~gi 93 (97)
||.=...|++||-.|+.|||
T Consensus 66 HP~l~~~lr~i~~sLa~MGI 85 (85)
T PF14357_consen 66 HPKLAGILRNIMDSLANMGI 85 (85)
T ss_pred CCcHHHHHHHHHHHHHHCCC
Confidence 77545579999999999996
No 361
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=31.88 E-value=59 Score=27.32 Aligned_cols=39 Identities=21% Similarity=0.393 Sum_probs=31.8
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+.. .+++|..+|+..++++. ....|.+..|...|++.
T Consensus 409 ~~~~e-n~~~T~~~L~~~l~is~---~~i~r~i~~Lv~~g~~~ 447 (467)
T COG2865 409 ELIKE-NGKVTARELREILGISS---ETIRRRIANLVKRGLLK 447 (467)
T ss_pred HHHhh-ccccCHHHHHHHhCcch---hhHHHHHHHHhcccHHH
Confidence 44433 47999999999999844 78999999999998875
No 362
>COG3978 Acetolactate synthase (isozyme II), small (regulatory) subunit [Function unknown]
Probab=31.73 E-value=32 Score=22.59 Aligned_cols=18 Identities=17% Similarity=0.185 Sum_probs=15.6
Q ss_pred CcccHHHHHHHHHhcCcc
Q 041844 77 KTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 77 ~~~~L~RlLR~Laa~gif 94 (97)
+|..|.|+||+--+.|+-
T Consensus 13 ~pe~leRVLrvtrhRGF~ 30 (86)
T COG3978 13 NPETLERVLRVTRHRGFR 30 (86)
T ss_pred ChHHHHHHHHHhhhcCeE
Confidence 679999999999998863
No 363
>PRK09526 lacI lac repressor; Reviewed
Probab=31.53 E-value=34 Score=25.42 Aligned_cols=24 Identities=17% Similarity=0.205 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+..|+.|||+..|++. ..+.|+|.
T Consensus 4 ~~~ti~dIA~~aGVS~---~TVSrvLn 27 (342)
T PRK09526 4 KPVTLYDVARYAGVSY---QTVSRVLN 27 (342)
T ss_pred CCCcHHHHHHHhCCCH---HHHHHHhc
Confidence 4578999999999843 56666664
No 364
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.51 E-value=87 Score=19.74 Aligned_cols=28 Identities=11% Similarity=-0.047 Sum_probs=19.3
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|...|..|||+.+|.+. .+..+.+.|+
T Consensus 16 ~G~v~TYg~iA~~~g~p~-~~RaVg~al~ 43 (80)
T TIGR00589 16 YGETKSYGQLAARIGNPK-AVRAVGGANG 43 (80)
T ss_pred CCCcCCHHHHHHHhCCCC-hHHHHHHHHH
Confidence 467899999999999532 3345555554
No 365
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=31.39 E-value=38 Score=21.43 Aligned_cols=28 Identities=18% Similarity=0.203 Sum_probs=18.6
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|...|..|||+.+| +|..+..+.+.|+
T Consensus 16 ~G~v~TYg~iA~~~g-~p~~ar~Vg~al~ 43 (85)
T PF01035_consen 16 YGKVTTYGEIARLLG-RPKAARAVGSALA 43 (85)
T ss_dssp TT-BEEHHHHHHHTT--TTCHHHHHHHHH
T ss_pred CCceEeHHHHHHHHh-hcccHHHHHHHhc
Confidence 467899999999999 3434455555554
No 366
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.36 E-value=46 Score=22.24 Aligned_cols=23 Identities=17% Similarity=0.199 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLV 85 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlL 85 (97)
.++|.++||.+++..+ .-|.+++
T Consensus 22 ~~LS~~~iA~~Ln~t~---~~lekil 44 (97)
T COG4367 22 CPLSDEEIATALNWTE---VKLEKIL 44 (97)
T ss_pred ccccHHHHHHHhCCCH---HHHHHHH
Confidence 7899999999999855 6788887
No 367
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=31.23 E-value=35 Score=19.75 Aligned_cols=19 Identities=16% Similarity=0.228 Sum_probs=13.1
Q ss_pred CHHHHHHHhCCCCCCcccHHHH
Q 041844 63 TLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
|+.|+|+.+|+++ ..|++-
T Consensus 2 s~~eva~~~gvs~---~tlr~w 20 (68)
T cd01104 2 TIGAVARLTGVSP---DTLRAW 20 (68)
T ss_pred CHHHHHHHHCcCH---HHHHHH
Confidence 6788888888854 544443
No 368
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=31.16 E-value=46 Score=20.70 Aligned_cols=17 Identities=24% Similarity=0.040 Sum_probs=15.1
Q ss_pred CcccHHHHHHHHHhcCc
Q 041844 77 KTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 77 ~~~~L~RlLR~Laa~gi 93 (97)
.|.+|++|.|.|...|+
T Consensus 11 RpGLL~~i~~~l~~~gl 27 (72)
T cd04895 11 KPGILLEAVQVLTDLDL 27 (72)
T ss_pred cCCHHHHHHHHHHHCCc
Confidence 56899999999999986
No 369
>PRK14999 histidine utilization repressor; Provisional
Probab=30.60 E-value=52 Score=23.99 Aligned_cols=33 Identities=9% Similarity=0.187 Sum_probs=28.5
Q ss_pred CCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+ |=.|||+..|++- ..++|-|..|+..|++.
T Consensus 34 ~~LPsE~eLa~~~gVSR---~TVR~Al~~L~~eGli~ 67 (241)
T PRK14999 34 DRIPSEAELVAQYGFSR---MTINRALRELTDEGWLV 67 (241)
T ss_pred CcCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 345 8999999999943 78999999999999875
No 370
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=30.58 E-value=38 Score=21.55 Aligned_cols=24 Identities=21% Similarity=0.430 Sum_probs=15.4
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCC
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIH 74 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~ 74 (97)
..+...+++ ..++..|||+.+|+.
T Consensus 5 ~~l~~~l~~--r~~~~~eLa~~igis 28 (73)
T COG3655 5 VRLDVMLAD--RKISLKELAEAIGIS 28 (73)
T ss_pred HhHHHHHHH--HhhhHHHHHHHHccc
Confidence 344455555 567777788777764
No 371
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=30.52 E-value=62 Score=25.49 Aligned_cols=34 Identities=15% Similarity=0.243 Sum_probs=29.1
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |..+||+.+|++. ..+++.++.|.+.|++.
T Consensus 26 g~~lps~r~la~~~~vsr---~tv~~a~~~L~~~g~i~ 60 (431)
T PRK15481 26 GDSLPPVRELASELGVNR---NTVAAAYKRLVTAGLAQ 60 (431)
T ss_pred CCcCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 3455 7899999999954 78999999999999875
No 372
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=30.41 E-value=35 Score=25.22 Aligned_cols=32 Identities=9% Similarity=0.107 Sum_probs=17.6
Q ss_pred CCHHHHHHHhCCCC------------CCcccHHHHHHHHHhcCc
Q 041844 62 MTLNQLLGALQIHP------------TKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 62 ~s~~ELA~~~g~~~------------~~~~~L~RlLR~Laa~gi 93 (97)
.|+.|||+.+|+++ ..++.-.||++....+|+
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY 45 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDY 45 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCC
Confidence 36677777777632 123445555555555554
No 373
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=30.41 E-value=40 Score=15.48 Aligned_cols=21 Identities=10% Similarity=0.066 Sum_probs=14.9
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHH
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
..|..++|..+|+.. ..+++.
T Consensus 21 ~~s~~~ia~~~~is~---~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSR---STLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCH---HHHHHh
Confidence 458999999999843 555543
No 374
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=30.37 E-value=61 Score=22.91 Aligned_cols=29 Identities=7% Similarity=0.008 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.-+|+.|+|+.+|+++ +-+|+-...|++.
