Query 045905
Match_columns 128
No_of_seqs 133 out of 857
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 06:44:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045905.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045905hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3178 Hydroxyindole-O-methyl 99.5 1.9E-13 4.1E-18 107.6 7.5 108 3-119 41-151 (342)
2 TIGR02716 C20_methyl_CrtF C-20 98.9 2.2E-09 4.7E-14 83.5 6.8 85 1-102 24-112 (306)
3 PF00891 Methyltransf_2: O-met 98.9 8.8E-10 1.9E-14 82.8 4.1 71 48-119 3-74 (241)
4 PF08100 Dimerisation: Dimeris 98.1 1.6E-06 3.6E-11 50.9 2.3 28 1-32 23-51 (51)
5 PF13463 HTH_27: Winged helix 97.2 0.00064 1.4E-08 41.1 4.2 50 1-57 19-68 (68)
6 smart00346 HTH_ICLR helix_turn 96.7 0.003 6.4E-08 40.2 4.1 46 1-58 21-66 (91)
7 PF09339 HTH_IclR: IclR helix- 96.7 0.0011 2.4E-08 38.5 1.8 33 1-40 19-51 (52)
8 COG1414 IclR Transcriptional r 96.6 0.0032 6.9E-08 47.9 4.1 49 1-61 20-68 (246)
9 PRK15090 DNA-binding transcrip 96.5 0.0044 9.6E-08 47.1 4.5 49 1-61 29-77 (257)
10 PF02082 Rrf2: Transcriptional 96.4 0.0031 6.7E-08 40.0 2.7 45 1-56 26-70 (83)
11 cd00092 HTH_CRP helix_turn_hel 96.2 0.0071 1.5E-07 36.1 3.6 42 1-55 26-67 (67)
12 smart00347 HTH_MARR helix_turn 96.2 0.013 2.7E-07 37.3 4.8 56 1-63 25-80 (101)
13 PRK09834 DNA-binding transcrip 96.2 0.0084 1.8E-07 45.8 4.6 50 1-62 27-76 (263)
14 smart00419 HTH_CRP helix_turn_ 96.2 0.0092 2E-07 33.2 3.6 33 1-40 9-41 (48)
15 PRK11569 transcriptional repre 96.1 0.0087 1.9E-07 46.0 4.4 48 1-60 44-91 (274)
16 smart00529 HTH_DTXR Helix-turn 96.1 0.012 2.6E-07 37.8 4.2 47 3-62 2-48 (96)
17 PRK10163 DNA-binding transcrip 96.0 0.011 2.3E-07 45.5 4.5 49 1-61 41-89 (271)
18 TIGR02431 pcaR_pcaU beta-ketoa 96.0 0.011 2.3E-07 44.7 4.2 47 1-61 25-71 (248)
19 TIGR02010 IscR iron-sulfur clu 95.8 0.014 3.1E-07 40.3 3.8 45 1-56 26-70 (135)
20 TIGR02337 HpaR homoprotocatech 95.7 0.027 5.8E-07 37.8 4.9 56 1-63 43-98 (118)
21 PRK03902 manganese transport t 95.7 0.023 4.9E-07 39.5 4.7 49 1-62 23-71 (142)
22 TIGR00738 rrf2_super rrf2 fami 95.5 0.02 4.4E-07 38.9 3.6 47 1-58 26-72 (132)
23 PF14947 HTH_45: Winged helix- 95.4 0.024 5.2E-07 35.6 3.4 47 2-62 21-67 (77)
24 PRK10857 DNA-binding transcrip 95.4 0.024 5.2E-07 40.8 3.8 45 1-56 26-70 (164)
25 PF01978 TrmB: Sugar-specific 95.2 0.02 4.4E-07 34.7 2.6 44 1-55 23-66 (68)
26 COG1959 Predicted transcriptio 95.1 0.032 6.9E-07 39.5 3.8 46 1-57 26-71 (150)
27 PRK11920 rirA iron-responsive 95.0 0.034 7.4E-07 39.4 3.7 46 1-57 25-70 (153)
28 PRK11512 DNA-binding transcrip 94.9 0.057 1.2E-06 37.4 4.6 56 1-63 55-110 (144)
29 cd00090 HTH_ARSR Arsenical Res 94.7 0.056 1.2E-06 32.1 3.7 49 1-60 21-69 (78)
30 TIGR02944 suf_reg_Xantho FeS a 94.7 0.036 7.8E-07 37.8 3.0 60 1-77 26-85 (130)
31 PRK03573 transcriptional regul 94.6 0.13 2.7E-06 35.5 5.7 56 1-63 47-102 (144)
32 PRK11050 manganese transport r 94.5 0.074 1.6E-06 37.6 4.4 49 1-62 52-100 (152)
33 PF01638 HxlR: HxlR-like helix 94.3 0.091 2E-06 33.7 4.2 54 2-62 20-74 (90)
34 TIGR01889 Staph_reg_Sar staphy 94.2 0.11 2.5E-06 34.4 4.7 56 1-63 44-99 (109)
35 PRK11014 transcriptional repre 94.1 0.069 1.5E-06 37.1 3.6 44 1-55 26-69 (141)
36 COG1321 TroR Mn-dependent tran 94.1 0.12 2.5E-06 36.9 4.7 50 1-63 25-74 (154)
37 PRK10870 transcriptional repre 93.9 0.13 2.8E-06 37.2 4.8 56 1-63 72-127 (176)
38 smart00418 HTH_ARSR helix_turn 93.6 0.15 3.3E-06 29.2 4.0 45 1-55 11-55 (66)
39 smart00550 Zalpha Z-DNA-bindin 93.6 0.13 2.9E-06 31.4 3.7 44 1-55 23-66 (68)
40 TIGR02702 SufR_cyano iron-sulf 93.2 0.18 3.9E-06 37.1 4.5 56 1-63 16-73 (203)
41 PF09012 FeoC: FeoC like trans 93.1 0.081 1.8E-06 32.3 2.2 34 1-41 15-48 (69)
42 COG4742 Predicted transcriptio 93.0 0.42 9.2E-06 36.9 6.5 49 1-63 27-75 (260)
43 TIGR01884 cas_HTH CRISPR locus 92.8 0.15 3.3E-06 37.4 3.8 46 1-57 158-203 (203)
44 PF12802 MarR_2: MarR family; 92.8 0.12 2.7E-06 30.2 2.6 35 1-42 22-56 (62)
45 PF13412 HTH_24: Winged helix- 92.7 0.16 3.4E-06 28.6 2.9 31 1-38 18-48 (48)
46 TIGR01610 phage_O_Nterm phage 92.7 0.2 4.4E-06 32.6 3.7 42 1-54 48-89 (95)
47 PRK14165 winged helix-turn-hel 92.6 0.25 5.4E-06 37.2 4.6 54 1-64 22-75 (217)
48 PF13601 HTH_34: Winged helix 92.5 0.22 4.7E-06 31.5 3.7 55 1-62 15-70 (80)
49 smart00345 HTH_GNTR helix_turn 91.7 0.38 8.2E-06 27.5 3.9 33 2-41 22-54 (60)
50 COG2345 Predicted transcriptio 91.6 0.41 9E-06 36.1 4.8 57 1-64 26-84 (218)
51 cd07377 WHTH_GntR Winged helix 91.3 0.38 8.2E-06 28.1 3.6 32 2-40 27-58 (66)
52 PF12840 HTH_20: Helix-turn-he 91.1 0.18 4E-06 29.8 2.1 34 1-41 25-58 (61)
53 COG3355 Predicted transcriptio 91.0 0.46 9.9E-06 32.9 4.1 35 1-42 43-77 (126)
54 PF07381 DUF1495: Winged helix 90.6 0.53 1.1E-05 30.7 4.0 52 1-62 26-88 (90)
55 smart00420 HTH_DEOR helix_turn 90.5 0.44 9.5E-06 26.5 3.2 34 1-41 15-48 (53)
56 COG1846 MarR Transcriptional r 90.4 0.48 1E-05 30.8 3.8 54 4-64 40-93 (126)
57 PF00325 Crp: Bacterial regula 90.4 0.29 6.2E-06 25.8 2.1 30 1-37 3-32 (32)
58 PF01047 MarR: MarR family; I 90.1 0.3 6.6E-06 28.3 2.3 34 1-41 18-51 (59)
59 PRK13777 transcriptional regul 88.6 1.1 2.4E-05 32.8 4.9 56 1-63 60-115 (185)
60 smart00344 HTH_ASNC helix_turn 88.2 0.67 1.5E-05 30.2 3.2 31 1-38 18-48 (108)
61 KOG2165 Anaphase-promoting com 88.2 0.68 1.5E-05 40.3 3.9 46 1-55 617-662 (765)
62 cd07153 Fur_like Ferric uptake 88.1 1 2.2E-05 29.7 4.1 48 1-54 17-66 (116)
63 COG1733 Predicted transcriptio 88.1 1.3 2.9E-05 30.1 4.7 52 3-61 39-91 (120)
64 PF13545 HTH_Crp_2: Crp-like h 87.3 1.2 2.6E-05 27.0 3.8 34 1-41 29-62 (76)
65 PRK10141 DNA-binding transcrip 86.9 3.3 7.3E-05 28.1 6.1 46 1-56 31-76 (117)
66 COG1378 Predicted transcriptio 86.9 1.4 3E-05 33.7 4.7 50 1-61 31-80 (247)
67 PF05732 RepL: Firmicute plasm 86.8 0.97 2.1E-05 32.5 3.6 44 1-57 76-119 (165)
68 PF01022 HTH_5: Bacterial regu 86.5 0.64 1.4E-05 26.1 2.0 30 2-38 17-46 (47)
69 PF03444 HrcA_DNA-bdg: Winged 86.3 2.1 4.5E-05 27.2 4.5 48 2-61 25-73 (78)
70 PF01325 Fe_dep_repress: Iron 86.3 0.98 2.1E-05 26.9 2.9 34 1-41 23-56 (60)
71 PRK09334 30S ribosomal protein 86.2 1.1 2.5E-05 28.9 3.3 34 1-41 42-75 (86)
72 PF13814 Replic_Relax: Replica 86.0 2 4.3E-05 30.7 4.9 59 1-63 10-72 (191)
73 PF01726 LexA_DNA_bind: LexA D 85.9 1.1 2.5E-05 27.2 3.1 34 2-41 27-60 (65)
74 PRK06474 hypothetical protein; 85.6 1.5 3.2E-05 31.8 4.1 53 1-60 27-82 (178)
75 PF00392 GntR: Bacterial regul 85.6 1.4 3E-05 26.2 3.4 33 2-41 26-58 (64)
76 PRK04172 pheS phenylalanyl-tRN 85.5 1.4 3E-05 36.8 4.4 53 1-64 21-73 (489)
77 COG1497 Predicted transcriptio 85.5 1.7 3.6E-05 33.4 4.4 81 2-95 27-109 (260)
78 PF04967 HTH_10: HTH DNA bindi 84.8 1.4 3E-05 25.8 3.0 28 1-31 24-51 (53)
79 PF02796 HTH_7: Helix-turn-hel 84.5 0.76 1.6E-05 25.6 1.7 22 1-29 22-43 (45)
80 TIGR00122 birA_repr_reg BirA b 84.1 2.2 4.7E-05 25.7 3.8 47 1-60 14-60 (69)
81 PF08220 HTH_DeoR: DeoR-like h 84.1 1.4 3E-05 25.9 2.8 34 1-41 15-48 (57)
82 PF03297 Ribosomal_S25: S25 ri 83.8 1.5 3.3E-05 29.3 3.2 34 1-41 60-93 (105)
83 PF04703 FaeA: FaeA-like prote 83.5 1.2 2.6E-05 26.9 2.4 33 2-41 17-49 (62)
84 PF13730 HTH_36: Helix-turn-he 83.2 1.9 4.1E-05 24.6 3.1 29 2-37 27-55 (55)
85 PRK04214 rbn ribonuclease BN/u 82.2 2 4.4E-05 35.0 4.0 34 1-41 311-344 (412)
86 PF14394 DUF4423: Domain of un 82.0 2 4.4E-05 31.0 3.5 43 2-57 41-85 (171)
87 PF03428 RP-C: Replication pro 81.4 2.5 5.3E-05 30.9 3.8 33 2-41 72-105 (177)
88 COG4901 Ribosomal protein S25 81.3 2 4.3E-05 28.7 2.9 34 1-41 60-93 (107)
89 PRK00215 LexA repressor; Valid 81.3 2.4 5.2E-05 30.9 3.8 34 1-41 24-58 (205)
90 PRK05638 threonine synthase; V 81.2 2.8 6E-05 34.5 4.4 55 1-62 385-439 (442)
91 PRK06266 transcription initiat 80.6 2.3 5.1E-05 30.9 3.4 34 1-41 37-70 (178)
92 PF08279 HTH_11: HTH domain; 80.2 3.5 7.5E-05 23.4 3.5 33 1-40 16-48 (55)
93 COG4190 Predicted transcriptio 80.0 2.4 5.2E-05 29.7 3.1 33 1-40 79-111 (144)
94 TIGR00498 lexA SOS regulatory 79.8 3 6.4E-05 30.3 3.8 34 2-41 27-60 (199)
95 PF00165 HTH_AraC: Bacterial r 79.4 1.6 3.5E-05 23.6 1.8 25 1-32 9-33 (42)
96 PF06163 DUF977: Bacterial pro 79.4 3.3 7.2E-05 28.7 3.6 34 1-41 27-60 (127)
97 TIGR03433 padR_acidobact trans 79.0 3.5 7.6E-05 26.8 3.6 41 23-63 41-83 (100)
98 PF12793 SgrR_N: Sugar transpo 78.9 2.7 5.8E-05 28.4 3.1 34 1-41 20-53 (115)
99 TIGR00373 conserved hypothetic 78.7 3 6.4E-05 29.7 3.4 33 1-40 29-61 (158)
100 PF13936 HTH_38: Helix-turn-he 78.7 1.8 3.9E-05 24.0 1.9 22 1-29 21-42 (44)
101 PRK11161 fumarate/nitrate redu 78.6 3.3 7.1E-05 30.4 3.8 34 1-41 185-218 (235)
102 PF06969 HemN_C: HemN C-termin 78.5 3.8 8.3E-05 24.2 3.4 45 2-59 22-66 (66)
103 PRK11753 DNA-binding transcrip 78.4 2.6 5.7E-05 30.2 3.2 34 1-41 169-202 (211)
104 PF08461 HTH_12: Ribonuclease 78.2 3.7 8.1E-05 24.9 3.3 49 1-59 14-64 (66)
105 TIGR03697 NtcA_cyano global ni 78.0 2.7 5.9E-05 29.7 3.1 34 1-41 144-177 (193)
106 COG1522 Lrp Transcriptional re 78.0 3 6.5E-05 28.7 3.2 33 1-40 23-55 (154)
107 cd04761 HTH_MerR-SF Helix-Turn 77.7 4.4 9.6E-05 22.2 3.3 44 1-57 1-44 (49)
108 PRK11179 DNA-binding transcrip 77.4 3.2 7E-05 29.0 3.3 31 1-38 24-54 (153)
109 PRK10430 DNA-binding transcrip 77.3 2.8 6E-05 30.9 3.1 34 1-41 179-212 (239)
110 COG3432 Predicted transcriptio 77.2 2.3 5E-05 28.0 2.3 38 23-63 47-84 (95)
111 smart00422 HTH_MERR helix_turn 77.1 4.3 9.4E-05 24.0 3.4 48 1-60 1-48 (70)
112 PRK09391 fixK transcriptional 76.8 4 8.8E-05 30.2 3.8 33 1-40 180-212 (230)
113 TIGR01764 excise DNA binding d 76.5 2.6 5.6E-05 22.8 2.1 27 1-38 2-28 (49)
114 PRK15431 ferrous iron transpor 76.4 4.7 0.0001 25.6 3.4 34 1-41 17-50 (78)
115 TIGR02719 repress_PhaQ poly-be 75.9 24 0.00051 24.7 7.2 44 16-63 56-101 (138)
116 cd04780 HTH_MerR-like_sg5 Heli 75.9 4.6 9.9E-05 26.2 3.5 47 1-59 1-47 (95)
117 PF03551 PadR: Transcriptional 75.8 2.8 6.2E-05 25.6 2.4 41 16-60 30-72 (75)
118 PF09929 DUF2161: Uncharacteri 75.4 4 8.7E-05 27.9 3.1 41 2-58 75-115 (118)
119 PRK09462 fur ferric uptake reg 75.0 5.1 0.00011 27.8 3.7 48 1-54 34-83 (148)
120 PF09821 AAA_assoc_C: C-termin 74.8 4.9 0.00011 27.4 3.5 46 5-64 2-47 (120)
121 PRK13918 CRP/FNR family transc 74.8 4 8.7E-05 29.1 3.3 33 1-40 150-182 (202)
122 TIGR03879 near_KaiC_dom probab 74.7 1.9 4E-05 27.0 1.3 30 1-37 33-62 (73)
123 PF04492 Phage_rep_O: Bacterio 74.7 4.9 0.00011 26.6 3.4 33 1-40 55-87 (100)
124 PRK11639 zinc uptake transcrip 74.6 4.7 0.0001 28.9 3.5 37 1-41 42-80 (169)
125 PHA00738 putative HTH transcri 74.5 6.1 0.00013 26.6 3.8 48 1-58 27-74 (108)
126 PRK11169 leucine-responsive tr 74.1 4.1 9E-05 28.8 3.2 31 1-38 29-59 (164)
127 PF01418 HTH_6: Helix-turn-hel 73.6 2.1 4.5E-05 26.6 1.3 28 1-35 35-62 (77)
128 PF10007 DUF2250: Uncharacteri 73.4 7.1 0.00015 25.5 3.8 52 4-62 25-90 (92)
129 COG1725 Predicted transcriptio 73.4 6.4 0.00014 27.2 3.8 33 2-41 37-69 (125)
130 smart00342 HTH_ARAC helix_turn 73.3 3.8 8.2E-05 24.4 2.5 27 1-34 2-28 (84)
131 PF12728 HTH_17: Helix-turn-he 72.8 3.5 7.6E-05 23.1 2.1 22 1-29 2-23 (51)
132 PF08784 RPA_C: Replication pr 72.4 4.1 8.8E-05 26.4 2.6 33 1-40 66-98 (102)
133 PRK14096 pgi glucose-6-phospha 71.9 4.5 9.8E-05 34.4 3.3 30 1-35 479-508 (528)
134 PF13404 HTH_AsnC-type: AsnC-t 70.6 3.9 8.5E-05 22.6 1.9 14 1-14 18-31 (42)
135 PF08281 Sigma70_r4_2: Sigma-7 70.4 5.8 0.00013 22.4 2.7 14 1-14 27-40 (54)
136 cd04762 HTH_MerR-trunc Helix-T 70.0 4.4 9.6E-05 21.7 2.1 46 1-59 1-46 (49)
137 PF09382 RQC: RQC domain; Int 69.3 8.8 0.00019 24.8 3.7 40 23-64 58-97 (106)
138 PRK11886 bifunctional biotin-- 68.3 7.5 0.00016 30.4 3.7 33 1-40 19-51 (319)
139 PRK12423 LexA repressor; Provi 68.0 7.8 0.00017 28.4 3.6 33 2-41 27-60 (202)
140 COG1675 TFA1 Transcription ini 67.8 7.1 0.00015 28.5 3.2 33 2-41 34-66 (176)
141 PF02002 TFIIE_alpha: TFIIE al 66.9 8.3 0.00018 25.1 3.2 33 2-41 29-61 (105)
142 PTZ00326 phenylalanyl-tRNA syn 66.3 11 0.00025 31.7 4.5 52 2-64 23-74 (494)
143 PLN02853 Probable phenylalanyl 66.3 11 0.00025 31.7 4.5 52 2-64 20-71 (492)
144 PF13384 HTH_23: Homeodomain-l 65.9 2.9 6.4E-05 23.2 0.7 28 1-35 18-45 (50)
145 cd04766 HTH_HspR Helix-Turn-He 64.9 11 0.00023 24.0 3.3 46 1-59 2-47 (91)
146 PF04760 IF2_N: Translation in 64.1 4 8.7E-05 23.4 1.1 27 1-37 4-31 (54)
147 PRK13509 transcriptional repre 64.0 7.8 0.00017 29.4 3.0 34 1-41 20-53 (251)
148 PRK09416 lstR lineage-specific 63.7 21 0.00046 24.9 4.8 41 16-62 76-116 (135)
149 PF13518 HTH_28: Helix-turn-he 63.3 10 0.00022 20.9 2.7 28 2-36 14-41 (52)
150 PRK11534 DNA-binding transcrip 63.1 13 0.00028 27.2 3.9 34 1-41 31-64 (224)
151 cd01109 HTH_YyaN Helix-Turn-He 62.9 14 0.0003 24.4 3.7 47 1-59 1-47 (113)
152 cd00592 HTH_MerR-like Helix-Tu 62.9 12 0.00027 23.8 3.4 46 1-59 1-46 (100)
153 COG3703 ChaC Uncharacterized p 62.8 11 0.00024 27.8 3.4 33 3-39 138-170 (190)
154 TIGR00635 ruvB Holliday juncti 62.5 11 0.00023 28.9 3.5 32 2-40 257-289 (305)
155 TIGR02277 PaaX_trns_reg phenyl 62.3 13 0.00029 28.8 4.0 50 3-62 23-72 (280)
156 PRK10402 DNA-binding transcrip 62.2 12 0.00026 27.4 3.7 33 2-41 171-203 (226)
157 PF14338 Mrr_N: Mrr N-terminal 62.1 7.8 0.00017 24.7 2.3 31 28-64 61-91 (92)
158 PF00356 LacI: Bacterial regul 62.0 6 0.00013 22.3 1.5 12 2-13 1-12 (46)
159 cd01108 HTH_CueR Helix-Turn-He 62.0 14 0.0003 25.1 3.6 47 1-59 1-47 (127)
160 TIGR03338 phnR_burk phosphonat 61.1 15 0.00032 26.6 3.9 33 2-41 36-68 (212)
161 PRK10401 DNA-binding transcrip 61.0 2.5 5.4E-05 32.7 -0.2 50 1-63 2-57 (346)
162 PF01381 HTH_3: Helix-turn-hel 60.9 4.3 9.3E-05 22.8 0.8 22 1-29 10-31 (55)
163 TIGR02787 codY_Gpos GTP-sensin 60.8 11 0.00024 29.0 3.2 34 1-41 199-232 (251)
164 COG3682 Predicted transcriptio 60.7 11 0.00023 26.0 2.9 47 1-56 21-68 (123)
165 PF13411 MerR_1: MerR HTH fami 60.6 11 0.00024 22.2 2.7 47 1-60 1-47 (69)
166 PRK10046 dpiA two-component re 59.5 11 0.00025 27.4 3.1 33 2-41 179-211 (225)
167 COG4565 CitB Response regulato 59.2 13 0.00029 28.1 3.4 33 1-40 174-206 (224)
168 PF03979 Sigma70_r1_1: Sigma-7 58.8 13 0.00027 23.4 2.8 34 1-38 22-55 (82)
169 PF10975 DUF2802: Protein of u 58.5 6.2 0.00014 24.3 1.3 23 1-27 45-67 (70)
170 PF00376 MerR: MerR family reg 57.8 9.3 0.0002 20.5 1.8 26 2-38 1-26 (38)
171 TIGR02147 Fsuc_second hypothet 57.7 18 0.00039 28.1 4.0 45 2-57 139-183 (271)
172 TIGR02531 yecD_yerC TrpR-relat 57.7 9 0.0002 24.7 2.0 24 1-31 51-74 (88)
173 PRK13824 replication initiatio 57.6 15 0.00033 30.1 3.7 33 2-41 84-117 (404)
174 cd04773 HTH_TioE_rpt2 Second H 57.2 20 0.00043 23.6 3.7 48 1-60 1-48 (108)
175 cd04763 HTH_MlrA-like Helix-Tu 57.2 19 0.00042 21.3 3.3 46 1-59 1-47 (68)
176 COG1349 GlpR Transcriptional r 57.0 24 0.00051 26.9 4.5 34 1-41 20-53 (253)
177 PRK00135 scpB segregation and 57.0 24 0.00053 25.9 4.4 48 1-58 105-153 (188)
178 PRK11557 putative DNA-binding 56.5 8.9 0.00019 29.1 2.1 29 1-36 31-59 (278)
179 TIGR02044 CueR Cu(I)-responsiv 56.3 18 0.0004 24.4 3.5 47 1-59 1-47 (127)
180 PRK13749 transcriptional regul 56.2 19 0.00041 24.6 3.5 47 1-59 4-50 (121)
181 PRK09492 treR trehalose repres 56.2 3 6.4E-05 31.7 -0.6 50 1-63 5-60 (315)
182 PF13591 MerR_2: MerR HTH fami 56.0 20 0.00043 22.6 3.4 44 1-58 1-44 (84)
183 cd01111 HTH_MerD Helix-Turn-He 56.0 19 0.00042 23.8 3.4 48 1-60 1-48 (107)
184 PRK10219 DNA-binding transcrip 56.0 12 0.00025 24.2 2.4 48 1-63 22-69 (107)
185 PRK11511 DNA-binding transcrip 55.7 11 0.00025 25.4 2.4 48 1-63 26-73 (127)
186 PRK09775 putative DNA-binding 55.7 17 0.00037 30.2 3.7 31 1-40 14-44 (442)
187 PF02981 FokI_N: Restriction e 55.5 13 0.00029 26.2 2.7 33 25-62 110-142 (145)
188 PF04545 Sigma70_r4: Sigma-70, 55.4 11 0.00024 20.9 2.0 23 1-30 21-43 (50)
189 TIGR02047 CadR-PbrR Cd(II)/Pb( 55.3 20 0.00043 24.3 3.5 46 1-58 1-46 (127)
190 COG2390 DeoR Transcriptional r 54.8 17 0.00036 29.0 3.5 34 1-41 27-60 (321)
191 PF01475 FUR: Ferric uptake re 54.3 8.6 0.00019 25.5 1.6 48 2-55 25-74 (120)
192 PF13542 HTH_Tnp_ISL3: Helix-t 54.3 13 0.00028 20.7 2.1 22 2-30 29-50 (52)
193 cd01279 HTH_HspR-like Helix-Tu 54.2 21 0.00046 23.0 3.4 46 1-59 2-47 (98)
194 PF04539 Sigma70_r3: Sigma-70 54.1 11 0.00025 22.8 2.0 30 2-38 22-51 (78)
195 PF07848 PaaX: PaaX-like prote 54.1 21 0.00046 21.9 3.2 45 3-57 26-70 (70)
196 PRK11302 DNA-binding transcrip 53.8 10 0.00022 28.7 2.1 29 1-36 35-63 (284)
197 PF02319 E2F_TDP: E2F/DP famil 53.5 21 0.00046 21.7 3.1 36 1-41 25-63 (71)
198 COG1737 RpiR Transcriptional r 53.1 8.7 0.00019 29.6 1.6 29 1-36 37-65 (281)
199 PF01710 HTH_Tnp_IS630: Transp 52.8 14 0.0003 24.8 2.4 28 1-38 72-99 (119)
200 TIGR00475 selB selenocysteine- 52.8 35 0.00076 29.3 5.3 54 2-68 490-543 (581)
201 cd04764 HTH_MlrA-like_sg1 Heli 52.6 25 0.00055 20.6 3.3 47 1-60 1-47 (67)
202 PRK10906 DNA-binding transcrip 52.1 17 0.00037 27.6 3.1 34 1-41 20-53 (252)
203 cd01106 HTH_TipAL-Mta Helix-Tu 52.0 27 0.00059 22.6 3.7 46 1-58 1-46 (103)
204 smart00421 HTH_LUXR helix_turn 52.0 18 0.00039 19.7 2.5 14 1-14 19-32 (58)
205 PRK09392 ftrB transcriptional 51.5 18 0.0004 26.4 3.1 28 2-36 175-202 (236)
206 PRK10421 DNA-binding transcrip 51.5 26 0.00056 26.2 4.0 33 2-41 28-60 (253)
207 cd04786 HTH_MerR-like_sg7 Heli 51.4 25 0.00053 24.1 3.5 46 1-58 1-46 (131)
208 PF03965 Penicillinase_R: Peni 51.3 51 0.0011 21.7 5.0 37 1-41 18-55 (115)
209 PRK05660 HemN family oxidoredu 51.1 26 0.00056 28.2 4.1 48 2-63 323-370 (378)
210 cd04770 HTH_HMRTR Helix-Turn-H 51.1 26 0.00057 23.3 3.6 46 1-58 1-46 (123)
211 cd04789 HTH_Cfa Helix-Turn-Hel 50.8 25 0.00055 22.8 3.3 45 1-58 2-46 (102)
212 TIGR02054 MerD mercuric resist 50.5 25 0.00055 23.8 3.4 47 1-59 4-50 (120)
213 PRK08208 coproporphyrinogen II 50.4 26 0.00057 28.7 4.1 48 2-63 363-410 (430)
214 PRK09802 DNA-binding transcrip 50.2 17 0.00037 27.9 2.8 34 1-41 32-65 (269)
215 PRK10014 DNA-binding transcrip 49.9 6.1 0.00013 30.4 0.3 53 1-63 7-62 (342)
216 PF08221 HTH_9: RNA polymerase 49.8 14 0.0003 22.0 1.8 31 2-39 29-59 (62)
217 PRK11642 exoribonuclease R; Pr 49.8 24 0.00052 31.6 4.0 37 1-41 35-72 (813)
218 PRK09954 putative kinase; Prov 49.4 19 0.00042 28.4 3.1 31 1-38 18-48 (362)
219 COG1802 GntR Transcriptional r 49.2 27 0.00059 25.7 3.7 34 1-41 40-73 (230)
220 PF05331 DUF742: Protein of un 49.2 31 0.00066 23.4 3.6 35 1-42 56-90 (114)
221 PF09079 Cdc6_C: CDC6, C termi 49.2 31 0.00067 21.4 3.5 35 3-41 25-59 (85)
222 cd04788 HTH_NolA-AlbR Helix-Tu 49.1 30 0.00064 22.2 3.5 47 1-59 1-47 (96)
223 TIGR02404 trehalos_R_Bsub treh 49.1 30 0.00065 25.5 3.9 33 2-41 26-58 (233)
224 PRK00082 hrcA heat-inducible t 49.0 29 0.00064 27.7 4.1 45 1-57 26-72 (339)
225 PRK09464 pdhR transcriptional 49.0 32 0.00069 25.7 4.1 33 2-41 36-68 (254)
226 cd04782 HTH_BltR Helix-Turn-He 48.9 31 0.00067 22.2 3.5 47 1-59 1-47 (97)
227 PRK00118 putative DNA-binding 48.6 15 0.00033 24.4 2.0 14 1-14 34-47 (104)
228 PRK04424 fatty acid biosynthes 48.5 11 0.00023 27.5 1.4 32 1-39 22-53 (185)
229 PRK11414 colanic acid/biofilm 48.3 31 0.00068 25.2 3.9 33 2-41 36-68 (221)
230 cd01107 HTH_BmrR Helix-Turn-He 48.2 35 0.00076 22.3 3.8 48 1-59 1-48 (108)
231 cd04784 HTH_CadR-PbrR Helix-Tu 48.2 29 0.00064 23.3 3.5 46 1-58 1-46 (127)
232 PRK04984 fatty acid metabolism 48.0 32 0.00069 25.4 3.9 33 2-41 33-65 (239)
233 PF05584 Sulfolobus_pRN: Sulfo 47.8 39 0.00085 21.1 3.6 33 1-40 19-51 (72)
234 COG2188 PhnF Transcriptional r 47.7 28 0.0006 26.0 3.6 40 4-55 35-74 (236)
235 TIGR02812 fadR_gamma fatty aci 47.4 36 0.00077 25.1 4.1 33 2-41 32-64 (235)
236 PHA02943 hypothetical protein; 47.3 33 0.00071 24.7 3.6 35 1-42 25-59 (165)
237 TIGR02698 CopY_TcrY copper tra 47.3 35 0.00076 23.3 3.8 88 1-95 19-118 (130)
238 TIGR02405 trehalos_R_Ecol treh 47.3 7.5 0.00016 29.6 0.4 50 1-63 2-57 (311)
239 TIGR02325 C_P_lyase_phnF phosp 47.1 33 0.00073 25.1 3.9 33 2-41 34-66 (238)