T Consensus 10 ~~~~IgevAk~~gvs~-------~TlRyYE~~GLi~ 38 (154)
T PRK15002 10 ALLTPGEVAKRSGVAV-------SALHFYESKGLIT 38 (154)
T ss_pred ccccHHHHHHHHCcCH-------HHHHHHHHCCCCC
Confidence 5689999999999954 4789999999875
No 375
>PF13309 HTH_22: HTH domain
Probab=30.34 E-value=46 Score=20.00 Aligned_cols=36 Identities=11% Similarity=0.046 Sum_probs=25.1
Q ss_pred HHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 40 SLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 40 aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+++.. -+-|+|+. .-++..+|+.+|++. ..++|-||
T Consensus 29 iV~~L--~~~G~F~l------Kgav~~vA~~L~iS~---~TVY~YLr 64 (64)
T PF13309_consen 29 IVRQL--YEKGIFLL------KGAVEYVAEKLGISR---ATVYRYLR 64 (64)
T ss_pred HHHHH--HHCCCccc------CcHHHHHHHHHCCCH---HHHHHHcC
Confidence 34444 67788865 235899999999954 67887654
No 376
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=30.25 E-value=48 Score=22.31 Aligned_cols=14 Identities=21% Similarity=0.223 Sum_probs=8.7
Q ss_pred CCCCHHHHHHHhCC
Q 041844 60 KPMTLNQLLGALQI 73 (97)
Q Consensus 60 gp~s~~ELA~~~g~ 73 (97)
..+|..|+|..+|+
T Consensus 17 ~Glsq~eLA~~~Gi 30 (120)
T PRK13890 17 RHMTKKELSERSGV 30 (120)
T ss_pred cCCCHHHHHHHHCc
Confidence 45666666666665
No 377
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=29.66 E-value=35 Score=19.30 Aligned_cols=22 Identities=9% Similarity=0.191 Sum_probs=17.0
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
++..|+++.+|++. ..++|+++
T Consensus 4 l~~~ev~~~~g~s~---~ti~~~~k 25 (51)
T PF05930_consen 4 LRIKEVAELLGVSR---STIYRLIK 25 (51)
T ss_dssp E-HHHHHHHHSS-H---HHHHHHHH
T ss_pred ccHHHHHHHHCCCH---HHHHHHHh
Confidence 56889999999944 78888887
No 378
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=29.57 E-value=43 Score=25.48 Aligned_cols=35 Identities=20% Similarity=0.313 Sum_probs=26.9
Q ss_pred CCCCHHHHH--HHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLL--GALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA--~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+-.|++||. +++.+ |.|+....|.|+.|...|+++
T Consensus 120 ~i~si~DL~~Gk~IAi-p~d~~n~~r~L~lL~~~Gli~ 156 (271)
T PRK11063 120 KIKSLDELQDGSQVAV-PNDPTNLGRSLLLLQKVGLIK 156 (271)
T ss_pred CCCCHHHhcCCCEEEe-cCCCccHHHHHHHHHHCCCEE
Confidence 467899996 33444 436789999999999999865
No 379
>COG2412 Uncharacterized conserved protein [Function unknown]
Probab=29.42 E-value=1e+02 Score=20.79 Aligned_cols=42 Identities=14% Similarity=0.234 Sum_probs=28.4
Q ss_pred CccccCCCCcHHHHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhH
Q 041844 4 PQSYGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPD 53 (97)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D 53 (97)
|.-||+...++|......+- -. +....--.++.+| ++.|+.|
T Consensus 40 esFYgge~v~~d~~~~~l~~-----At-i~nl~Ge~av~~a--I~~Gli~ 81 (101)
T COG2412 40 ESFYGGELVEEDEAIKALEE-----AT-IANLVGEKAVEIA--IDAGLID 81 (101)
T ss_pred ccccCCcccCHHHHHHHHHH-----hH-HHHHhhhhhhHHH--HhcCccC
Confidence 45688888888877766654 11 3344456678888 9988876
No 380
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=29.22 E-value=92 Score=23.04 Aligned_cols=55 Identities=15% Similarity=0.228 Sum_probs=37.4
Q ss_pred HhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCC--------CCCcccHH-----HHHHHHHhcC
Q 041844 33 FSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIH--------PTKTRCLH-----FLVCSLVRSG 92 (97)
Q Consensus 33 ~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~--------~~~~~~L~-----RlLR~Laa~g 92 (97)
.||..-+.--.| |++|-.|.|++ |..+++|..++.-. |++|..+. +|-|+|+..+
T Consensus 88 TGy~sIATAV~A--vKlGA~~YLaK---PAdaDdi~aAl~~~~~d~~~~~~~~pmS~~rl~WEhIqrvl~e~~ 155 (182)
T COG4567 88 TGYASIATAVEA--VKLGACDYLAK---PADADDILAALLRREPDEDTAPPENPMSADRLRWEHIQRVLEECE 155 (182)
T ss_pred ecchHHHHHHHH--HHhhhhhhcCC---CCChHHHHHHHhhcCCCcccCCCCCCCchhHhhHHHHHHHHHHhC
Confidence 366666665567 99999999964 99999998876532 33444443 4667776544
No 381
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=29.19 E-value=63 Score=27.35 Aligned_cols=32 Identities=9% Similarity=-0.077 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
.|.++.|+++.++.+ +..+.+++|.|+..|.+
T Consensus 487 ~~~~~~~~~~~~~~~---~~~~~~~l~~l~~~g~~ 518 (581)
T TIGR00475 487 KGAWVREFAEEVNGD---EKVMLKRVRKAGHRGGE 518 (581)
T ss_pred CCCCHHHHHhhhCCC---HHHHHHHHHHHHhCCCE
Confidence 799999999999984 47899999999998854
No 382
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=29.11 E-value=81 Score=17.07 Aligned_cols=29 Identities=14% Similarity=0.041 Sum_probs=19.1
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+.|...+ -+..+-|..+|+++ ..|+|-|+
T Consensus 12 ~aL~~~~--gn~~~aA~~Lgisr---~tL~~klk 40 (42)
T PF02954_consen 12 QALERCG--GNVSKAARLLGISR---RTLYRKLK 40 (42)
T ss_dssp HHHHHTT--T-HHHHHHHHTS-H---HHHHHHHH
T ss_pred HHHHHhC--CCHHHHHHHHCCCH---HHHHHHHH
Confidence 4455533 34678899999954 78888776
No 383
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.99 E-value=49 Score=20.77 Aligned_cols=17 Identities=6% Similarity=-0.043 Sum_probs=15.0
Q ss_pred CcccHHHHHHHHHhcCc
Q 041844 77 KTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 77 ~~~~L~RlLR~Laa~gi 93 (97)
.|.+|+|+.|.+...|+
T Consensus 10 RpGLL~~i~~~l~~~~l 26 (75)
T cd04896 10 QKGLLYDILRTSKDCNI 26 (75)
T ss_pred cccHHHHHHHHHHHCCe
Confidence 56899999999998885
No 384
>COG1164 Oligoendopeptidase F [Amino acid transport and metabolism]
Probab=28.93 E-value=2.7e+02 Score=23.84 Aligned_cols=65 Identities=11% Similarity=0.033 Sum_probs=41.9
Q ss_pred HhccCcc--hhhHHhHHHHHHHHHHHHHhcC--------hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 22 LNCANPC--LDNTFSFINSMSLKCVKLIQVG--------IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 22 ~~~~~p~--~~l~~~~~~s~aL~~a~~veLg--------I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
.+|.+|+ ....+|++.+.++..- +.-+ +.+.|. .||.+++.||....|+|..+++.+.-.+..+.
T Consensus 512 Hfy~~pFYvy~Ya~G~~~a~~l~~~--~~~~~~~~~~~~y~~~Lk-~GgS~~p~ell~~~GiD~~~~~~~~~a~~~~~ 586 (598)
T COG1164 512 HFYHSPFYVYQYATGQLAALALYAK--ILTNDAEAFEKYYIAFLK-SGGSKSPLELLKIAGIDLTTPDPWEEALAEFE 586 (598)
T ss_pred eeeecCceehHhHHHHHHHHHHHHH--HHhccHHHHHHHHHHHHh-CCCCCCHHHHHHHcCCCCCCchHHHHHHHHHH
Confidence 4566676 4555566555444433 3333 335554 57899999999999998777777766665443
No 385
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=28.88 E-value=37 Score=27.96 Aligned_cols=44 Identities=9% Similarity=0.112 Sum_probs=32.6
Q ss_pred cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+.+.|+=.+|..|+-|||+++|++ ...+.-+.+.|...|+++
T Consensus 343 ~~~l~~L~~~DG~~slldIA~~~~~~---~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 343 MAMLWVLNYSDGKNSLLDIAERIGLP---FDELADAARKLLEAGLLK 386 (386)
T ss_dssp HHHHHHHHH-EEEEEHHHHHHHHT-----HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHhccCCCcHHHHHHHHCcC---HHHHHHHHHHHHHcCCCC
Confidence 34566676677999999999999994 478888999998888763
No 386
>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=28.47 E-value=61 Score=23.40 Aligned_cols=33 Identities=9% Similarity=0.196 Sum_probs=28.2
Q ss_pred CCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+ |=.|||+..|++- ..++|-|..|+..|++.
T Consensus 23 ~~LPsE~eLa~~~~VSR---~TVR~Al~~L~~eGli~ 56 (230)
T TIGR02018 23 HRIPSEHELVAQYGCSR---MTVNRALRELTDAGLLE 56 (230)
T ss_pred CcCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 345 8889999999943 78999999999999875
No 387
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=28.45 E-value=1.1e+02 Score=18.99 Aligned_cols=40 Identities=8% Similarity=0.109 Sum_probs=24.7
Q ss_pred hhHHHhhCCCCCCHHHHHHHh----CCCCC-CcccHHHHHHHHHhcCcc
Q 041844 51 IPDIIHNHTKPMTLNQLLGAL----QIHPT-KTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~----g~~~~-~~~~L~RlLR~Laa~gif 94 (97)
|++.| +|+.|+.||++.+ ++ +. -..-+..+++.|...|++
T Consensus 36 Iw~ll---dg~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli 80 (81)
T TIGR03859 36 ILELC---DGKRSLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWL 80 (81)
T ss_pred HHHHc---cCCCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCc
Confidence 44554 3688999999887 55 31 112355566666677765
No 388
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=28.39 E-value=65 Score=27.39 Aligned_cols=56 Identities=13% Similarity=0.034 Sum_probs=0.0
Q ss_pred ccCcchhhHHhHHHHHHHHHHHHHhcChhHHH---------------hhCCCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 24 CANPCLDNTFSFINSMSLKCVKLIQVGIPDII---------------HNHTKPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 24 ~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~L---------------a~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
||++|++ +.+.-..-..+ -...||-++ ...|..-|..|||+.+|++. +-+.++|+.
T Consensus 436 YA~~wIr---~aI~~~i~~~~--r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~---~~v~~~~~~ 506 (619)
T PRK05658 436 YATWWIR---QAITRSIADQA--RTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPE---DKVRKVLKI 506 (619)
T ss_pred HhHHHHH---HHHHHHHHHcC--CceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCH---HHHHHHHHh
No 389
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=28.33 E-value=54 Score=22.30 Aligned_cols=29 Identities=10% Similarity=0.229 Sum_probs=17.4
Q ss_pred hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
++++.+ ..|++||.+.+++|| =.|.+|-+
T Consensus 17 ~eAlrr---G~sveeI~e~T~ID~---wFL~~i~~ 45 (123)
T PF02787_consen 17 AEALRR---GYSVEEIHELTKIDP---WFLEQIKN 45 (123)
T ss_dssp HHHHHT---TB-HHHHHHHH---H---HHHHHHHH
T ss_pred HHHHHc---CCCHHHHHHHHCccH---HHHHHHHH
Confidence 455543 589999999999954 66666654
No 390
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=28.30 E-value=1.1e+02 Score=23.12 Aligned_cols=44 Identities=20% Similarity=0.197 Sum_probs=31.6
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCC-----CCCcccHHHHHHHHHhcCccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIH-----PTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~-----~~~~~~L~RlLR~Laa~gif~ 95 (97)
|.+.|. .+||+|..||.+.++.. +.......++++.|...|.+.
T Consensus 90 v~~~L~-~~gplt~~eL~~~l~~~~~~~~~~~~~~~~~~l~~l~~~G~l~ 138 (327)
T PF06224_consen 90 VLDALR-ADGPLTRAELREALAEAGWWGWGGPSSPWKHLLEYLWYRGLLC 138 (327)
T ss_pred HHHHHH-hcCCCCHHHHHHHhhhccccCCCCCCchHHHHHHHHHhCCeEE
Confidence 445562 35899999999997664 112347899999999888653
No 391
>PRK09726 antitoxin HipB; Provisional
Probab=28.17 E-value=43 Score=20.95 Aligned_cols=15 Identities=20% Similarity=0.211 Sum_probs=12.1
Q ss_pred CCCCHHHHHHHhCCC
Q 041844 60 KPMTLNQLLGALQIH 74 (97)
Q Consensus 60 gp~s~~ELA~~~g~~ 74 (97)
..+|..|+|..+|+.
T Consensus 24 ~gltq~elA~~~gvs 38 (88)
T PRK09726 24 NGWTQSELAKKIGIK 38 (88)
T ss_pred cCCCHHHHHHHHCcC
Confidence 568888999988874
No 392
>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=28.15 E-value=57 Score=21.29 Aligned_cols=22 Identities=9% Similarity=0.238 Sum_probs=16.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
...|..|||+.+|+.+ ..++..
T Consensus 128 ~~~~~~eIA~~lgis~---~tv~~~ 149 (161)
T TIGR02985 128 EGKSYKEIAEELGISV---KTVEYH 149 (161)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHH
Confidence 5789999999999954 554433
No 393
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=28.04 E-value=71 Score=22.18 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
..+|+.|+|+.+|+.+ +-+|+--..|++.
T Consensus 6 ~~~~IgevAk~~Gvs~-------~TLRyYE~~GLl~ 34 (144)
T PRK13752 6 ENLTIGVFAKAAGVNV-------ETIRFYQRKGLLP 34 (144)
T ss_pred CcccHHHHHHHHCcCH-------HHHHHHHHCCCCC
Confidence 3589999999999954 5789988999885
No 394
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=28.03 E-value=40 Score=25.05 Aligned_cols=24 Identities=8% Similarity=0.091 Sum_probs=16.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+..|+.|||+..|++. ..+.|+|+
T Consensus 4 ~~~ti~dIA~~agVS~---~TVSrvLn 27 (331)
T PRK14987 4 KRPVLQDVADRVGVTK---MTVSRFLR 27 (331)
T ss_pred CCCcHHHHHHHhCCCH---HHhhhhhC
Confidence 3568899999999843 55555553
No 395
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=27.98 E-value=76 Score=26.83 Aligned_cols=56 Identities=13% Similarity=0.067 Sum_probs=0.0
Q ss_pred ccCcchhhHHhHHHHHHHHHHHHHhcChhHHH---------------hhCCCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844 24 CANPCLDNTFSFINSMSLKCVKLIQVGIPDII---------------HNHTKPMTLNQLLGALQIHPTKTRCLHFLVCS 87 (97)
Q Consensus 24 ~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~L---------------a~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~ 87 (97)
||++|++ +.+.-....-. -...||-++ ...|..-|..|||+.+|+.+ .-+.++++.