240 cd01105 HTH_GlnR-like Helix-Tu 47.0 34 0.00074 21.6 3.4 46 1-58 2-47 (88)
241 cd04785 HTH_CadR-PbrR-like Hel 47.0 32 0.00069 23.2 3.5 47 1-59 1-47 (126)
242 PRK11337 DNA-binding transcrip 46.9 17 0.00036 27.9 2.3 29 1-36 47-75 (292)
243 PRK04217 hypothetical protein; 46.9 20 0.00043 24.1 2.4 14 1-14 59-72 (110)
244 COG0735 Fur Fe2+/Zn2+ uptake r 46.5 33 0.00072 23.9 3.6 50 2-57 38-89 (145)
245 PRK08599 coproporphyrinogen II 46.4 36 0.00079 27.1 4.3 48 3-63 321-368 (377)
246 smart00354 HTH_LACI helix_turn 46.3 17 0.00038 21.8 1.9 13 1-13 1-13 (70)
247 PRK10225 DNA-binding transcrip 46.2 35 0.00076 25.5 3.9 33 2-41 35-67 (257)
248 cd04790 HTH_Cfa-like_unk Helix 46.0 32 0.00069 24.7 3.5 46 1-58 2-47 (172)
249 PRK12520 RNA polymerase sigma 45.9 24 0.00051 25.1 2.8 28 1-31 148-175 (191)
250 PRK09990 DNA-binding transcrip 45.8 38 0.00083 25.2 4.1 33 2-41 33-65 (251)
251 TIGR03070 couple_hipB transcri 45.8 18 0.00039 20.0 1.9 21 1-28 16-36 (58)
252 cd04783 HTH_MerR1 Helix-Turn-H 45.7 34 0.00073 23.0 3.4 46 1-58 1-46 (126)
253 PRK15482 transcriptional regul 45.6 19 0.00041 27.5 2.4 29 1-36 35-63 (285)
254 PRK10227 DNA-binding transcrip 45.5 34 0.00074 23.5 3.5 48 1-60 1-48 (135)
255 cd04781 HTH_MerR-like_sg6 Heli 45.2 33 0.00073 22.8 3.4 45 1-58 1-45 (120)
256 PRK03837 transcriptional regul 45.2 41 0.0009 24.7 4.2 33 2-41 39-71 (241)
257 PRK14999 histidine utilization 44.9 36 0.00079 25.3 3.8 33 2-41 38-70 (241)
258 PRK12533 RNA polymerase sigma 44.8 24 0.00053 26.0 2.9 30 1-33 151-180 (216)
259 COG1386 scpB Chromosome segreg 44.8 52 0.0011 24.1 4.5 46 1-56 107-153 (184)
260 PF10668 Phage_terminase: Phag 44.6 17 0.00036 21.9 1.6 14 1-14 23-36 (60)
261 PRK09514 zntR zinc-responsive 44.5 35 0.00077 23.5 3.5 47 1-59 2-48 (140)
262 PF08535 KorB: KorB domain; I 44.4 15 0.00033 23.4 1.5 24 1-31 4-27 (93)
263 PF04182 B-block_TFIIIC: B-blo 44.3 31 0.00067 21.1 2.9 33 2-41 20-52 (75)
264 TIGR02947 SigH_actino RNA poly 44.3 27 0.00059 24.8 3.0 29 1-32 148-176 (193)
265 COG2186 FadR Transcriptional r 44.3 38 0.00082 25.5 3.8 40 3-54 37-76 (241)
266 PRK13347 coproporphyrinogen II 44.1 26 0.00057 28.9 3.2 50 3-63 384-433 (453)
267 PRK09764 DNA-binding transcrip 44.1 40 0.00087 25.0 3.9 33 2-41 31-63 (240)
268 PRK10434 srlR DNA-bindng trans 44.1 23 0.00049 26.9 2.6 34 1-41 20-53 (256)
269 COG1695 Predicted transcriptio 44.1 39 0.00084 22.8 3.6 44 16-63 43-88 (138)
270 PF00126 HTH_1: Bacterial regu 43.9 63 0.0014 18.6 4.6 43 2-58 15-60 (60)
271 COG3695 Predicted methylated D 43.5 19 0.00042 24.0 1.9 28 1-33 24-51 (103)
272 PRK10411 DNA-binding transcrip 43.5 40 0.00086 25.4 3.9 33 1-40 19-51 (240)
273 PF05930 Phage_AlpA: Prophage 43.5 16 0.00035 20.6 1.4 27 1-38 4-30 (51)
274 cd04768 HTH_BmrR-like Helix-Tu 43.3 43 0.00093 21.4 3.5 48 1-60 1-48 (96)
275 cd06171 Sigma70_r4 Sigma70, re 43.3 24 0.00051 18.7 2.1 23 1-30 27-49 (55)
276 PRK05799 coproporphyrinogen II 43.2 39 0.00085 26.9 4.0 34 23-63 334-367 (374)
277 PF07789 DUF1627: Protein of u 42.9 46 0.001 23.8 3.8 34 1-41 7-40 (155)
278 cd08768 Cdc6_C Winged-helix do 42.6 50 0.0011 20.2 3.7 35 3-41 32-66 (87)
279 PF06413 Neugrin: Neugrin; In 42.3 21 0.00046 27.0 2.2 21 2-29 31-51 (225)
280 PRK12532 RNA polymerase sigma 42.3 29 0.00062 24.7 2.8 28 1-31 153-180 (195)
281 cd04769 HTH_MerR2 Helix-Turn-H 42.1 42 0.00092 22.2 3.5 47 1-60 1-47 (116)
282 TIGR02018 his_ut_repres histid 41.8 45 0.00097 24.5 3.9 33 2-41 27-59 (230)
283 PRK15418 transcriptional regul 41.7 36 0.00078 26.9 3.5 33 1-40 30-62 (318)
284 PF09269 DUF1967: Domain of un 41.5 20 0.00043 21.8 1.6 32 3-40 18-49 (69)
285 PF02387 IncFII_repA: IncFII R 41.3 59 0.0013 25.5 4.6 61 1-61 96-163 (281)
286 PRK10572 DNA-binding transcrip 41.3 25 0.00053 26.7 2.5 55 1-71 200-254 (290)
287 PRK12511 RNA polymerase sigma 41.2 34 0.00073 24.4 3.0 29 1-32 128-156 (182)
288 PRK12540 RNA polymerase sigma 40.9 32 0.00068 24.5 2.9 29 1-32 128-156 (182)
289 COG1510 Predicted transcriptio 40.7 30 0.00065 25.3 2.6 33 1-40 42-74 (177)
290 smart00753 PAM PCI/PINT associ 40.7 40 0.00088 20.7 3.0 33 1-40 25-57 (88)
291 smart00088 PINT motif in prote 40.7 40 0.00088 20.7 3.0 33 1-40 25-57 (88)
292 cd01282 HTH_MerR-like_sg3 Heli 40.6 46 0.00099 21.9 3.4 47 1-60 1-47 (112)
293 PF00440 TetR_N: Bacterial reg 40.4 17 0.00036 20.0 1.1 14 1-14 17-30 (47)
294 PF10078 DUF2316: Uncharacteri 40.4 25 0.00055 22.8 2.0 22 1-29 24-45 (89)
295 cd04767 HTH_HspR-like_MBC Heli 40.1 44 0.00095 22.8 3.3 45 1-59 2-46 (120)
296 PRK13626 transcriptional regul 40.0 31 0.00068 29.0 3.1 34 1-41 24-57 (552)
297 PF13443 HTH_26: Cro/C1-type H 40.0 17 0.00037 20.9 1.2 22 1-29 11-32 (63)
298 PF03374 ANT: Phage antirepres 40.0 27 0.00059 22.7 2.2 29 1-39 25-53 (111)
299 TIGR02297 HpaA 4-hydroxyphenyl 39.9 28 0.00062 26.1 2.6 59 1-75 203-261 (287)
300 PF09106 SelB-wing_2: Elongati 39.6 58 0.0013 18.8 3.4 36 2-41 19-54 (59)
301 PRK13752 putative transcriptio 39.6 44 0.00095 23.3 3.3 47 1-59 8-54 (144)
302 PRK11402 DNA-binding transcrip 39.1 53 0.0011 24.3 3.9 33 2-41 35-67 (241)
303 PRK11523 DNA-binding transcrip 39.0 52 0.0011 24.6 3.9 32 3-41 35-66 (253)
304 PRK10265 chaperone-modulator p 38.9 42 0.00091 21.9 3.0 30 1-41 8-37 (101)
305 PRK08898 coproporphyrinogen II 38.7 57 0.0012 26.4 4.3 47 3-63 341-387 (394)
306 cd04775 HTH_Cfa-like Helix-Tur 38.7 57 0.0012 21.1 3.6 45 1-58 2-46 (102)
307 PF02042 RWP-RK: RWP-RK domain 38.7 33 0.00072 20.0 2.2 23 1-30 16-38 (52)
308 cd06170 LuxR_C_like C-terminal 38.7 39 0.00085 18.4 2.5 14 1-14 16-29 (57)
309 PF08222 HTH_CodY: CodY helix- 38.6 39 0.00084 20.3 2.4 33 2-41 6-38 (61)
310 cd04772 HTH_TioE_rpt1 First He 38.5 55 0.0012 21.1 3.5 46 1-58 1-46 (99)
311 PF04297 UPF0122: Putative hel 38.4 48 0.001 22.0 3.2 27 1-30 34-60 (101)
312 PRK09526 lacI lac repressor; R 38.2 12 0.00027 28.6 0.4 53 1-63 6-61 (342)
313 COG2524 Predicted transcriptio 38.1 45 0.00098 26.2 3.4 47 3-60 28-74 (294)
314 TIGR00331 hrcA heat shock gene 38.0 54 0.0012 26.1 4.0 34 1-41 22-57 (337)
315 PF13986 DUF4224: Domain of un 37.9 55 0.0012 18.4 3.0 32 1-41 3-34 (47)
316 PF05402 PqqD: Coenzyme PQQ sy 37.9 63 0.0014 18.8 3.5 31 4-37 37-67 (68)
317 cd06445 ATase The DNA repair p 37.8 34 0.00073 21.2 2.3 25 1-30 18-42 (79)
318 COG3828 Uncharacterized protei 37.6 18 0.0004 27.1 1.2 44 78-127 64-107 (239)
319 PF14490 HHH_4: Helix-hairpin- 37.6 45 0.00097 21.3 2.9 17 2-18 58-74 (94)
320 cd04774 HTH_YfmP Helix-Turn-He 37.6 58 0.0013 20.9 3.5 47 1-60 1-47 (96)
321 PF14502 HTH_41: Helix-turn-he 37.5 82 0.0018 18.1 3.6 33 2-41 8-40 (48)
322 PRK12516 RNA polymerase sigma 37.4 38 0.00083 24.2 2.8 29 1-32 133-161 (187)
323 PF01371 Trp_repressor: Trp re 37.4 36 0.00079 21.9 2.4 25 1-32 50-74 (87)
324 PF13551 HTH_29: Winged helix- 37.3 33 0.00071 21.8 2.3 27 2-35 14-40 (112)
325 PF13560 HTH_31: Helix-turn-he 36.7 23 0.0005 20.6 1.3 22 1-29 15-36 (64)
326 PRK09647 RNA polymerase sigma 36.4 40 0.00086 24.5 2.8 29 1-32 155-183 (203)
327 cd04787 HTH_HMRTR_unk Helix-Tu 36.2 56 0.0012 22.2 3.4 46 1-58 1-46 (133)
328 COG0789 SoxR Predicted transcr 36.1 54 0.0012 21.5 3.3 45 1-57 1-45 (124)
329 smart00531 TFIIE Transcription 35.8 44 0.00095 23.2 2.8 29 1-36 16-44 (147)
330 PHA01976 helix-turn-helix prot 35.8 31 0.00067 20.1 1.8 21 1-28 16-36 (67)
331 TIGR02063 RNase_R ribonuclease 35.8 52 0.0011 28.9 3.9 37 1-41 19-56 (709)
332 PRK15121 right oriC-binding tr 35.6 33 0.00073 26.2 2.4 47 1-62 22-68 (289)
333 PRK13503 transcriptional activ 35.5 36 0.00079 25.4 2.6 58 1-74 188-245 (278)
334 COG2512 Predicted membrane-ass 35.5 44 0.00096 25.8 3.0 33 2-41 212-244 (258)
335 TIGR02043 ZntR Zn(II)-responsi 35.1 62 0.0013 22.0 3.5 47 1-59 2-48 (131)
336 PF06971 Put_DNA-bind_N: Putat 35.1 21 0.00045 20.6 0.9 14 1-14 29-42 (50)
337 PRK10736 hypothetical protein; 35.0 55 0.0012 26.7 3.6 34 1-41 322-355 (374)
338 TIGR00180 parB_part ParB-like 34.9 41 0.00089 24.2 2.7 25 1-32 121-145 (187)
339 PHA00542 putative Cro-like pro 34.9 34 0.00075 21.3 2.0 22 1-29 32-53 (82)
340 cd01110 HTH_SoxR Helix-Turn-He 34.8 61 0.0013 22.3 3.4 46 1-59 2-47 (139)
341 PRK12535 RNA polymerase sigma 34.7 48 0.001 23.9 3.0 28 1-31 150-177 (196)
342 PF13744 HTH_37: Helix-turn-he 34.4 25 0.00053 21.8 1.2 14 1-14 32-45 (80)
343 PRK10703 DNA-binding transcrip 34.3 12 0.00026 28.7 -0.2 53 1-63 2-57 (341)
344 PRK15340 transcriptional regul 34.2 37 0.00079 25.6 2.3 31 1-38 126-156 (216)
345 COG4367 Uncharacterized protei 34.2 41 0.0009 21.9 2.2 23 1-30 24-46 (97)
346 PRK12524 RNA polymerase sigma 34.1 45 0.00098 23.8 2.8 29 1-32 153-181 (196)
347 PRK09906 DNA-binding transcrip 34.1 59 0.0013 24.3 3.5 48 2-63 17-67 (296)
348 PRK10079 phosphonate metabolis 34.0 70 0.0015 23.7 3.9 32 3-41 38-69 (241)
349 PF04433 SWIRM: SWIRM domain; 34.0 74 0.0016 19.8 3.5 30 2-38 55-85 (86)
350 PF01498 HTH_Tnp_Tc3_2: Transp 34.0 47 0.001 19.7 2.5 32 1-40 14-48 (72)
351 PRK00080 ruvB Holliday junctio 34.0 43 0.00092 26.1 2.8 43 2-58 278-321 (328)
352 PRK12543 RNA polymerase sigma 33.9 46 0.00099 23.3 2.8 14 1-14 134-147 (179)
353 PRK00400 hisE phosphoribosyl-A 33.9 40 0.00086 22.5 2.2 19 19-37 62-80 (105)
354 TIGR03826 YvyF flagellar opero 33.8 42 0.00091 23.5 2.4 23 1-30 47-69 (137)
355 TIGR03337 phnR transcriptional 33.8 69 0.0015 23.3 3.8 33 2-41 27-59 (231)
356 PRK03601 transcriptional regul 33.2 56 0.0012 24.4 3.3 48 2-63 17-67 (275)
357 PF09202 Rio2_N: Rio2, N-termi 32.8 63 0.0014 20.4 3.0 45 3-58 27-71 (82)
358 PF11972 HTH_13: HTH DNA bindi 32.7 70 0.0015 18.8 2.9 25 1-32 14-38 (54)
359 PRK12546 RNA polymerase sigma 32.4 52 0.0011 23.6 2.9 29 1-32 130-158 (188)
360 TIGR02051 MerR Hg(II)-responsi 32.4 70 0.0015 21.4 3.4 46 2-59 1-46 (124)
361 PF02037 SAP: SAP domain; Int 32.3 71 0.0015 16.6 2.7 24 4-31 10-35 (35)