T Consensus 327 YA~wWIR---qaI~raI~d~~--r~IRvP~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~---e~V~~~~~~ 397 (509)
T PRK05901 327 YATWWIR---QAITRAMADQA--RTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTP---EKVREIQKY 397 (509)
T ss_pred hhHHHHH---HHHHHHHHHcC--CceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCH---HHHHHHHHh
No 396
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=27.94 E-value=29 Score=19.05 Aligned_cols=33 Identities=9% Similarity=0.160 Sum_probs=18.4
Q ss_pred CCHHHHHHHhCCCC-CCcccHHHHHHHHHhcCcc
Q 041844 62 MTLNQLLGALQIHP-TKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 62 ~s~~ELA~~~g~~~-~~~~~L~RlLR~Laa~gif 94 (97)
+|.+.+...+.-++ ..+....|++.....+|+-
T Consensus 9 vs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~ 42 (52)
T cd01392 9 VSVATVSRVLNGKPRVSEETRERVLAAAEELGYR 42 (52)
T ss_pred cCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCC
Confidence 34444444444321 1446677788887777753
No 397
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=27.69 E-value=1.9e+02 Score=22.31 Aligned_cols=53 Identities=8% Similarity=-0.001 Sum_probs=35.0
Q ss_pred HhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 33 FSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 33 ~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+..|...+++.. +. + .++..++.+||.+++..= ...-++..|..|...|+++.
T Consensus 119 ~~~W~~~virel--~~-----~---~~~~~~~~~ia~~l~p~i-s~~ev~~sL~~L~~~glikk 171 (271)
T TIGR02147 119 YRHWYNSVIREL--LG-----V---MPFADDPEELAKRCFPKI-SAEQVKESLDLLERLGLIKK 171 (271)
T ss_pred HHHHHHHHHHHH--hh-----c---CCCCCCHHHHHHHhCCCC-CHHHHHHHHHHHHHCCCeeE
Confidence 345555566666 32 2 234556889999988311 33668899999999998863
No 398
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=27.58 E-value=2.2e+02 Score=19.90 Aligned_cols=47 Identities=6% Similarity=0.006 Sum_probs=32.2
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhC---CCCCCcccHHHHHHHHHhcCccc
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQ---IHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g---~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+++=|.-+|.. +|+.=-||.+.+. .-..++..|+++|+-|...|++.
T Consensus 25 l~~~IL~~L~~--~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~ 74 (138)
T TIGR02719 25 LVPFLLLCLKD--WNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLIS 74 (138)
T ss_pred HHHHHHHHHcc--CCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEE
Confidence 44444555644 6777777766643 22235688999999999999886
No 399
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=27.45 E-value=80 Score=23.10 Aligned_cols=29 Identities=24% Similarity=0.366 Sum_probs=22.4
Q ss_pred CCCC-CCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844 58 HTKP-MTLNQLLGALQIHPTKTRCLHFLVCSLV 89 (97)
Q Consensus 58 ~~gp-~s~~ELA~~~g~~~~~~~~L~RlLR~La 89 (97)
.+.| +|+.+|++.++.++ .-+..++..|.
T Consensus 16 sg~pgls~~~La~~l~~~~---~~v~~~l~~L~ 45 (188)
T PRK00135 16 SGEEGLSLEQLAEILELEP---TEVQQLLEELQ 45 (188)
T ss_pred cCCCCCCHHHHHHHHCCCH---HHHHHHHHHHH
Confidence 4566 99999999999854 56777777664
No 400
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=27.38 E-value=85 Score=20.57 Aligned_cols=40 Identities=18% Similarity=0.270 Sum_probs=26.0
Q ss_pred HHHhhCCCCCCHHHHHHH-hCCCCCCcccHHHHHHHHHhcC
Q 041844 53 DIIHNHTKPMTLNQLLGA-LQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~-~g~~~~~~~~L~RlLR~Laa~g 92 (97)
+..-..+.+-.+.+++.+ +..+|.+...-..+||.+...|
T Consensus 70 ~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g 110 (146)
T PF03704_consen 70 EALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQG 110 (146)
T ss_dssp HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT
T ss_pred HHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCc
Confidence 433334444445555555 4568888899999999999887
No 401
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=27.23 E-value=95 Score=15.63 Aligned_cols=13 Identities=23% Similarity=0.319 Sum_probs=7.1
Q ss_pred CCCHHHHHHHhCC
Q 041844 61 PMTLNQLLGALQI 73 (97)
Q Consensus 61 p~s~~ELA~~~g~ 73 (97)
.+|..++|..+|.
T Consensus 12 ~~s~~~~a~~~~~ 24 (58)
T cd00093 12 GLTQEELAEKLGV 24 (58)
T ss_pred CCCHHHHHHHHCC
Confidence 3455555555554
No 402
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=27.17 E-value=66 Score=23.50 Aligned_cols=34 Identities=12% Similarity=0.139 Sum_probs=28.8
Q ss_pred CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|..+ |=.|||+..|++- ..+++-|..|+..|++.
T Consensus 26 G~~LPsE~eL~~~~~VSR---~TvR~Al~~L~~eGli~ 60 (240)
T PRK09764 26 GDALPTESALQTEFGVSR---VTVRQALRQLVEQQILE 60 (240)
T ss_pred CCcCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 3456 7799999999943 78999999999999875
No 403
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=26.80 E-value=43 Score=24.92 Aligned_cols=22 Identities=5% Similarity=0.152 Sum_probs=14.1
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.|+.|||+.+|++. ..+.|+|+
T Consensus 2 ~Ti~dIA~~agVS~---~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVST---TTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCH---HHHHHHHc
Confidence 47788888888732 44555543
No 404
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=26.72 E-value=67 Score=23.38 Aligned_cols=31 Identities=19% Similarity=0.212 Sum_probs=27.3
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
-|=.|||+..|+.- ..++|-|..|+..|++.
T Consensus 34 PsE~eLa~~~~VSR---~TvR~Al~~L~~eGli~ 64 (241)
T PRK11402 34 PTENELCTQYNVSR---ITIRKAISDLVADGVLI 64 (241)
T ss_pred cCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 47899999999943 78999999999999875
No 405
>PLN03239 histone acetyltransferase; Provisional
Probab=26.46 E-value=1.3e+02 Score=24.56 Aligned_cols=48 Identities=10% Similarity=0.216 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 34 ~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+||....++.. .+. . ..+..+|+.+|+..||+.+ .-|+-.|..+|++.
T Consensus 265 ~YW~~~il~~L--~~~-----~-~~~~~~si~dis~~Tgi~~------~DIi~tL~~l~~l~ 312 (351)
T PLN03239 265 PYWGSTIVDFL--LNH-----S-GNDSSLSIMDIAKKTSIMA------EDIVFALNQLGILK 312 (351)
T ss_pred HHHHHHHHHHH--Hhc-----c-CCCCCccHHHHHHHhCCCH------HHHHHHHHHCCcEE
Confidence 66666666555 321 1 1124799999999999954 33777788888764
No 406
>TIGR02216 phage_TIGR02216 phage conserved hypothetical protein. This model describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA.
Probab=26.35 E-value=91 Score=19.13 Aligned_cols=27 Identities=22% Similarity=0.279 Sum_probs=18.8
Q ss_pred CCCHHHHHHHhCC------CCCCcccHHHHHHH
Q 041844 61 PMTLNQLLGALQI------HPTKTRCLHFLVCS 87 (97)
Q Consensus 61 p~s~~ELA~~~g~------~~~~~~~L~RlLR~ 87 (97)
.+|..||+..+|. .|-+-..|.++||.
T Consensus 24 ~lTP~EL~~~lg~~~~~~~apl~Ra~Ld~Lm~~ 56 (60)
T TIGR02216 24 RLTPAELAAAIAGLQGAAAAPLDRAALDALLAA 56 (60)
T ss_pred hCCHHHHHHHhCCccCCCCCCCCHHHHHHHHHH
Confidence 4789999999983 22244568888874
No 407
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.30 E-value=64 Score=21.56 Aligned_cols=16 Identities=19% Similarity=0.287 Sum_probs=14.0
Q ss_pred CCCCHHHHHHHhCCCC
Q 041844 60 KPMTLNQLLGALQIHP 75 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~ 75 (97)
..+|..|||+.+|+++
T Consensus 124 ~~~s~~EIA~~lgis~ 139 (163)
T PRK07037 124 HGETQKDIARELGVSP 139 (163)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5789999999999954
No 408
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=26.14 E-value=3.1e+02 Score=21.34 Aligned_cols=31 Identities=10% Similarity=-0.026 Sum_probs=26.2
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHH
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSL 88 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~L 88 (97)
.||..+..|+.+.+|+++.++..+.+.+..+
T Consensus 396 ~Ggs~~~~ell~~~g~d~~~~~~~~~~~~~~ 426 (427)
T cd06459 396 AGGSKSPLELLKKAGVDLTSPDFWEEAIDVI 426 (427)
T ss_pred ccCCCCHHHHHHHcCcCCCChHHHHHHHHhh
Confidence 4778999999999999888888888877653
No 409
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=25.87 E-value=85 Score=23.32 Aligned_cols=29 Identities=14% Similarity=0.217 Sum_probs=19.2
Q ss_pred CCCHHHHHHHhCC-------------CCCCcccHHHHHHHHHh
Q 041844 61 PMTLNQLLGALQI-------------HPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 61 p~s~~ELA~~~g~-------------~~~~~~~L~RlLR~Laa 90 (97)
.+|-.|||..+|+ || ..+.+.||+|+|..
T Consensus 18 GitQ~dLA~~aGVSQ~~IArlE~G~vdP-rlSt~k~Il~aL~e 59 (187)
T COG3620 18 GITQKDLARRAGVSQPYIARLEAGKVDP-RLSTVKRILEALEE 59 (187)
T ss_pred CCCHHHHHHHcCccHHHHHHHhcCCCCc-cHHHHHHHHHHHHH
Confidence 3455666666653 45 55669999999874
No 410
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=25.83 E-value=51 Score=20.11 Aligned_cols=30 Identities=13% Similarity=0.161 Sum_probs=23.8
Q ss_pred CHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844 63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92 (97)
Q Consensus 63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g 92 (97)
+++.+|.+.|....+.+.+.+++..|+.-+
T Consensus 3 AvD~la~~~g~~i~~~~~~k~vsaalv~g~ 32 (93)
T PF11761_consen 3 AVDLLARELGWRIENREAVKRVSAALVNGE 32 (93)
T ss_pred CcchhhhhCCCEEcCHHHHHHHHHHHHCCC
Confidence 467889999986556789999999998643
No 411
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=25.56 E-value=58 Score=25.59 Aligned_cols=23 Identities=17% Similarity=0.252 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHH
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
+.++|+.|||..+|+.. ..+++|
T Consensus 280 ~~~~Tl~eIa~~lgvS~---eRVrQI 302 (324)
T PRK07921 280 GQPRTLDQIGKLFGLSR---ERVRQI 302 (324)
T ss_pred CCCcCHHHHHHHHCCCH---HHHHHH
Confidence 36899999999999955 666665
No 412
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=25.54 E-value=66 Score=25.00 Aligned_cols=23 Identities=22% Similarity=0.348 Sum_probs=18.3
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHH
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
+.++|+.|||+.+|+.. ..++++
T Consensus 274 ~~~~Tl~EIa~~lgiS~---erVRqi 296 (317)
T PRK07405 274 GQPLTLAKIGERLNISR---ERVRQI 296 (317)
T ss_pred CCCcCHHHHHHHHCcCH---HHHHHH
Confidence 37899999999999954 555555
No 413
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=25.27 E-value=71 Score=18.89 Aligned_cols=23 Identities=9% Similarity=0.060 Sum_probs=17.6
Q ss_pred CCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 61 PMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 61 p~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.++..|-|..+|+.+ ..|.|+-|
T Consensus 15 hlp~~eAA~~Lgv~~---T~LKr~CR 37 (52)
T PF02042_consen 15 HLPIKEAAKELGVSV---TTLKRRCR 37 (52)
T ss_pred CCCHHHHHHHhCCCH---HHHHHHHH
Confidence 467888888888844 67888877
No 414
>PRK04158 transcriptional repressor CodY; Validated
Probab=25.12 E-value=25 Score=27.31 Aligned_cols=45 Identities=11% Similarity=0.143 Sum_probs=35.8
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccccC
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR 97 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e~ 97 (97)
-||+-|.-..|-+.++.||.++|+-- +.+---||-|.+.|+++.|
T Consensus 190 hIf~eL~g~EG~lvASkiADrvgITR---SVIVNALRK~ESAGvIESr 234 (256)
T PRK04158 190 HIFEELDGNEGLLVASKIADRVGITR---SVIVNALRKLESAGVIESR 234 (256)
T ss_pred HHHHhcCCCcceEEeeecccccCCch---hhhhhhhhhhhcccceeec
Confidence 45666644448899999999999844 6788899999999998754
No 415
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=24.99 E-value=1e+02 Score=24.06 Aligned_cols=36 Identities=14% Similarity=0.217 Sum_probs=30.8
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
+.......|||..+|+.+ ..+.--++-|+.-|++.+
T Consensus 22 ~qp~v~q~eIA~~lgiT~---QaVsehiK~Lv~eG~i~~ 57 (260)
T COG1497 22 RQPRVKQKEIAKKLGITL---QAVSEHIKELVKEGLIEK 57 (260)
T ss_pred hCCCCCHHHHHHHcCCCH---HHHHHHHHHHHhccceee
Confidence 346789999999999955 889999999999998764
No 416
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=24.96 E-value=63 Score=24.58 Aligned_cols=24 Identities=13% Similarity=0.127 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.++|..|||+.+|+++ ..++++.+
T Consensus 247 ~~~Tl~EIA~~lgvS~---~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSA---ERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCH---HHHHHHHH
Confidence 5899999999999955 67777665
No 417
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=24.84 E-value=1.9e+02 Score=18.35 Aligned_cols=35 Identities=23% Similarity=0.151 Sum_probs=22.6
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
.+.+.+..+|...++.++ +...+..+.|.+...|+
T Consensus 24 ~g~~~~~~~l~~~~~~~~-~~~~~~~l~~~a~~~Gl 58 (136)
T cd02418 24 YGKNYSLAKLRELAGTDR-EGTSLLGLVKAAEKLGF 58 (136)
T ss_pred hCCCCCHHHHHHHcCCCC-CCcCHHHHHHHHHHCCC
Confidence 346778888887776543 23456666666667764
No 418
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=24.82 E-value=48 Score=24.85 Aligned_cols=13 Identities=8% Similarity=0.235 Sum_probs=9.1
Q ss_pred CCHHHHHHHhCCC
Q 041844 62 MTLNQLLGALQIH 74 (97)
Q Consensus 62 ~s~~ELA~~~g~~ 74 (97)
.|+.|||+..|++
T Consensus 2 ~ti~dIA~~aGVS 14 (346)
T PRK10401 2 ITIRDVARQAGVS 14 (346)
T ss_pred CCHHHHHHHhCCC
Confidence 4677777777763
No 419
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=24.70 E-value=60 Score=22.21 Aligned_cols=33 Identities=21% Similarity=0.198 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.-+|.+=|.+++.++. .+-++.||.|...|++.