362 TIGR01950 SoxR redox-sensitive 32.3 70 0.0015 22.2 3.4 45 1-58 2-46 (142)
363 TIGR03188 histidine_hisI phosp 31.9 46 0.001 21.2 2.2 19 19-37 58-76 (84)
364 PRK13502 transcriptional activ 31.7 38 0.00083 25.4 2.2 57 1-73 193-249 (282)
365 COG1339 Transcriptional regula 31.4 1.2E+02 0.0027 22.7 4.7 54 1-64 20-73 (214)
366 PRK12545 RNA polymerase sigma 31.4 54 0.0012 23.6 2.8 14 1-14 156-169 (201)
367 PRK09726 antitoxin HipB; Provi 31.1 37 0.0008 21.3 1.7 22 1-29 26-47 (88)
368 PF11761 CbiG_mid: Cobalamin b 31.0 50 0.0011 20.4 2.3 30 2-35 3-32 (93)
369 TIGR02959 SigZ RNA polymerase 31.0 57 0.0012 22.7 2.9 30 1-33 117-146 (170)
370 smart00530 HTH_XRE Helix-turn- 31.0 41 0.00089 17.3 1.7 13 1-13 11-23 (56)
371 TIGR02960 SigX5 RNA polymerase 30.9 52 0.0011 25.3 2.8 29 1-32 159-187 (324)
372 PF09286 Pro-kuma_activ: Pro-k 30.9 49 0.0011 22.6 2.4 31 1-38 48-78 (143)
373 cd01104 HTH_MlrA-CarA Helix-Tu 30.8 35 0.00077 19.8 1.5 45 1-57 1-45 (68)
374 PRK08241 RNA polymerase factor 30.8 52 0.0011 25.6 2.8 30 1-33 170-199 (339)
375 cd04765 HTH_MlrA-like_sg2 Heli 30.5 82 0.0018 20.4 3.3 46 1-59 1-47 (99)
376 PF01035 DNA_binding_1: 6-O-me 30.4 45 0.00098 21.0 2.0 25 1-30 20-44 (85)
377 PRK13501 transcriptional activ 30.4 49 0.0011 25.1 2.6 55 1-71 193-247 (290)
378 TIGR02607 antidote_HigA addict 30.1 52 0.0011 19.6 2.2 22 1-29 19-40 (78)
379 PRK10837 putative DNA-binding 29.7 88 0.0019 23.2 3.8 48 2-63 19-69 (290)
380 cd04778 HTH_MerR-like_sg2 Heli 29.4 75 0.0016 23.8 3.3 46 1-59 2-47 (219)
381 COG2207 AraC AraC-type DNA-bin 29.4 58 0.0013 20.6 2.5 49 1-64 37-85 (127)
382 TIGR02216 phage_TIGR02216 phag 29.3 84 0.0018 18.9 2.9 26 1-30 25-56 (60)
383 TIGR03595 Obg_CgtA_exten Obg f 29.2 93 0.002 18.8 3.2 30 4-39 19-48 (69)
384 PRK06704 RNA polymerase factor 29.2 58 0.0013 24.5 2.7 29 1-32 133-161 (228)
385 COG1309 AcrR Transcriptional r 29.2 47 0.001 21.8 2.1 14 1-14 33-46 (201)
386 PRK15002 redox-sensitivie tran 29.0 85 0.0019 22.2 3.4 45 1-58 12-56 (154)
387 cd04779 HTH_MerR-like_sg4 Heli 28.8 97 0.0021 21.3 3.6 46 1-59 1-46 (134)
388 PRK10371 DNA-binding transcrip 28.7 51 0.0011 25.5 2.4 55 1-71 208-262 (302)
389 PRK11062 nhaR transcriptional 28.6 73 0.0016 24.0 3.3 48 2-63 20-70 (296)
390 PF00888 Cullin: Cullin family 28.5 21 0.00046 29.8 0.3 33 1-40 535-567 (588)
391 PF06056 Terminase_5: Putative 28.3 51 0.0011 19.4 1.8 14 1-14 14-27 (58)
392 PRK11131 ATP-dependent RNA hel 28.3 1.8E+02 0.004 27.8 6.2 55 13-76 451-506 (1294)
393 KOG1767 40S ribosomal protein 28.2 56 0.0012 21.9 2.2 34 1-41 61-94 (110)
394 PRK14101 bifunctional glucokin 28.2 45 0.00098 28.7 2.2 29 1-36 375-403 (638)
395 PRK11233 nitrogen assimilation 28.1 82 0.0018 23.9 3.5 48 2-63 17-67 (305)
396 PRK12542 RNA polymerase sigma 28.1 68 0.0015 22.5 2.8 28 1-31 139-166 (185)
397 cd00093 HTH_XRE Helix-turn-hel 28.0 53 0.0012 17.0 1.9 14 1-14 13-26 (58)
398 TIGR03882 cyclo_dehyd_2 bacter 27.9 88 0.0019 22.8 3.4 35 2-41 44-78 (193)
399 PF14357 DUF4404: Domain of un 27.8 50 0.0011 21.0 1.9 17 20-36 69-85 (85)
400 PF01399 PCI: PCI domain; Int 27.7 59 0.0013 20.2 2.3 33 1-40 61-93 (105)
401 PRK09986 DNA-binding transcrip 27.6 92 0.002 23.1 3.6 47 2-62 23-72 (294)
402 PRK12538 RNA polymerase sigma 27.6 64 0.0014 24.1 2.7 29 1-32 188-216 (233)
403 PRK15411 rcsA colanic acid cap 27.5 77 0.0017 23.1 3.1 29 1-32 153-181 (207)
404 smart00351 PAX Paired Box doma 27.5 78 0.0017 21.3 2.9 32 1-39 34-65 (125)
405 PRK08629 coproporphyrinogen II 27.4 1E+02 0.0022 25.4 4.1 49 2-63 360-408 (433)
406 cd00569 HTH_Hin_like Helix-tur 27.4 43 0.00094 15.6 1.3 11 2-12 23-33 (42)
407 PF07574 SMC_Nse1: Nse1 non-SM 27.0 74 0.0016 23.2 2.9 29 23-57 168-196 (200)
408 PRK09057 coproporphyrinogen II 26.9 96 0.0021 24.9 3.8 47 2-63 327-373 (380)
409 PRK09685 DNA-binding transcrip 26.8 52 0.0011 24.9 2.2 23 1-30 215-237 (302)
410 PRK15481 transcriptional regul 26.8 1E+02 0.0022 24.8 4.0 33 2-41 31-63 (431)
411 PRK09636 RNA polymerase sigma 26.8 68 0.0015 24.6 2.8 31 1-34 132-162 (293)
412 PRK12682 transcriptional regul 26.4 77 0.0017 24.0 3.1 49 2-63 18-69 (309)
413 PRK11063 metQ DL-methionine tr 25.9 47 0.001 25.5 1.8 35 2-41 123-159 (271)
414 PRK10512 selenocysteinyl-tRNA- 25.9 1.2E+02 0.0025 26.4 4.3 33 2-41 508-540 (614)
415 PRK12517 RNA polymerase sigma 25.8 79 0.0017 22.5 2.9 14 1-14 145-158 (188)
416 PRK13500 transcriptional activ 25.6 63 0.0014 25.0 2.5 56 1-72 223-278 (312)
417 TIGR02424 TF_pcaQ pca operon t 25.3 83 0.0018 23.6 3.0 48 2-63 19-69 (300)
418 PF04738 Lant_dehyd_C: Lantibi 25.3 63 0.0014 26.4 2.5 36 1-40 1-38 (500)
419 TIGR01321 TrpR trp operon repr 25.2 65 0.0014 21.1 2.1 25 1-32 56-80 (94)
420 TIGR00281 segregation and cond 25.2 1.7E+02 0.0037 21.4 4.5 46 1-56 102-148 (186)
421 PF09681 Phage_rep_org_N: N-te 25.1 1.4E+02 0.0031 20.2 3.9 47 2-61 55-101 (121)
422 COG0140 HisI Phosphoribosyl-AT 24.9 72 0.0016 20.8 2.2 19 19-37 58-76 (92)
423 PRK12679 cbl transcriptional r 24.9 93 0.002 23.8 3.3 49 2-63 18-69 (316)
424 PRK11922 RNA polymerase sigma 24.8 81 0.0017 23.2 2.8 14 1-14 166-179 (231)
425 PRK15201 fimbriae regulatory p 24.8 85 0.0019 23.3 2.8 29 1-32 149-177 (198)
426 PF04552 Sigma54_DBD: Sigma-54 24.8 24 0.00053 25.2 0.0 22 1-29 50-71 (160)
427 PRK11303 DNA-binding transcrip 24.6 57 0.0012 24.7 2.0 22 1-29 1-22 (328)
428 PRK09791 putative DNA-binding 24.3 81 0.0018 23.7 2.8 48 2-63 21-71 (302)
429 TIGR00589 ogt O-6-methylguanin 24.2 95 0.0021 19.4 2.7 25 1-30 20-44 (80)
430 cd01392 HTH_LacI Helix-turn-he 24.1 40 0.00087 18.4 0.8 8 5-12 2-9 (52)
431 TIGR00721 tfx DNA-binding prot 24.1 88 0.0019 21.8 2.7 29 1-32 22-50 (137)
432 cd04777 HTH_MerR-like_sg1 Heli 24.0 96 0.0021 20.0 2.8 42 1-56 1-42 (107)
433 PRK09637 RNA polymerase sigma 23.9 99 0.0021 21.8 3.0 29 1-32 123-151 (181)
434 KOG3789 Nitrogen permease regu 23.6 51 0.0011 26.9 1.6 53 2-63 219-271 (396)
435 PRK09393 ftrA transcriptional 23.4 75 0.0016 24.6 2.5 55 1-71 235-289 (322)
436 PRK10094 DNA-binding transcrip 23.4 1.2E+02 0.0026 23.2 3.6 48 2-63 18-68 (308)
437 PRK10632 transcriptional regul 23.3 90 0.002 23.7 2.9 48 2-63 18-68 (309)
438 TIGR03001 Sig-70_gmx1 RNA poly 23.3 86 0.0019 23.6 2.7 29 1-32 178-206 (244)
439 PF13309 HTH_22: HTH domain 23.3 43 0.00094 19.9 0.9 21 2-29 44-64 (64)
440 PRK10341 DNA-binding transcrip 23.0 96 0.0021 23.6 3.0 48 2-63 23-73 (312)
441 PRK09480 slmA division inhibit 23.0 62 0.0014 22.5 1.8 14 1-14 31-44 (194)
442 TIGR00637 ModE_repress ModE mo 22.9 1.1E+02 0.0025 19.7 3.0 52 2-62 18-72 (99)
443 PF08280 HTH_Mga: M protein tr 22.9 1.1E+02 0.0024 17.6 2.6 13 1-13 20-32 (59)
444 TIGR03339 phn_lysR aminoethylp 22.8 1.3E+02 0.0028 21.9 3.7 48 2-63 13-63 (279)
445 cd00186 TOP1Ac DNA Topoisomera 22.8 1.7E+02 0.0037 23.6 4.5 60 25-95 304-363 (381)
446 PRK11151 DNA-binding transcrip 22.7 1.1E+02 0.0024 23.0 3.3 48 2-63 17-67 (305)
447 PF13022 HTH_Tnp_1_2: Helix-tu 22.7 64 0.0014 22.8 1.8 21 2-29 36-56 (142)
448 TIGR02394 rpoS_proteo RNA poly 22.7 88 0.0019 23.9 2.7 28 1-31 243-270 (285)
449 PRK15044 transcriptional regul 22.6 73 0.0016 25.2 2.3 55 1-72 209-263 (295)
450 PF08820 DUF1803: Domain of un 22.4 85 0.0018 20.5 2.2 25 23-54 43-67 (93)
451 PRK09978 DNA-binding transcrip 22.3 70 0.0015 24.9 2.1 55 1-72 159-213 (274)
452 PRK09975 DNA-binding transcrip 22.1 73 0.0016 22.7 2.1 14 1-14 32-45 (213)
453 PRK09249 coproporphyrinogen II 22.0 1.6E+02 0.0034 24.3 4.2 30 27-63 404-433 (453)
454 COG2771 CsgD DNA-binding HTH d 21.9 1.3E+02 0.0028 16.8 2.8 29 1-32 20-48 (65)
455 COG3311 AlpA Predicted transcr 21.8 84 0.0018 19.4 2.0 23 1-30 14-36 (70)
456 PF00196 GerE: Bacterial regul 21.8 96 0.0021 17.5 2.2 28 1-31 19-46 (58)
457 PRK09635 sigI RNA polymerase s 21.6 97 0.0021 24.0 2.8 30 1-33 135-164 (290)
458 TIGR02957 SigX4 RNA polymerase 21.5 1E+02 0.0022 23.6 2.8 30 1-33 125-154 (281)
459 PRK09940 transcriptional regul 21.4 76 0.0017 24.4 2.1 54 1-72 151-204 (253)
460 cd04896 ACT_ACR-like_3 ACT dom 21.4 90 0.0019 19.4 2.1 18 23-40 13-30 (75)
461 cd04895 ACT_ACR_1 ACT domain-c 21.4 95 0.0021 19.1 2.2 19 23-41 14-32 (72)
462 PRK13890 conjugal transfer pro 21.4 68 0.0015 21.5 1.7 13 1-13 19-31 (120)
463 PF07037 DUF1323: Putative tra 21.4 99 0.0021 21.3 2.4 31 1-41 1-31 (122)
464 TIGR00538 hemN oxygen-independ 21.2 1.7E+02 0.0037 24.1 4.2 30 27-63 404-433 (455)
465 PRK15185 transcriptional regul 21.1 78 0.0017 25.2 2.2 57 1-74 223-279 (309)
466 TIGR01481 ccpA catabolite cont 21.1 64 0.0014 24.5 1.7 53 1-63 2-57 (329)
467 TIGR02844 spore_III_D sporulat 21.1 78 0.0017 20.0 1.8 21 1-28 20-40 (80)
468 PF08721 Tn7_Tnp_TnsA_C: TnsA 21.1 1.3E+02 0.0029 17.7 2.9 16 23-38 61-76 (79)
469 COG1983 PspC Putative stress-r 20.9 1.1E+02 0.0024 18.9 2.4 24 4-35 19-42 (70)
470 PRK05472 redox-sensing transcr 20.8 94 0.002 22.7 2.5 28 1-35 33-60 (213)
471 COG1485 Predicted ATPase [Gene 20.6 88 0.0019 25.5 2.4 18 23-40 149-166 (367)
472 PF13413 HTH_25: Helix-turn-he 20.4 74 0.0016 18.8 1.5 14 1-14 11-24 (62)
473 COG0664 Crp cAMP-binding prote 20.4 1.5E+02 0.0033 20.4 3.4 34 1-41 172-205 (214)
474 PRK11202 DNA-binding transcrip 20.4 82 0.0018 22.6 2.1 14 1-14 33-46 (203)
475 PRK07379 coproporphyrinogen II 20.3 1.9E+02 0.0042 23.4 4.3 49 2-63 337-387 (400)
476 PTZ00407 DNA topoisomerase IA; 20.2 2.2E+02 0.0047 25.9 4.9 60 26-95 601-660 (805)
No 1
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.45 E-value=1.9e-13 Score=107.62 Aligned_cols=108 Identities=19% Similarity=0.245 Sum_probs=92.1
Q ss_pred HHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC-CCcHHHHHHHhcChh
Q 045905 3 LNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI-TLTVRSFLQAVLDPI 79 (128)
Q Consensus 3 ~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~-~~s~~~~~~~~~~~~ 79 (128)
..|||..++. +|.++. .++||||.|++++||++.... .+ .|++||+++.+..+. ..|++++++..+++.