T Consensus 59 k~it~svl~dRlkIng---sLAr~alr~L~~kG~Ik 91 (110)
T KOG1767|consen 59 KLITPSVLSDRLKING---SLARAALRELSNKGVIK 91 (110)
T ss_pred eeecHHHhhhhhhhch---HHHHHHHHHHHhcchHH
Confidence 5578999999999954 88899999999999875
No 420
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=24.60 E-value=99 Score=19.04 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=27.2
Q ss_pred HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
|.+..+++++++.+|.+.+..-..++..++--|--|++.|+++
T Consensus 12 dy~~~~g~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~ 54 (70)
T PF07848_consen 12 DYLRPRGGWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLE 54 (70)
T ss_dssp HHCCTTTS-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEE
T ss_pred HHhccCCCceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCcee
Confidence 5566667888887777765532224467777777778888775
No 421
>PF10376 Mei5: Double-strand recombination repair protein ; InterPro: IPR018468 Mei5 is one of a pair of meiosis-specific proteins which facilitate the loading of Dmc1 on to Rad51 on DNA at double-strand breaks during recombination. Recombination is carried out by a large protein complex based around the two RecA homologues, Rad51 and Dmc1 []. This complex may play both a catalytic and a structural role in the interaction between homologous chromosomes during meiosis. Mei5 is seen to contain a coiled-coli region.
Probab=24.33 E-value=1.1e+02 Score=22.98 Aligned_cols=36 Identities=17% Similarity=0.235 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHhcChhHHHhh-CCCCCCHHHHHHHhCCCC
Q 041844 36 INSMSLKCVKLIQVGIPDIIHN-HTKPMTLNQLLGALQIHP 75 (97)
Q Consensus 36 ~~s~aL~~a~~veLgI~D~La~-~~gp~s~~ELA~~~g~~~ 75 (97)
|.+.+-.++ .+|. ..+.. .+...|..||...+|+|+
T Consensus 179 wr~~~q~~l--~eL~--~~~~~~e~~~~TM~eL~~~l~ID~ 215 (221)
T PF10376_consen 179 WRSASQEAL--YELQ--SEMSEEEGEKFTMGELIKRLGIDY 215 (221)
T ss_pred HHHHHHHHH--HHHH--HHHhhccccCccHHHHHHHhCCCc
Confidence 445555666 6554 55666 567899999999999965
No 422
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=24.20 E-value=68 Score=23.13 Aligned_cols=23 Identities=22% Similarity=0.107 Sum_probs=18.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLV 85 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlL 85 (97)
..+|..|||+.+|+++ ..++++.
T Consensus 198 ~~~t~~eIA~~lgis~---~~V~~~~ 220 (231)
T TIGR02885 198 KDKTQTEVANMLGISQ---VQVSRLE 220 (231)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHH
Confidence 6789999999999965 6666655
No 423
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=24.04 E-value=2e+02 Score=18.17 Aligned_cols=35 Identities=20% Similarity=0.188 Sum_probs=23.9
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
++.+.+..+|...++.++ +...+..+.|.+...|+
T Consensus 24 ~g~~~~~~~l~~~~~~~~-~~~~~~~l~~~a~~~Gl 58 (127)
T cd02419 24 HGHHVDLASLRQRFPVSL-KGATLADLIDIAQQLGL 58 (127)
T ss_pred cCCCCCHHHHHHHcCCCC-CCcCHHHHHHHHHHCCC
Confidence 457888888888777643 33556667777767774
No 424
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=23.71 E-value=3.4e+02 Score=20.73 Aligned_cols=34 Identities=21% Similarity=0.226 Sum_probs=28.6
Q ss_pred CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc-Ccc
Q 041844 58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS-GFF 94 (97)
Q Consensus 58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~-gif 94 (97)
-|+-+|..|||-.+++++ ..+++-++.+-.. |++
T Consensus 102 QgglLT~~Dla~LL~~S~---~TI~~~i~~yq~e~g~v 136 (220)
T PF07900_consen 102 QGGLLTQEDLAMLLGISP---RTISKDIKEYQKEHGVV 136 (220)
T ss_pred cCCcccHHHHHHHHCCCH---HHHHHHHHHHHHHcCce
Confidence 468899999999999965 8999999988876 643
No 425
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=23.58 E-value=50 Score=24.52 Aligned_cols=13 Identities=15% Similarity=0.138 Sum_probs=9.1
Q ss_pred CCHHHHHHHhCCC
Q 041844 62 MTLNQLLGALQIH 74 (97)
Q Consensus 62 ~s~~ELA~~~g~~ 74 (97)
.|+.|||+..|+.
T Consensus 2 ~ti~dIA~~agVS 14 (327)
T PRK10339 2 ATLKDIAIEAGVS 14 (327)
T ss_pred CCHHHHHHHhCCC
Confidence 3677788877763
No 426
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=23.50 E-value=78 Score=24.13 Aligned_cols=25 Identities=16% Similarity=0.282 Sum_probs=19.5
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
..++|..|||+.+|++. ..+++++.
T Consensus 267 ~~~~Tl~EIa~~lgiS~---erVrq~~~ 291 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSR---ERVRQIEA 291 (298)
T ss_pred CCCcCHHHHHHHHCcCH---HHHHHHHH
Confidence 37999999999999954 66666543
No 427
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=23.43 E-value=2e+02 Score=18.07 Aligned_cols=35 Identities=14% Similarity=0.025 Sum_probs=22.4
Q ss_pred CC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844 58 HT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 58 ~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi 93 (97)
.+ .+.+..+|...++.++ +...+..+.|.+...|+
T Consensus 24 ~g~~~~~~~~l~~~~~~~~-~~~s~~~l~~~a~~~Gl 59 (129)
T cd02423 24 YGGINITEQEVLKLMLIRS-EGFSMLDLKRYAEALGL 59 (129)
T ss_pred cCCCCCCHHHHHHHhCccc-CCcCHHHHHHHHHHCCC
Confidence 45 6788888888877643 22445556666666664
No 428
>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=23.10 E-value=1.5e+02 Score=20.67 Aligned_cols=45 Identities=16% Similarity=0.260 Sum_probs=34.9
Q ss_pred hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844 51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e 96 (97)
|.+.|.....|-|+.+|..-++-. -.-..+.+.|..|+..|-+.+
T Consensus 6 Il~y~~~qNRPys~~di~~nL~~~-~~K~~v~k~Ld~L~~~g~i~~ 50 (169)
T PF07106_consen 6 ILEYMKEQNRPYSAQDIFDNLHNK-VGKTAVQKALDSLVEEGKIVE 50 (169)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHhh-ccHHHHHHHHHHHHhCCCeee
Confidence 567776667999999999998631 133689999999999997654
No 429
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=22.78 E-value=72 Score=22.39 Aligned_cols=29 Identities=14% Similarity=0.140 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCC--CCcc-----cHHHHHHHHHhcC
Q 041844 64 LNQLLGALQIHP--TKTR-----CLHFLVCSLVRSG 92 (97)
Q Consensus 64 ~~ELA~~~g~~~--~~~~-----~L~RlLR~Laa~g 92 (97)
-.|||.++|+.. ++.. +.+.+|+-|+.+|
T Consensus 88 RkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~kLA~NG 123 (127)
T PF12200_consen 88 RKELAKELGYTGDYNDSASMNIWLHKQVMQKLAENG 123 (127)
T ss_dssp HHHHHHHHT---SS-HHHHHHHHHHHHHHHHHGGGS
T ss_pred HHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHhC
Confidence 679999999732 1211 5678999999887
No 430
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.70 E-value=90 Score=22.74 Aligned_cols=31 Identities=19% Similarity=0.280 Sum_probs=27.2
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
=|=.|||+..|++- ..++|-|..|+..|++.
T Consensus 36 PsE~eLa~~~~VSR---~TVR~Al~~L~~eGli~ 66 (241)
T PRK10079 36 PAEQQLAARYEVNR---HTLRRAIDQLVEKGWVQ 66 (241)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence 37889999999944 78999999999999875
No 431
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=22.59 E-value=55 Score=24.49 Aligned_cols=31 Identities=3% Similarity=0.036 Sum_probs=17.7
Q ss_pred CHHHHHHHhCCCC------------CCcccHHHHHHHHHhcCc
Q 041844 63 TLNQLLGALQIHP------------TKTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 63 s~~ELA~~~g~~~------------~~~~~L~RlLR~Laa~gi 93 (97)
|+.|||+..|++. ..++.=.||++....+|+
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY 45 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSY 45 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCC
Confidence 6677777777531 123445566666666654
No 432
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=22.36 E-value=86 Score=18.59 Aligned_cols=15 Identities=7% Similarity=0.257 Sum_probs=12.6
Q ss_pred CCCCHHHHHHHhCCC
Q 041844 60 KPMTLNQLLGALQIH 74 (97)
Q Consensus 60 gp~s~~ELA~~~g~~ 74 (97)
...+..|||+.+|++
T Consensus 12 ~G~~~~eIA~~Lg~~ 26 (58)
T PF06056_consen 12 QGWSIKEIAEELGVP 26 (58)
T ss_pred cCCCHHHHHHHHCCC
Confidence 467899999999984
No 433
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=22.07 E-value=1e+02 Score=21.85 Aligned_cols=24 Identities=13% Similarity=0.120 Sum_probs=19.0
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
+..|..+||..+|+.. ..++|++.
T Consensus 171 ~g~s~~~iak~lgis~---~Tv~r~~k 194 (200)
T PRK13413 171 KGTSKSEIARKLGVSR---TTLARFLK 194 (200)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 3579999999999944 67777765
No 434
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=21.89 E-value=92 Score=22.90 Aligned_cols=26 Identities=15% Similarity=0.189 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSL 88 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~L 88 (97)
..+|..|||+.+|+.. ..++|+.+.+
T Consensus 198 ~~~t~~EIA~~lgis~---~~V~q~~~~~ 223 (231)
T PRK12427 198 HEMSLKEIALVLDLTE---ARICQLNKKI 223 (231)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 6899999999999954 6677665543
No 435
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.80 E-value=1.8e+02 Score=22.46 Aligned_cols=44 Identities=20% Similarity=0.299 Sum_probs=34.7
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
+.+|...+..+ ...+++|+.+-++.+ ...++=.+|.|-+.+..+
T Consensus 103 R~~Iy~~i~~n-PG~~lsEl~~nl~i~---R~TlRyhlriLe~~~li~ 146 (240)
T COG3398 103 RDGIYNYIKPN-PGFSLSELRANLYIN---RSTLRYHLRILESNPLIE 146 (240)
T ss_pred HHHHHHHhccC-CCccHHHHHHhcCCC---hHHHHHHHHHHHhCcchh
Confidence 45666666553 579999999999994 488999999999888764
No 436
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=21.78 E-value=1.1e+02 Score=22.00 Aligned_cols=40 Identities=5% Similarity=-0.022 Sum_probs=27.8
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCC-cccHHHHHHHHH
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTK-TRCLHFLVCSLV 89 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~-~~~L~RlLR~La 89 (97)
-|..|...+++ ..|-.|||+++++.+.- ...+.||++-|-
T Consensus 141 RE~eVL~lla~---G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 141 TESSMLRMWMA---GQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred HHHHHHHHHHc---CCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 56777777754 78999999999985410 123667777654
No 437
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=21.73 E-value=96 Score=20.62 Aligned_cols=16 Identities=6% Similarity=0.191 Sum_probs=14.1
Q ss_pred CCCCHHHHHHHhCCCC
Q 041844 60 KPMTLNQLLGALQIHP 75 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~ 75 (97)
..+|..|||+.+|+.+
T Consensus 140 ~~~~~~eIA~~lgis~ 155 (179)
T PRK11924 140 EGLSYREIAEILGVPV 155 (179)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5789999999999965
No 438
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI 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 Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=21.72 E-value=67 Score=23.72 Aligned_cols=21 Identities=5% Similarity=0.151 Sum_probs=13.6
Q ss_pred CCHHHHHHHhCCCCCCcccHHHHH
Q 041844 62 MTLNQLLGALQIHPTKTRCLHFLV 85 (97)
Q Consensus 62 ~s~~ELA~~~g~~~~~~~~L~RlL 85 (97)
.|+.|||+..|++. ..+.|+|
T Consensus 2 ~ti~dIA~~agVS~---sTVSr~L 22 (311)
T TIGR02405 2 LTIKDIARLAGVGK---STVSRVL 22 (311)
T ss_pred CcHHHHHHHhCCCH---HHHHHHh
Confidence 47788888888743 4555554
No 439
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=21.48 E-value=91 Score=22.75 Aligned_cols=23 Identities=13% Similarity=0.287 Sum_probs=18.1
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHH
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
..++|..|||..+|+++ ..++++
T Consensus 194 ~~~~t~~EIA~~lgis~---~~V~q~ 216 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTR---ERIRQI 216 (238)
T ss_pred CCCccHHHHHHHHCCCH---HHHHHH
Confidence 37899999999999954 555554
No 440
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=21.42 E-value=1.1e+02 Score=23.07 Aligned_cols=40 Identities=10% Similarity=0.110 Sum_probs=26.4
Q ss_pred HhcChhHHHhhCCCCCCHHHHHHHhCCCCCC-cccHHHHHHHHH
Q 041844 47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTK-TRCLHFLVCSLV 89 (97)
Q Consensus 47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~-~~~L~RlLR~La 89 (97)
-|..|+..+++ ..|..|||+.+++++.- ...+.|+|+-|-
T Consensus 137 RErEVLrLLAq---GkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 137 TERHLLKLIAS---GYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred HHHHHHHHHHC---CCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 46667777754 78999999999986511 123566666443
No 441
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=21.38 E-value=85 Score=23.21 Aligned_cols=24 Identities=13% Similarity=-0.018 Sum_probs=18.9
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.++|..|||..+|+.+ ..++++.+
T Consensus 221 ~~~t~~eIA~~lgis~---~~V~~~~~ 244 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQ---AQVSRLEK 244 (254)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 6789999999999954 66666644
No 442
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=21.30 E-value=99 Score=25.79 Aligned_cols=36 Identities=14% Similarity=0.217 Sum_probs=26.0
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHH
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSL 88 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~L 88 (97)
+..|.+.|.+ +++|..+||+.+|++. ..++|=+..+
T Consensus 6 ~~~iL~~L~~--~~~t~~~LA~~l~VS~---RTIr~dI~~i 41 (584)
T PRK09863 6 ELKIVDLLEQ--QDRSGGELAQQLGVSR---RTIVRDIAYI 41 (584)
T ss_pred HHHHHHHHHc--CCCCHHHHHHHhCCCH---HHHHHHHHHH
Confidence 3456667743 7999999999999954 6666655543
No 443
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=21.18 E-value=2.7e+02 Score=19.91 Aligned_cols=36 Identities=17% Similarity=0.303 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCC------CC-----CcccHHHHHHHHHhcCccc
Q 041844 60 KPMTLNQLLGALQIH------PT-----KTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 60 gp~s~~ELA~~~g~~------~~-----~~~~L~RlLR~Laa~gif~ 95 (97)
+|+.+..|....|.. |+ .-..++.+|+.|...|+++
T Consensus 66 gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVe 112 (150)
T PRK09333 66 GPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVE 112 (150)
T ss_pred CCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCee
Confidence 699999999999861 21 1234999999999999986
No 444
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=21.14 E-value=1.3e+02 Score=24.80 Aligned_cols=45 Identities=11% Similarity=0.236 Sum_probs=27.6
Q ss_pred hHHHHHHHHHHHHHhcChhHHHhhCCCCCC-HHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844 34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMT-LNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN 95 (97)
Q Consensus 34 ~~~~s~aL~~a~~veLgI~D~La~~~gp~s-~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~ 95 (97)
.||.-++++.. ++ ++++.+ +.|||..+|..+. -++-.|.+.+++.