T Consensus 41 p~~ia~~l~~~~~~~~p~----ll~r~lr~L~s~~i~k~~~~~---~~-~Y~~~~~~~~~l~~~~~~S~a~~~~~~~~~v 112 (342)
T KOG3178|consen 41 PSEIASLLPTPKNPEAPV----LLDRILRLLVSYSILKCRLVG---GE-VYSATPVCKYFLKDSGGGSLAPLVLLNTSKV 112 (342)
T ss_pred HHHHHHhccCCCCCCChh----HHHHHHHHHHHhhhceeeeec---ce-eeeccchhhhheecCCCCchhHHHHHhcccc
Confidence 4688888883 454667 999999999999999987631 13 899999999998544 479999999999999
Q ss_pred hHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905 80 LTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI 119 (128)
Q Consensus 80 ~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~ 119 (128)
.++.|.+++++++.+. .+|..+||+.+|+|...|+.++.
T Consensus 113 ~~~~w~~l~dai~eg~-~~~~~~~G~~l~~~~~~~~~~~~ 151 (342)
T KOG3178|consen 113 IMNTWQFLKDAILEGG-DAFATAHGMMLGGYGGADERFSK 151 (342)
T ss_pred hhhhHHHHHHHHHhcc-cCCccccchhhhhhcccccccHH
Confidence 9999999999999988 68999999999999999886443
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=98.94 E-value=2.2e-09 Score=83.46 Aligned_cols=85 Identities=7% Similarity=0.031 Sum_probs=61.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCc----HHHHHHHhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLT----VRSFLQAVL 76 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s----~~~~~~~~~ 76 (128)
+|++|||+++++++ . .++||||+|+++|+|.+.. ++|++|++|+.+..+.+.+ +.+++.+..
T Consensus 24 ~t~~eLA~~~~~~~---~----~~~~lL~~L~~lgll~~~~-------~~y~~t~~~~~~l~~~~~~~~~~~~~~~~~~~ 89 (306)
T TIGR02716 24 KDLATLAADTGSVP---P----RLEMLLETLRQMRVINLED-------GKWSLTEFADYMFSPTPKEPNLHQTPVAKAMA 89 (306)
T ss_pred CCHHHHHHHcCCCh---H----HHHHHHHHHHhCCCeEecC-------CcEecchhHHhhccCCccchhhhcCchHHHHH
Confidence 48999999999955 8 9999999999999998753 6899999999777654321 123333332
Q ss_pred ChhhHHHHHhHHHhhhcCCCChhhhc
Q 045905 77 DPILTTPCQHVTTWFQNDDLRCLTRH 102 (128)
Q Consensus 77 ~~~~~~~~~~l~~~~~~g~~~~f~~a 102 (128)
. .....|..|.+++++ . ++|...
T Consensus 90 ~-~~~~~~~~l~~~~r~-~-~~~~~~ 112 (306)
T TIGR02716 90 F-LADDFYMGLSQAVRG-Q-KNFKGQ 112 (306)
T ss_pred H-HHHHHHHhHHHHhcC-C-cccccc
Confidence 1 233678999999984 3 345543
No 3
>PF00891 Methyltransf_2: O-methyltransferase; InterPro: IPR001077 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This domain includes a range of O-methyltransferases some of which utilise S-adenosyl methionine as substrate []. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. O-methyltransferases have a common catalytic domain structure, which might be universal among S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases []. Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32-71% sequence identity, and can be grouped according to the different compounds they utilise as substrates [].; GO: 0008171 O-methyltransferase activity; PDB: 1FPQ_A 1FP1_D 3P9K_B 3P9I_D 3P9C_A 3I53_A 3I5U_A 3I64_A 3I58_A 1ZG3_A ....
Probab=98.93 E-value=8.8e-10 Score=82.79 Aligned_cols=71 Identities=21% Similarity=0.254 Sum_probs=62.3
Q ss_pred ccceechHhhhhhhcCCC-CcHHHHHHHhcChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905 48 ERSYVATNASKLLLKDIT-LTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI 119 (128)
Q Consensus 48 ~~~y~~T~~s~~L~~~~~-~s~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~ 119 (128)
+++|+||++|+.|+.+.. .++..++.+...+..+.+|.+|.+++++|. ++|+.++|.++|+|++++|+..+
T Consensus 3 ~~~y~~t~~s~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~-~~~~~~~g~~~~~~~~~~~~~~~ 74 (241)
T PF00891_consen 3 GDRYSLTPLSELLLSDHSSPSMRGFVLFMISPELYPAWFRLTEAVRTGK-PPFEKAFGTPFFEYLEEDPELAK 74 (241)
T ss_dssp TEEEEE-HHHHGGSTTTTTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS--HHHHHHSS-HHHHHHCSHHHHH
T ss_pred CCEEeChHHHHHHhCCCCcCcHHHHHHHhcCHHHHHHHHHHHhhhccCC-CHHHHhcCCcHHHhhhhChHHHH
Confidence 578999999999998765 689999989889999999999999999998 89999999999999999997765
No 4
>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=98.13 E-value=1.6e-06 Score=50.85 Aligned_cols=28 Identities=32% Similarity=0.558 Sum_probs=23.9
Q ss_pred CCHHHHHHhCC-CCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALP-FHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|++|||++++ .+|.++. .|+||||+|+
T Consensus 23 ls~~eia~~l~~~~p~~~~----~L~RimR~L~ 51 (51)
T PF08100_consen 23 LSLSEIAARLPTSNPSAPP----MLDRIMRLLV 51 (51)
T ss_dssp BEHHHHHHTSTCT-TTHHH----HHHHHHHHHH
T ss_pred CCHHHHHHHcCCCCcchHH----HHHHHHHHhC
Confidence 58999999999 7776777 9999999996
No 5
>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=97.23 E-value=0.00064 Score=41.05 Aligned_cols=50 Identities=22% Similarity=0.292 Sum_probs=36.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
++..+|+..+++ +.. .+.|+++-|...|++.......|+....|.+||.|
T Consensus 19 ~t~~~l~~~~~~---~~~----~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 19 MTQSDLAERLGI---SKS----TVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp BEHHHHHHHTT-----HH----HHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred cCHHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 467899999999 447 89999999999999966554333323579999975
No 6
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=96.70 E-value=0.003 Score=40.19 Aligned_cols=46 Identities=22% Similarity=0.248 Sum_probs=37.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|+.|||+.++++. . .++|+|+.|...|++..... .+.|.+++-..
T Consensus 21 ~t~~~ia~~l~i~~---~----tv~r~l~~L~~~g~l~~~~~-----~~~y~l~~~~~ 66 (91)
T smart00346 21 LTLAELAERLGLSK---S----TAHRLLNTLQELGYVEQDGQ-----NGRYRLGPKVL 66 (91)
T ss_pred cCHHHHHHHhCCCH---H----HHHHHHHHHHHCCCeeecCC-----CCceeecHHHH
Confidence 47899999999955 7 89999999999999976531 46798887543
No 7
>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=96.67 E-value=0.0011 Score=38.47 Aligned_cols=33 Identities=30% Similarity=0.497 Sum_probs=28.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|+.|||+++|++. . .++|+|+.|+..|++..+
T Consensus 19 ~t~~eia~~~gl~~---s----tv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 19 LTLSEIARALGLPK---S----TVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp EEHHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEC
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCcCeecC
Confidence 37899999999955 7 899999999999999754
No 8
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=96.57 E-value=0.0032 Score=47.91 Aligned_cols=49 Identities=24% Similarity=0.246 Sum_probs=41.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL 61 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~ 61 (128)
+++.|||+++|+|. . .++|+|..|+..|++..++. .++|.+++-.-.|-
T Consensus 20 l~l~ela~~~glpk---s----T~~RlL~tL~~~G~v~~d~~-----~g~Y~Lg~~~~~lg 68 (246)
T COG1414 20 LSLAELAERLGLPK---S----TVHRLLQTLVELGYVEQDPE-----DGRYRLGPRLLELG 68 (246)
T ss_pred CCHHHHHHHhCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCcEeehHHHHHHH
Confidence 47999999999966 7 89999999999999998762 46899999765553
No 9
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=96.49 E-value=0.0044 Score=47.10 Aligned_cols=49 Identities=24% Similarity=0.288 Sum_probs=40.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL 61 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~ 61 (128)
+|+.|||+++|++. . .++|||+.|+..|++..... .+.|.+++-...|.
T Consensus 29 l~l~eia~~lgl~k---s----tv~Rll~tL~~~G~l~~~~~-----~~~Y~lG~~~~~lg 77 (257)
T PRK15090 29 IGITELSQRVMMSK---S----TVYRFLQTMKTLGYVAQEGE-----SEKYSLTLKLFELG 77 (257)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCcEEecHHHHHHH
Confidence 57899999999965 7 89999999999999987642 47899998765554
No 10
>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=96.41 E-value=0.0031 Score=40.04 Aligned_cols=45 Identities=16% Similarity=0.321 Sum_probs=34.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA 56 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~ 56 (128)
+|..|||+++++++ . .|+++|+.|...|++..... ..+.|.++.-
T Consensus 26 ~s~~eiA~~~~i~~---~----~l~kil~~L~~~Gli~s~~G----~~GGy~L~~~ 70 (83)
T PF02082_consen 26 VSSKEIAERLGISP---S----YLRKILQKLKKAGLIESSRG----RGGGYRLARP 70 (83)
T ss_dssp BEHHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEETS----TTSEEEESS-
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHhhCCeeEecCC----CCCceeecCC
Confidence 47899999999965 8 99999999999999876541 1356776643
No 11
>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=96.25 E-value=0.0071 Score=36.10 Aligned_cols=42 Identities=19% Similarity=0.278 Sum_probs=34.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN 55 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~ 55 (128)
+|..|||+.+|+++ . .+.|+|+.|...|++.... .+.|.++|
T Consensus 26 ~s~~ela~~~g~s~---~----tv~r~l~~L~~~g~i~~~~------~~~~~l~~ 67 (67)
T cd00092 26 LTRQEIADYLGLTR---E----TVSRTLKELEEEGLISRRG------RGKYRVNP 67 (67)
T ss_pred cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecC------CCeEEeCC
Confidence 47899999999944 7 8999999999999998653 25687764
No 12
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.20 E-value=0.013 Score=37.32 Aligned_cols=56 Identities=18% Similarity=0.254 Sum_probs=43.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|..+||..+++++ . .+.|.++-|...|++.......+.....|.+|+.+..+...
T Consensus 25 ~~~~~la~~~~~s~---~----~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 25 LSVSELAKRLGVSP---S----TVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred cCHHHHHHHHCCCc---h----hHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 47889999999954 7 89999999999999986543221123479999999877654
No 13
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=96.20 E-value=0.0084 Score=45.80 Aligned_cols=50 Identities=20% Similarity=0.230 Sum_probs=41.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
+|+.|||+++|++. . .++|+|+.|...|++..... .+.|.+++....|..