T Consensus 314 ~YW~~~v~~~L--~k---------~~~~~~~I~~Is~~TgM~~d------DVI~tLe~L~il~ 359 (395)
T COG5027 314 AYWSEIVAKLL--LK---------MDKEITDINEISKETGMSTD------DVIHTLEALNILR 359 (395)
T ss_pred HHHHHHHHHHH--Hh---------cCcccccHHHHHhhhCCchh------hHHHHHHHhccch
Confidence 55555555555 44 344444 9999999998542 2555566666654
No 445
>PF15467 SGIII: Secretogranin-3
Probab=21.03 E-value=1.1e+02 Score=25.41 Aligned_cols=45 Identities=18% Similarity=0.369 Sum_probs=34.8
Q ss_pred hHHHhhC-CCCCCHHHHHHHhCC---CCCCcccHHHHHHHHHhcCcccc
Q 041844 52 PDIIHNH-TKPMTLNQLLGALQI---HPTKTRCLHFLVCSLVRSGFFNL 96 (97)
Q Consensus 52 ~D~La~~-~gp~s~~ELA~~~g~---~~~~~~~L~RlLR~Laa~gif~e 96 (97)
||-++.- |.|+|+.+|..+.-. ...|.....||.--|-..|++++
T Consensus 120 PdglhQlDGTPLTAeDIVqKIAtrIYEEnDRGVFDkIVSKLLnLGLITe 168 (453)
T PF15467_consen 120 PDGLHQLDGTPLTAEDIVQKIATRIYEENDRGVFDKIVSKLLNLGLITE 168 (453)
T ss_pred chhhhccCCCCCcHHHHHHHHHHHHHhcccchHHHHHHHHHHhccccch
Confidence 5566553 589999999998653 23366789999999999999876
No 446
>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.70 E-value=90 Score=19.56 Aligned_cols=17 Identities=24% Similarity=0.571 Sum_probs=15.2
Q ss_pred CcccHHHHHHHHHhcCc
Q 041844 77 KTRCLHFLVCSLVRSGF 93 (97)
Q Consensus 77 ~~~~L~RlLR~Laa~gi 93 (97)
.|.+|++|-|.|+.+|+
T Consensus 11 RpGLL~~i~~~l~~~~l 27 (75)
T cd04897 11 RPKLLFDVVCTLTDMDY 27 (75)
T ss_pred cCcHHHHHHHHHHhCCe
Confidence 56899999999999986
No 447
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=20.65 E-value=74 Score=20.76 Aligned_cols=14 Identities=36% Similarity=0.584 Sum_probs=10.3
Q ss_pred CCHHHHHHHhCCCC
Q 041844 62 MTLNQLLGALQIHP 75 (97)
Q Consensus 62 ~s~~ELA~~~g~~~ 75 (97)
+|+.|+|+.+|+++
T Consensus 1 ~~i~eva~~~gvs~ 14 (108)
T cd04773 1 MTIGELAHLLGVPP 14 (108)
T ss_pred CCHHHHHHHHCcCH
Confidence 46788888888744
No 448
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=20.64 E-value=69 Score=21.43 Aligned_cols=24 Identities=13% Similarity=0.188 Sum_probs=14.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
...|++|||+.+|++. ..++-.++
T Consensus 32 eDlSlsEIAe~~~iSR---qaV~d~ik 55 (101)
T PF04297_consen 32 EDLSLSEIAEELGISR---QAVYDSIK 55 (101)
T ss_dssp S---HHHHHHHCTS-H---HHHHHHHH
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 6799999999999943 55554444
No 449
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=20.55 E-value=1e+02 Score=17.67 Aligned_cols=37 Identities=11% Similarity=0.043 Sum_probs=26.9
Q ss_pred hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844 48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90 (97)
Q Consensus 48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa 90 (97)
++.+|..+.+.+ |...-|+.+++++ +.+.|-++.|..
T Consensus 3 ~l~~f~~v~~~g---s~~~AA~~l~is~---~~vs~~i~~LE~ 39 (60)
T PF00126_consen 3 QLRYFLAVAETG---SISAAAEELGISQ---SAVSRQIKQLEE 39 (60)
T ss_dssp HHHHHHHHHHHS---SHHHHHHHCTSSH---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---CHHHHHHHhhccc---hHHHHHHHHHHH
Confidence 455667776632 7888889999954 788888887753
No 450
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=20.51 E-value=1.2e+02 Score=26.04 Aligned_cols=32 Identities=9% Similarity=0.222 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif 94 (97)
.|-++.||++.++.++ .....+|+.|+..|.+
T Consensus 505 ~p~~~~~~~~~l~~~~---~~~~~~l~~l~~~g~l 536 (614)
T PRK10512 505 EPWWVRDLAKETGTDE---QAMRLTLRQAAQQGII 536 (614)
T ss_pred CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCE
Confidence 7889999999999844 7889999999998854
No 451
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.44 E-value=90 Score=19.53 Aligned_cols=14 Identities=14% Similarity=0.230 Sum_probs=9.9
Q ss_pred CCHHHHHHHhCCCC
Q 041844 62 MTLNQLLGALQIHP 75 (97)
Q Consensus 62 ~s~~ELA~~~g~~~ 75 (97)
+|+.|+|+.+|+++
T Consensus 1 ~~~~eva~~~gi~~ 14 (100)
T cd00592 1 YTIGEVAKLLGVSV 14 (100)
T ss_pred CCHHHHHHHHCcCH
Confidence 36778888888754
No 452
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=20.39 E-value=90 Score=23.85 Aligned_cols=24 Identities=21% Similarity=0.138 Sum_probs=18.7
Q ss_pred CCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844 60 KPMTLNQLLGALQIHPTKTRCLHFLVC 86 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~~~~~~L~RlLR 86 (97)
.++|..|||+.+|+++ ..++++++
T Consensus 244 ~~~t~~EIa~~lgvs~---~~V~q~~~ 267 (289)
T PRK07500 244 DGATLEALGEELGISK---ERVRQIEA 267 (289)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 6899999999999954 55655543
No 453
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.34 E-value=1.1e+02 Score=21.04 Aligned_cols=16 Identities=25% Similarity=0.256 Sum_probs=14.1
Q ss_pred CCCCHHHHHHHhCCCC
Q 041844 60 KPMTLNQLLGALQIHP 75 (97)
Q Consensus 60 gp~s~~ELA~~~g~~~ 75 (97)
..+|..|||+.+|+++
T Consensus 142 ~g~s~~EIA~~lgis~ 157 (178)
T PRK12529 142 DGMKQKDIAQALDIAL 157 (178)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 6789999999999954
No 454
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.33 E-value=1.9e+02 Score=19.41 Aligned_cols=25 Identities=16% Similarity=0.347 Sum_probs=20.3
Q ss_pred ChhHHHhhCCCCCCHHHHHHHhCCC
Q 041844 50 GIPDIIHNHTKPMTLNQLLGALQIH 74 (97)
Q Consensus 50 gI~D~La~~~gp~s~~ELA~~~g~~ 74 (97)
+|+..|-..+.|.|+.||...++..
T Consensus 7 kii~lL~e~~eplt~~ei~~~~~~~ 31 (97)
T COG3357 7 KIISLLLESDEPLTVAEIFELLNGE 31 (97)
T ss_pred HHHHHHHcCCCcchHHHHHHHHcCC
Confidence 4666776667899999999999874
No 455
>PRK05949 RNA polymerase sigma factor; Validated
Probab=20.20 E-value=97 Score=24.29 Aligned_cols=23 Identities=17% Similarity=0.226 Sum_probs=17.5
Q ss_pred CCCCCHHHHHHHhCCCCCCcccHHHH
Q 041844 59 TKPMTLNQLLGALQIHPTKTRCLHFL 84 (97)
Q Consensus 59 ~gp~s~~ELA~~~g~~~~~~~~L~Rl 84 (97)
+.++|..|||+.+|+.. ..++++
T Consensus 284 ~e~~Tl~EIa~~lgiS~---erVrq~ 306 (327)
T PRK05949 284 GKELSLAKVGERLNLSR---ERVRQL 306 (327)
T ss_pred CCCCCHHHHHHHHCcCH---HHHHHH
Confidence 37899999999999954 444444
Done!