T Consensus 27 ls~~eia~~lgl~k---s----tv~RlL~tL~~~g~v~~~~~-----~~~Y~Lg~~~~~l~~ 76 (263)
T PRK09834 27 ATVGLLAELTGLHR---T----TVRRLLETLQEEGYVRRSAS-----DDSFRLTLKVRQLSE 76 (263)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEecC-----CCcEEEcHHHHHHHH
Confidence 47899999999955 7 89999999999999987642 468999987766543
No 14
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=96.18 E-value=0.0092 Score=33.24 Aligned_cols=33 Identities=21% Similarity=0.303 Sum_probs=28.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|..|||+.+++++ . .+.|+|+.|...|++...
T Consensus 9 ~s~~~la~~l~~s~---~----tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 9 LTRQEIAELLGLTR---E----TVSRTLKRLEKEGLISRE 41 (48)
T ss_pred cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEe
Confidence 47899999999944 7 899999999999999754
No 15
>PRK11569 transcriptional repressor IclR; Provisional
Probab=96.13 E-value=0.0087 Score=46.04 Aligned_cols=48 Identities=15% Similarity=0.181 Sum_probs=39.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+|+.|||+.+|++. . .++|||+.|+..|++..+.. .++|.+.+-...|
T Consensus 44 ~~lseia~~lglpk---s----Tv~RlL~tL~~~G~l~~~~~-----~~~Y~lG~~l~~L 91 (274)
T PRK11569 44 VALTELAQQAGLPN---S----TTHRLLTTMQQQGFVRQVGE-----LGHWAIGAHAFIV 91 (274)
T ss_pred cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCeEecCHHHHHH
Confidence 58999999999965 7 89999999999999976542 4789998776554
No 16
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.06 E-value=0.012 Score=37.82 Aligned_cols=47 Identities=19% Similarity=0.262 Sum_probs=40.2
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
+.|||..+++++ . .+.|+++.|...|++.... ...|.+|+.++.+..
T Consensus 2 ~~ela~~l~is~---s----tvs~~l~~L~~~glI~r~~------~~~~~lT~~g~~~~~ 48 (96)
T smart00529 2 TSEIAERLNVSP---P----TVTQMLKKLEKDGLVEYEP------YRGITLTEKGRRLAR 48 (96)
T ss_pred HHHHHHHhCCCh---H----HHHHHHHHHHHCCCEEEcC------CCceEechhHHHHHH
Confidence 579999999954 8 9999999999999998765 357999999988764
No 17
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=96.02 E-value=0.011 Score=45.47 Aligned_cols=49 Identities=10% Similarity=0.057 Sum_probs=40.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL 61 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~ 61 (128)
+|+.|||+.+|++. . .++|||..|+..|++..+.. .+.|.+++--..|.
T Consensus 41 ~tl~eIa~~lglpk---S----tv~RlL~tL~~~G~l~~~~~-----~~~Y~lG~~l~~Lg 89 (271)
T PRK10163 41 SSVSDISLNLDLPL---S----TTFRLLKVLQAADFVYQDSQ-----LGWWHIGLGVFNVG 89 (271)
T ss_pred cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCeEEecHHHHHHH
Confidence 57899999999965 7 89999999999999976542 47899887665443
No 18
>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=95.98 E-value=0.011 Score=44.71 Aligned_cols=47 Identities=23% Similarity=0.295 Sum_probs=39.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL 61 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~ 61 (128)
+|+.|||+++|++. . .++|||..|+..|++..+ .+.|.+++.-..|.
T Consensus 25 ~~l~eia~~lglpk---s----T~~RlL~tL~~~G~l~~~-------~~~Y~lG~~~~~lg 71 (248)
T TIGR02431 25 LTLTDVAEATGLTR---A----AARRFLLTLVELGYVTSD-------GRLFWLTPRVLRLG 71 (248)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeC-------CCEEEecHHHHHHH
Confidence 58999999999966 7 899999999999999753 36799998765553
No 19
>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=95.77 E-value=0.014 Score=40.32 Aligned_cols=45 Identities=13% Similarity=0.168 Sum_probs=35.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA 56 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~ 56 (128)
+|.+|||+.+++++ . .|.+||+.|...|++..... ..|.|.++.-
T Consensus 26 ~s~~~ia~~~~ip~---~----~l~kil~~L~~~glv~s~~G----~~Ggy~l~~~ 70 (135)
T TIGR02010 26 VTLADISERQGISL---S----YLEQLFAKLRKAGLVKSVRG----PGGGYQLGRP 70 (135)
T ss_pred CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCceEEEeC----CCCCEeccCC
Confidence 47899999999966 8 99999999999999975431 1345776654
No 20
>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=95.74 E-value=0.027 Score=37.75 Aligned_cols=56 Identities=13% Similarity=0.121 Sum_probs=43.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|..|||..+++++ . .+.|+++-|...|++.......|.....|.+|+.|+.+.+.
T Consensus 43 ~t~~ela~~~~~~~---~----tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~ 98 (118)
T TIGR02337 43 MEFTQLANQACILR---P----SLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS 98 (118)
T ss_pred cCHHHHHHHhCCCc---h----hHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence 47889999999944 7 89999999999999976543222212479999999988754
No 21
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.72 E-value=0.023 Score=39.52 Aligned_cols=49 Identities=22% Similarity=0.316 Sum_probs=40.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
+++.|||..+++++ + .+.++++.|...|++.... .+.|.+|+.|+.+..
T Consensus 23 ~~~~ela~~l~vs~---~----svs~~l~~L~~~Gli~~~~------~~~i~LT~~G~~~a~ 71 (142)
T PRK03902 23 ARVSDIAEALSVHP---S----SVTKMVQKLDKDEYLIYEK------YRGLVLTPKGKKIGK 71 (142)
T ss_pred cCHHHHHHHhCCCh---h----HHHHHHHHHHHCCCEEEec------CceEEECHHHHHHHH
Confidence 36789999999954 7 8999999999999987543 367999999987653
No 22
>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=95.46 E-value=0.02 Score=38.94 Aligned_cols=47 Identities=11% Similarity=0.227 Sum_probs=36.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|..|||+.+++++ . .++++|+.|...|++..... ..+.|.++.-..
T Consensus 26 ~s~~eia~~~~i~~---~----~v~~il~~L~~~gli~~~~g----~~ggy~l~~~~~ 72 (132)
T TIGR00738 26 VSVKEIAERQGISR---S----YLEKILRTLRRAGLVESVRG----PGGGYRLARPPE 72 (132)
T ss_pred CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEeccC----CCCCccCCCCHH
Confidence 47899999999965 8 99999999999999876431 134577765443
No 23
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=95.36 E-value=0.024 Score=35.59 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=36.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
+..+|+..++++. . .+.+.+..|...|++... .+.|.+|+-|+-+.+
T Consensus 21 ~~t~i~~~~~L~~---~----~~~~yL~~L~~~gLI~~~-------~~~Y~lTekG~~~l~ 67 (77)
T PF14947_consen 21 KKTEIMYKANLNY---S----TLKKYLKELEEKGLIKKK-------DGKYRLTEKGKEFLE 67 (77)
T ss_dssp -HHHHHTTST--H---H----HHHHHHHHHHHTTSEEEE-------TTEEEE-HHHHHHHH
T ss_pred CHHHHHHHhCcCH---H----HHHHHHHHHHHCcCeeCC-------CCEEEECccHHHHHH
Confidence 4678999999944 7 899999999999999553 478999999988764
No 24
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=95.35 E-value=0.024 Score=40.76 Aligned_cols=45 Identities=11% Similarity=0.183 Sum_probs=35.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA 56 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~ 56 (128)
+|++|||+++++|+ . .|.+||+.|...|++..... ..|.|.|..-
T Consensus 26 vs~~eIA~~~~ip~---~----~l~kIl~~L~~aGLv~s~rG----~~GGy~Lar~ 70 (164)
T PRK10857 26 VPLADISERQGISL---S----YLEQLFSRLRKNGLVSSVRG----PGGGYLLGKD 70 (164)
T ss_pred CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeCCC----CCCCeeccCC
Confidence 58899999999966 8 99999999999999986532 1345776543
No 25
>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=95.16 E-value=0.02 Score=34.72 Aligned_cols=44 Identities=23% Similarity=0.304 Sum_probs=33.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN 55 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~ 55 (128)
+|+.|||..++++. . .+++.|+-|...|++..... ....|...+
T Consensus 23 ~t~~eIa~~l~i~~---~----~v~~~L~~L~~~GlV~~~~~----~~~~Y~a~~ 66 (68)
T PF01978_consen 23 ATAEEIAEELGISR---S----TVYRALKSLEEKGLVEREEG----RPKVYRAVP 66 (68)
T ss_dssp EEHHHHHHHHTSSH---H----HHHHHHHHHHHTTSEEEEEE----CCEEEEEE-
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEEcC----ceEEEEEeC
Confidence 47899999999944 7 89999999999999986652 134566544
No 26
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=95.10 E-value=0.032 Score=39.51 Aligned_cols=46 Identities=13% Similarity=0.234 Sum_probs=36.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
+|+++||+..+++| . .|.|||..|...|++.-... ..|.|.|..-.
T Consensus 26 ~s~~~IA~~~~is~---~----~L~kil~~L~kaGlV~S~rG----~~GGy~Lar~~ 71 (150)
T COG1959 26 VSSAEIAERQGISP---S----YLEKILSKLRKAGLVKSVRG----KGGGYRLARPP 71 (150)
T ss_pred ccHHHHHHHhCcCH---H----HHHHHHHHHHHcCCEEeecC----CCCCccCCCCh
Confidence 46899999999966 8 99999999999999976542 13567776544
No 27
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=95.00 E-value=0.034 Score=39.42 Aligned_cols=46 Identities=11% Similarity=0.200 Sum_probs=36.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
+|..|||++.++++ . .|.+||+.|...|++.-... ..|.|.|+.--
T Consensus 25 ~s~~eIA~~~~is~---~----~L~kIl~~L~~aGlv~S~rG----~~GGy~La~~p 70 (153)
T PRK11920 25 SRIPEIARAYGVSE---L----FLFKILQPLVEAGLVETVRG----RNGGVRLGRPA 70 (153)
T ss_pred CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeecC----CCCCeeecCCH
Confidence 47899999999966 8 99999999999999976642 23567776543
No 28
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=94.91 E-value=0.057 Score=37.41 Aligned_cols=56 Identities=16% Similarity=0.133 Sum_probs=43.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|..|||..++++ +. .+.|++.-|...|++......+|.-...+.+|+.|+.+...
T Consensus 55 ~t~~eLa~~l~i~---~~----tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 55 ITPVELKKVLSVD---LG----ALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 5789999999994 48 99999999999999976543333222468999999988654
No 29
>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=94.73 E-value=0.056 Score=32.07 Aligned_cols=49 Identities=24% Similarity=0.342 Sum_probs=37.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
++..||+..++++. . .++|.|+.|...|++...... ....|.+|+ ++.+
T Consensus 21 ~~~~ei~~~~~i~~---~----~i~~~l~~L~~~g~i~~~~~~---~~~~~~~~~-g~~~ 69 (78)
T cd00090 21 LTVSELAERLGLSQ---S----TVSRHLKKLEEAGLVESRREG---RRVYYSLTD-AERL 69 (78)
T ss_pred cCHHHHHHHHCcCH---h----HHHHHHHHHHHCCCeEEEEec---cEEEEEeCC-chHH
Confidence 47889999999944 7 899999999999999865421 136788887 5544
No 30
>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=94.66 E-value=0.036 Score=37.82 Aligned_cols=60 Identities=18% Similarity=0.217 Sum_probs=41.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLD 77 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~ 77 (128)
+|..|||+++++++ . .+.++|+.|...|++..... ..+.|.+... ....++.+++..+-+
T Consensus 26 ~s~~eia~~l~is~---~----~v~~~l~~L~~~Gli~~~~g----~~ggy~l~~~------~~~it~~~v~~~l~~ 85 (130)
T TIGR02944 26 YSAAEIAEQTGLNA---P----TVSKILKQLSLAGIVTSKRG----VEGGYTLARA------PRDITVADIVKAVEG 85 (130)
T ss_pred ccHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEecCC----CCCChhhcCC------ccccCHHHHHHHHcC
Confidence 47899999999955 8 99999999999999965431 1345766442 112246666555543
No 31
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=94.58 E-value=0.13 Score=35.54 Aligned_cols=56 Identities=14% Similarity=0.217 Sum_probs=43.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|..|||..+++++ . .+.|++.-|...|++......+|.-...+.+|+.|+.+...
T Consensus 47 ~t~~eLa~~l~~~~---~----tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~ 102 (144)
T PRK03573 47 QSQIQLAKAIGIEQ---P----SLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISE 102 (144)
T ss_pred CCHHHHHHHhCCCh---h----hHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHH
Confidence 36789999999944 7 89999999999999976653333212468999999988764
No 32
>PRK11050 manganese transport regulator MntR; Provisional
Probab=94.49 E-value=0.074 Score=37.58 Aligned_cols=49 Identities=14% Similarity=0.142 Sum_probs=40.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
++..|||+.+++++ . .+.|.++.|...|++.... .+.+.+|+.|+.+..
T Consensus 52 ~t~~eLA~~l~is~---s----tVsr~l~~Le~~GlI~r~~------~~~v~LT~~G~~l~~ 100 (152)
T PRK11050 52 ARQVDIAARLGVSQ---P----TVAKMLKRLARDGLVEMRP------YRGVFLTPEGEKLAQ 100 (152)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEec------CCceEECchHHHHHH
Confidence 47889999999944 7 8999999999999987554 356899999988854
No 33
>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=94.31 E-value=0.091 Score=33.73 Aligned_cols=54 Identities=20% Similarity=0.277 Sum_probs=38.2
Q ss_pred CHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 2 TLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 2 S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
...||...+ ++++ . .|.+-|+.|...|++...........-.|.+|+.|+.|..
T Consensus 20 rf~el~~~l~~is~---~----~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~ 74 (90)
T PF01638_consen 20 RFSELQRRLPGISP---K----VLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP 74 (90)
T ss_dssp EHHHHHHHSTTS-H---H----HHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred cHHHHHHhcchhHH---H----HHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence 367899998 5743 7 8999999999999997653211111236999999998863
No 34
>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=94.24 E-value=0.11 Score=34.40 Aligned_cols=56 Identities=11% Similarity=0.285 Sum_probs=42.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|..|||..++++ .. .+.|+++.|...|++....+.+|.-.-.+.+|+.|+-+.+.
T Consensus 44 ~t~~eL~~~l~~~---~s----tvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~ 99 (109)
T TIGR01889 44 LTLKEIIKEILIK---QS----ALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIES 99 (109)
T ss_pred CcHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHH
Confidence 4789999999994 48 99999999999999976543332112358899999887653
No 35
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=94.15 E-value=0.069 Score=37.09 Aligned_cols=44 Identities=7% Similarity=0.120 Sum_probs=34.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN 55 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~ 55 (128)
+|..|||+.+++++ . .|+++|+.|...|++..... ..+.|.++.
T Consensus 26 ~s~~~ia~~~~is~---~----~vrk~l~~L~~~Glv~s~~G----~~GG~~l~~ 69 (141)
T PRK11014 26 TSISEVTEVYGVSR---N----HMVKIINQLSRAGYVTAVRG----KNGGIRLGK 69 (141)
T ss_pred cCHHHHHHHHCcCH---H----HHHHHHHHHHhCCEEEEecC----CCCCeeecC
Confidence 36789999999955 8 99999999999999976542 134566654
No 36
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=94.07 E-value=0.12 Score=36.88 Aligned_cols=50 Identities=14% Similarity=0.145 Sum_probs=41.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+...+||+.+++.| + .+..+++-|...|++.... .+.|.||+.|+.+...
T Consensus 25 ~~~~diA~~L~Vsp---~----sVt~ml~rL~~~GlV~~~~------y~gi~LT~~G~~~a~~ 74 (154)
T COG1321 25 ARTKDIAERLKVSP---P----SVTEMLKRLERLGLVEYEP------YGGVTLTEKGREKAKE 74 (154)
T ss_pred ccHHHHHHHhCCCc---H----HHHHHHHHHHHCCCeEEec------CCCeEEChhhHHHHHH
Confidence 35689999999955 7 7888999999999998765 4789999999876644
No 37
>PRK10870 transcriptional repressor MprA; Provisional
Probab=93.92 E-value=0.13 Score=37.17 Aligned_cols=56 Identities=16% Similarity=0.141 Sum_probs=43.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|..|||..+++++ . .+.|++.-|...|++......+|.-...+.+|+.|+.+.+.
T Consensus 72 it~~eLa~~l~l~~---~----tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~ 127 (176)
T PRK10870 72 IQPSELSCALGSSR---T----NATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE 127 (176)
T ss_pred cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 36789999999944 7 89999999999999976553333222468999999988865
No 38
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=93.64 E-value=0.15 Score=29.23 Aligned_cols=45 Identities=18% Similarity=0.220 Sum_probs=34.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN 55 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~ 55 (128)
+|..||++.+++++ . .+++.|+.|...|++..... +....|.+|.
T Consensus 11 ~~~~~i~~~l~is~---~----~v~~~l~~L~~~g~i~~~~~---~~~~~~~~~~ 55 (66)
T smart00418 11 LCVCELAEILGLSQ---S----TVSHHLKKLREAGLVESRRE---GKRVYYSLTD 55 (66)
T ss_pred ccHHHHHHHHCCCH---H----HHHHHHHHHHHCCCeeeeec---CCEEEEEEch
Confidence 47889999999944 7 89999999999999975432 1134677766
No 39
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=93.56 E-value=0.13 Score=31.40 Aligned_cols=44 Identities=20% Similarity=0.185 Sum_probs=33.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN 55 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~ 55 (128)
+|+.|||.++|++. . .++|+|--|-..|++..... .++.|.++.
T Consensus 23 ~ta~eLa~~lgl~~---~----~v~r~L~~L~~~G~V~~~~~----~~~~W~i~~ 66 (68)
T smart00550 23 STALQLAKNLGLPK---K----EVNRVLYSLEKKGKVCKQGG----TPPLWKLTD 66 (68)
T ss_pred cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecCC----CCCceEeec
Confidence 57899999999955 7 89999999999999865431 135676653
No 40
>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=93.17 E-value=0.18 Score=37.09 Aligned_cols=56 Identities=20% Similarity=0.227 Sum_probs=42.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc-CCCCc-ccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF-GQNDQ-ERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~-~~~~~-~~~y~~T~~s~~L~~~ 63 (128)
+|..|||+.+++++ . .++|.|..|...|++..... ...|. ...|.+|+.++.+...
T Consensus 16 ~t~~eLA~~lgis~---~----tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~ 73 (203)
T TIGR02702 16 ATAAALAEALAISP---Q----AVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ 73 (203)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhccc
Confidence 57899999999944 8 99999999999999975521 11121 2358999999876644
No 41
>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=93.12 E-value=0.081 Score=32.33 Aligned_cols=34 Identities=21% Similarity=0.419 Sum_probs=28.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|+.|||..++++| + .|.-+|..|+.+|.+....
T Consensus 15 ~S~~eLa~~~~~s~---~----~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 15 VSLAELAREFGISP---E----AVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp EEHHHHHHHTT--H---H----HHHHHHHHHHCCTSCEEEE
T ss_pred cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEEec
Confidence 47899999999954 8 9999999999999998664
No 42
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=93.03 E-value=0.42 Score=36.93 Aligned_cols=49 Identities=18% Similarity=0.316 Sum_probs=41.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
.|.+||-..+++++ . .+.+=++-|...|++.+.+ +.|.||++|+.++..
T Consensus 27 kti~EI~~~l~vs~---~----ai~pqiKkL~~~~LV~~~~-------~~Y~LS~~G~iiv~k 75 (260)
T COG4742 27 KTIEEIKNELNVSS---S----AILPQIKKLKDKGLVVQEG-------DRYSLSSLGKIIVEK 75 (260)
T ss_pred CCHHHHHHHhCCCc---H----HHHHHHHHHhhCCCEEecC-------CEEEecchHHHHHHH
Confidence 37899999999955 6 7777788899999998764 789999999999865
No 43
>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=92.85 E-value=0.15 Score=37.43 Aligned_cols=46 Identities=15% Similarity=0.215 Sum_probs=37.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
+|..|||+.+++++ . .+.|.+..|...|++..... ....|.+|+.|
T Consensus 158 ~s~~eia~~l~is~---s----tv~r~L~~Le~~GlI~r~~~----r~~~~~lT~~G 203 (203)
T TIGR01884 158 KSVKNIAKKLGKSL---S----TISRHLRELEKKGLVEQKGR----KGKRYSLTKLG 203 (203)
T ss_pred cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEEcC----CccEEEeCCCC
Confidence 47899999999954 7 89999999999999987641 14679999864
No 44
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=92.75 E-value=0.12 Score=30.21 Aligned_cols=35 Identities=23% Similarity=0.251 Sum_probs=29.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF 42 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~ 42 (128)
+|..|||+.++++ +. .+.|+++.|...|++.....
T Consensus 22 ~t~~~la~~l~~~---~~----~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 22 LTQSELAERLGIS---KS----TVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp EEHHHHHHHHTS----HH----HHHHHHHHHHHTTSEEEEE-
T ss_pred cCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEeCC
Confidence 3688999999994 48 99999999999999976653
No 45
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=92.70 E-value=0.16 Score=28.57 Aligned_cols=31 Identities=26% Similarity=0.366 Sum_probs=25.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|..|||.++|+ ... .+.+.++-|...|++.
T Consensus 18 ~t~~ela~~~~i---s~~----tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 18 ITQKELAEKLGI---SRS----TVNRYLKKLEEKGLIE 48 (48)
T ss_dssp S-HHHHHHHHTS----HH----HHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHhCC---CHH----HHHHHHHHHHHCcCcC
Confidence 578999999999 447 8999999999999863
No 46
>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=92.65 E-value=0.2 Score=32.58 Aligned_cols=42 Identities=10% Similarity=-0.030 Sum_probs=33.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT 54 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T 54 (128)
+|-.|||+.+|+++ . .+.|+|..|...|++..... -+.|+.+
T Consensus 48 is~~eLa~~~g~sr---~----tVsr~L~~Le~~GlI~r~~~-----~~~~~~n 89 (95)
T TIGR01610 48 VTATVIAELTGLSR---T----HVSDAIKSLARRRIIFRQGM-----MGIVGVN 89 (95)
T ss_pred cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeeeecC-----CceeecC
Confidence 47789999999944 7 89999999999999975531 3566665
No 47
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=92.59 E-value=0.25 Score=37.20 Aligned_cols=54 Identities=13% Similarity=0.123 Sum_probs=43.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
+|..|||+.+++ +.+ .+.|+++.|...|++...... ....+.+|+.|+.+....
T Consensus 22 IS~~eLA~~L~i---S~~----Tvsr~Lk~LEe~GlI~R~~~~---r~~~v~LTekG~~ll~~~ 75 (217)
T PRK14165 22 ISSSEFANHTGT---SSK----TAARILKQLEDEGYITRTIVP---RGQLITITEKGLDVLYNE 75 (217)
T ss_pred cCHHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEEEEcC---CceEEEECHHHHHHHHHH
Confidence 578999999999 448 999999999999999755421 136799999999777543
No 48
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=92.52 E-value=0.22 Score=31.49 Aligned_cols=55 Identities=15% Similarity=0.195 Sum_probs=38.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCc-ccceechHhhhhhhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQ-ERSYVATNASKLLLK 62 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~-~~~y~~T~~s~~L~~ 62 (128)
++..||.+.++++ .. .|.+-|+.|...|++.......+.. ...|.+|+.|+....
T Consensus 15 ~~f~~L~~~l~lt---~g----~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~ 70 (80)
T PF13601_consen 15 ATFSELKEELGLT---DG----NLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFE 70 (80)
T ss_dssp EEHHHHHHHTT-----HH----HHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHH
T ss_pred CCHHHHHHHhCcC---HH----HHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHH
Confidence 3678999999994 47 9999999999999997654322111 236999999986543
No 49
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=91.74 E-value=0.38 Score=27.48 Aligned_cols=33 Identities=18% Similarity=0.140 Sum_probs=28.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|..|||+.++++. . .++|.|+.|...|++....
T Consensus 22 s~~~la~~~~vs~---~----tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 22 SERELAAQLGVSR---T----TVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEec
Confidence 6889999999944 7 8999999999999986543
No 50
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=91.62 E-value=0.41 Score=36.07 Aligned_cols=57 Identities=18% Similarity=0.200 Sum_probs=42.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC-CCc-ccceechHhhhhhhcCC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ-NDQ-ERSYVATNASKLLLKDI 64 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~-~~~-~~~y~~T~~s~~L~~~~ 64 (128)
+|+.|||+++|+++ . .++|-|-.|...|++....... -|- ...|.+|.-++......
T Consensus 26 ~sa~elA~~Lgis~---~----avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f~~~ 84 (218)
T COG2345 26 VSADELAEELGISP---M----AVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQFPKR 84 (218)
T ss_pred ccHHHHHHHhCCCH---H----HHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhcchh
Confidence 58999999999966 8 9999999999999886542211 121 24799999987755443
No 51
>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=91.33 E-value=0.38 Score=28.05 Aligned_cols=32 Identities=19% Similarity=0.185 Sum_probs=27.4
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
|..+||..++++. . .+++.|..|...|++...
T Consensus 27 ~~~~la~~~~is~---~----~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 27 SERELAEELGVSR---T----TVREALRELEAEGLVERR 58 (66)
T ss_pred CHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEec
Confidence 4789999999944 7 899999999999998644
No 52
>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=91.14 E-value=0.18 Score=29.83 Aligned_cols=34 Identities=24% Similarity=0.286 Sum_probs=29.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|+.|||+.+++++ . .+++-|+.|...|++....
T Consensus 25 ~t~~ela~~l~~~~---~----t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 25 MTVSELAEELGISQ---S----TVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp BEHHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEEE
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCeEEec
Confidence 47899999999954 7 8999999999999998664
No 53
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=90.96 E-value=0.46 Score=32.88 Aligned_cols=35 Identities=26% Similarity=0.424 Sum_probs=29.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF 42 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~ 42 (128)
+|.+|||+.++. +.. .++|.|+-|+..|++.....
T Consensus 43 ~tvdelae~lnr---~rS----tv~rsl~~L~~~GlV~Rek~ 77 (126)
T COG3355 43 LTVDELAEILNR---SRS----TVYRSLQNLLEAGLVEREKV 77 (126)
T ss_pred cCHHHHHHHHCc---cHH----HHHHHHHHHHHcCCeeeeee
Confidence 478999999999 557 89999999999999965543
No 54
>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=90.57 E-value=0.53 Score=30.68 Aligned_cols=52 Identities=15% Similarity=0.098 Sum_probs=37.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH----------HHhcCcc-eeeccCCCCcccceechHhhhhhhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI----------LVHSGFF-AQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~----------L~~~gvf-~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
+++.|||..+++++ . .+.-.|+- |+.+|++ .+... . +...|.+|+-|+.+++
T Consensus 26 ~~~~eIar~v~~~~---s----nV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~--~-g~k~Y~lT~~G~~~~~ 88 (90)
T PF07381_consen 26 AYPSEIARSVGSDY---S----NVLGALRGDGKRYNKEDSLVGLGLVEEEEEK--G-GFKYYRLTEKGKRIAE 88 (90)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHhcCCCCcCcchhHHHcCCeeEeeec--C-CeeEEEeChhhhhHHh
Confidence 46789999999944 7 77676664 8999999 33321 1 1458999999987653
No 55
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=90.49 E-value=0.44 Score=26.47 Aligned_cols=34 Identities=18% Similarity=0.246 Sum_probs=29.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|..+|+..+++++ . .++|.|..|...|++....
T Consensus 15 ~s~~~l~~~l~~s~---~----tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 15 VSVEELAELLGVSE---M----TIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEee
Confidence 47899999999944 7 8999999999999987553
No 56
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=90.40 E-value=0.48 Score=30.76 Aligned_cols=54 Identities=19% Similarity=0.214 Sum_probs=42.4
Q ss_pred HHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 4 NELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 4 ~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
.|||..+++++ . .+.|+++-|...|++......+|.-...+.+|+.|+.+....
T Consensus 40 ~~la~~l~i~~---~----~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~ 93 (126)
T COG1846 40 KELAERLGLDR---S----TVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQL 93 (126)
T ss_pred HHHHHHHCCCH---H----HHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHh
Confidence 79999999944 8 999999999999999766543332124699999999887653
No 57
>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=90.37 E-value=0.29 Score=25.81 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=23.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFF 37 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf 37 (128)
+|-.|||..+|+.+ . .+.|+|..|-..|+.
T Consensus 3 mtr~diA~~lG~t~---E----TVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTR---E----TVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-H---H----HHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcH---H----HHHHHHHHHHHcCCC
Confidence 57789999999944 7 999999999888863
No 58
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=90.07 E-value=0.3 Score=28.32 Aligned_cols=34 Identities=24% Similarity=0.320 Sum_probs=28.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|..|||..+++ +.. .+.|+++-|...|++....
T Consensus 18 ~~~~~la~~~~~---~~~----~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 18 ITQSELAEKLGI---SRS----TVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp EEHHHHHHHHTS----HH----HHHHHHHHHHHTTSEEEEE
T ss_pred CCHHHHHHHHCC---Chh----HHHHHHHHHHHCCCEEecc
Confidence 367899999999 448 9999999999999997554
No 59
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=88.64 E-value=1.1 Score=32.84 Aligned_cols=56 Identities=14% Similarity=0.201 Sum_probs=43.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|..|||..+.+++ + .+.|++.-|...|++......+|.-.....+|+.|+.+...
T Consensus 60 itq~eLa~~l~l~~---s----Tvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~ 115 (185)
T PRK13777 60 ASISEIAKFGVMHV---S----TAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLE 115 (185)
T ss_pred cCHHHHHHHHCCCH---h----hHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 47889999999844 7 89999999999999976543333212458999999988754
No 60
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=88.22 E-value=0.67 Score=30.20 Aligned_cols=31 Identities=23% Similarity=0.290 Sum_probs=27.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|..|||+.+|+++ . .++|.++.|...|++.
T Consensus 18 ~~~~~la~~l~~s~---~----tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 18 ISLAELAKKVGLSP---S----TVHNRVKRLEEEGVIK 48 (108)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCee
Confidence 47899999999955 7 8999999999999987
No 61
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=88.16 E-value=0.68 Score=40.33 Aligned_cols=46 Identities=15% Similarity=0.207 Sum_probs=37.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN 55 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~ 55 (128)
.|++|||+.+|+++ + .|+|.|-+....||+++.+...+ .+.|..++
T Consensus 617 wt~eelse~l~ip~---~----~lrrrL~fWi~~GvL~e~~~~s~--tgt~T~iE 662 (765)
T KOG2165|consen 617 WTLEELSESLGIPV---P----ALRRRLSFWIQKGVLREEPIISD--TGTLTVIE 662 (765)
T ss_pred ccHHHHHHHhCCCH---H----HHHHHHHHHHHcCeeecCCCCCC--Cceeeecc
Confidence 47899999999976 8 99999999999999998763211 35677766
No 62
>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=88.10 E-value=1 Score=29.67 Aligned_cols=48 Identities=23% Similarity=0.365 Sum_probs=33.7
Q ss_pred CCHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905 1 MTLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT 54 (128)
Q Consensus 1 ~S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T 54 (128)
+|++||.+++.- +..+.. .+||.|..|+..|++......+ +..+|.++
T Consensus 17 ~sa~ei~~~l~~~~~~i~~~----TVYR~L~~L~~~Gli~~~~~~~--~~~~y~~~ 66 (116)
T cd07153 17 LTAEEIYERLRKKGPSISLA----TVYRTLELLEEAGLVREIELGD--GKARYELN 66 (116)
T ss_pred CCHHHHHHHHHhcCCCCCHH----HHHHHHHHHHhCCCEEEEEeCC--CceEEEeC
Confidence 478899888842 112557 8999999999999998765311 13467664
No 63
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=88.08 E-value=1.3 Score=30.13 Aligned_cols=52 Identities=21% Similarity=0.317 Sum_probs=38.3
Q ss_pred HHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905 3 LNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL 61 (128)
Q Consensus 3 ~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~ 61 (128)
..||-..++ +++ . .|.+=||.|...|++......+....-.|++|+.|+-|.
T Consensus 39 F~eL~r~i~~Is~---k----~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~ 91 (120)
T COG1733 39 FNELRRSIGGISP---K----MLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLL 91 (120)
T ss_pred HHHHHHHccccCH---H----HHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHH
Confidence 568888877 644 7 899999999999999765432111124599999998775
No 64
>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=87.30 E-value=1.2 Score=26.96 Aligned_cols=34 Identities=21% Similarity=0.284 Sum_probs=29.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|-.|||..+|+.. . .+.|+|+.|...|++.-..
T Consensus 29 lt~~~iA~~~g~sr---~----tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 29 LTQEEIADMLGVSR---E----TVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp SSHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEEEET
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEcC
Confidence 46789999999944 7 8999999999999998553
No 65
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=86.94 E-value=3.3 Score=28.10 Aligned_cols=46 Identities=17% Similarity=0.224 Sum_probs=35.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA 56 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~ 56 (128)
+++.||++.+++++ + .+.+-|+.|...|++..... |....|.+.+.
T Consensus 31 ~~v~ela~~l~lsq---s----tvS~HL~~L~~AGLV~~~r~---Gr~~~Y~l~~~ 76 (117)
T PRK10141 31 LCVCDLCTALDQSQ---P----KISRHLALLRESGLLLDRKQ---GKWVHYRLSPH 76 (117)
T ss_pred cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCceEEEEE---cCEEEEEECch
Confidence 36789999999955 7 89999999999999976542 11346888763
No 66
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=86.90 E-value=1.4 Score=33.68 Aligned_cols=50 Identities=20% Similarity=0.253 Sum_probs=40.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL 61 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~ 61 (128)
+|+.||+...|+|- + .+|.+||-|...|++.... |.+..|..-+...++.
T Consensus 31 ~tA~eis~~sgvP~---~----kvY~vl~sLe~kG~v~~~~----g~P~~y~av~p~~~i~ 80 (247)
T COG1378 31 ATAKEISEASGVPR---P----KVYDVLRSLEKKGLVEVIE----GRPKKYRAVPPEELIE 80 (247)
T ss_pred ccHHHHHHHcCCCc---h----hHHHHHHHHHHCCCEEeeC----CCCceEEeCCHHHHHH
Confidence 58999999999954 6 8999999999999997653 2257898888877554
No 67
>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=86.84 E-value=0.97 Score=32.52 Aligned_cols=44 Identities=16% Similarity=0.143 Sum_probs=37.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
+|..+||+.++++ .+ .+.|.+..|...+|+.... .+.|-.+|-=
T Consensus 76 ~t~~~ia~~l~iS---~~----Tv~r~ik~L~e~~iI~k~~------~G~Y~iNP~~ 119 (165)
T PF05732_consen 76 ATQKEIAEKLGIS---KP----TVSRAIKELEEKNIIKKIR------NGAYMINPNF 119 (165)
T ss_pred eeHHHHHHHhCCC---HH----HHHHHHHHHHhCCcEEEcc------CCeEEECcHH
Confidence 3678999999994 37 8999999999999998664 4789999974
No 68
>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=86.51 E-value=0.64 Score=26.07 Aligned_cols=30 Identities=23% Similarity=0.300 Sum_probs=25.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
++.||++.+++ +.. .+.+-|+.|...|++.
T Consensus 17 ~~~el~~~l~~---s~~----~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 17 TVSELAEELGL---SQS----TVSHHLKKLREAGLVE 46 (47)
T ss_dssp EHHHHHHHHTS----HH----HHHHHHHHHHHTTSEE
T ss_pred chhhHHHhccc---cch----HHHHHHHHHHHCcCee
Confidence 57899999999 447 8999999999999874
No 69
>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=86.31 E-value=2.1 Score=27.19 Aligned_cols=48 Identities=17% Similarity=0.097 Sum_probs=36.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce-eeccCCCCcccceechHhhhhhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA-QQNFGQNDQERSYVATNASKLLL 61 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~-e~~~~~~~~~~~y~~T~~s~~L~ 61 (128)
...+||+.++.+| . .++-.|..|-.+|++. .+.+ .+.|-+|..+-.+.
T Consensus 25 gSk~ia~~l~~s~---a----TIRN~M~~Le~lGlve~~p~~-----s~GriPT~~aYr~~ 73 (78)
T PF03444_consen 25 GSKTIAEELGRSP---A----TIRNEMADLEELGLVESQPHP-----SGGRIPTDKAYRAL 73 (78)
T ss_pred CHHHHHHHHCCCh---H----HHHHHHHHHHHCCCccCCCCC-----CCCCCcCHHHHHHH
Confidence 4578999999854 8 9999999999999996 3322 35688888875444
No 70
>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=86.26 E-value=0.98 Score=26.94 Aligned_cols=34 Identities=15% Similarity=0.261 Sum_probs=28.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++..+||+.+++.| + .+..+++-|...|++....
T Consensus 23 v~~~~iA~~L~vs~---~----tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 23 VRTKDIAERLGVSP---P----TVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp BBHHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEET
T ss_pred ccHHHHHHHHCCCh---H----HHHHHHHHHHHCCCEEecC
Confidence 36789999999944 8 8999999999999997653
No 71
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=86.19 E-value=1.1 Score=28.92 Aligned_cols=34 Identities=12% Similarity=0.088 Sum_probs=29.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|...||+++++.- . .-+|+||.|...|++....
T Consensus 42 ITps~lserlkI~~---S----lAr~~Lr~L~~kG~Ik~V~ 75 (86)
T PRK09334 42 VTPYTLASKYGIKI---S----VAKKVLRELEKRGVLVLYS 75 (86)
T ss_pred EcHHHHHHHhcchH---H----HHHHHHHHHHHCCCEEEEe
Confidence 58899999999944 7 8899999999999987553
No 72
>PF13814 Replic_Relax: Replication-relaxation
Probab=86.04 E-value=2 Score=30.69 Aligned_cols=59 Identities=20% Similarity=0.143 Sum_probs=43.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccC---CC-CcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG---QN-DQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~---~~-~~~~~y~~T~~s~~L~~~ 63 (128)
+|.++|+..+..+..... .++|.|+-|...|++...... .. ..+..|.+|+.|..++.+
T Consensus 10 lt~~Qi~~l~~~~~~~~~----~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~ 72 (191)
T PF13814_consen 10 LTTDQIARLLFPSSKSER----TARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD 72 (191)
T ss_pred cCHHHHHHHHcCCCcchH----HHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence 578899998887553345 699999999999998765431 11 124689999999888753
No 73
>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=85.93 E-value=1.1 Score=27.16 Aligned_cols=34 Identities=24% Similarity=0.381 Sum_probs=28.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|+.|||+.+|+. .+. .+.+.|+.|...|++....
T Consensus 27 t~rEIa~~~g~~--S~~----tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 27 TVREIAEALGLK--STS----TVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp -HHHHHHHHTSS--SHH----HHHHHHHHHHHTTSEEEGC
T ss_pred CHHHHHHHhCCC--ChH----HHHHHHHHHHHCcCccCCC
Confidence 789999999994 246 8999999999999997654
No 74
>PRK06474 hypothetical protein; Provisional
Probab=85.63 E-value=1.5 Score=31.83 Aligned_cols=53 Identities=21% Similarity=0.308 Sum_probs=39.0
Q ss_pred CCHHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcceeeccCC--CCcccceechHhhhhh
Q 045905 1 MTLNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ--NDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~--~~~~~~y~~T~~s~~L 60 (128)
+|+.||+..++ + ... .++|.|+.|...|++....... ++.+..|.+++-+-.+
T Consensus 27 ~ta~el~~~l~~i---s~a----TvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~~ 82 (178)
T PRK06474 27 LTPLELVKILKDV---PQA----TLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAKI 82 (178)
T ss_pred CCHHHHHHHhcCC---CHH----HHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceeee
Confidence 47899999984 5 336 8999999999999998764321 1224679888877554
No 75
>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=85.57 E-value=1.4 Score=26.15 Aligned_cols=33 Identities=15% Similarity=0.136 Sum_probs=27.4
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|..+||++++++. . .+++.|+.|...|++.-..
T Consensus 26 s~~~la~~~~vsr---~----tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 26 SERELAERYGVSR---T----TVREALRRLEAEGLIERRP 58 (64)
T ss_dssp -HHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEET
T ss_pred CHHHHHHHhccCC---c----HHHHHHHHHHHCCcEEEEC
Confidence 6789999999944 7 8999999999999997554
No 76
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=85.50 E-value=1.4 Score=36.85 Aligned_cols=53 Identities=26% Similarity=0.249 Sum_probs=43.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
+|..|||++++++ .. .+.|++.-|...|++..... ....|.||+-|+.+++..
T Consensus 21 ~s~~eLA~~l~l~---~~----tVt~~i~~Le~kGlV~~~~~----~~~~i~LTeeG~~~~~~g 73 (489)
T PRK04172 21 ATLEELAEKLGLP---PE----AVMRAAEWLEEKGLVKVEER----VEEVYVLTEEGKKYAEEG 73 (489)
T ss_pred CCHHHHHHHhCcC---HH----HHHHHHHHHHhCCCEEEEee----eEEEEEECHHHHHHHHhc
Confidence 4788999999994 48 99999999999998875431 135799999999888754
No 77
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=85.49 E-value=1.7 Score=33.45 Aligned_cols=81 Identities=19% Similarity=0.184 Sum_probs=56.3
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHh-cChhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAV-LDPIL 80 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~-~~~~~ 80 (128)
...|||.++|+.+ + .+.--++-|+..|+..+.. .+.|..|.-|.-.+.++-..++.|+... ..-..
T Consensus 27 ~q~eIA~~lgiT~---Q----aVsehiK~Lv~eG~i~~~g------R~~Y~iTkkG~e~l~~~~~dlr~f~~ev~~~l~~ 93 (260)
T COG1497 27 KQKEIAKKLGITL---Q----AVSEHIKELVKEGLIEKEG------RGEYEITKKGAEWLLEQLSDLRRFSEEVELVLDY 93 (260)
T ss_pred CHHHHHHHcCCCH---H----HHHHHHHHHHhccceeecC------CeeEEEehhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4579999999944 7 8999999999999998764 4689999999644333222366665555 22245
Q ss_pred HHHHHhHHHh-hhcCC
Q 045905 81 TTPCQHVTTW-FQNDD 95 (128)
Q Consensus 81 ~~~~~~l~~~-~~~g~ 95 (128)
...|..+..- +++|+
T Consensus 94 ~~vw~AIA~edI~~Gd 109 (260)
T COG1497 94 VMVWTAIAKEDIKEGD 109 (260)
T ss_pred HHHHHHhhHhhhccCC
Confidence 6677776554 45554
No 78
>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=84.83 E-value=1.4 Score=25.83 Aligned_cols=28 Identities=29% Similarity=0.278 Sum_probs=19.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
+|+.|||+.+|+.+ .-+-+.|+|..+-+
T Consensus 24 ~tl~elA~~lgis~---st~~~~LRrae~kl 51 (53)
T PF04967_consen 24 ITLEELAEELGISK---STVSEHLRRAERKL 51 (53)
T ss_pred CCHHHHHHHhCCCH---HHHHHHHHHHHHHH
Confidence 58999999999954 42333566665544
No 79
>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=84.52 E-value=0.76 Score=25.64 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=16.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|||..+|+. .. .|+|+++
T Consensus 22 ~si~~IA~~~gvs---r~----TvyR~l~ 43 (45)
T PF02796_consen 22 MSIAEIAKQFGVS---RS----TVYRYLN 43 (45)
T ss_dssp --HHHHHHHTTS----HH----HHHHHHC
T ss_pred CCHHHHHHHHCcC---HH----HHHHHHh
Confidence 4789999999994 37 8888874
No 80
>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=84.14 E-value=2.2 Score=25.65 Aligned_cols=47 Identities=19% Similarity=0.128 Sum_probs=33.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+|..|||+++++.. . .++|-++.|-..|+..+.. ...|.+.+...+|
T Consensus 14 ~~~~eLa~~l~vS~---~----tv~~~l~~L~~~g~~i~~~------~~g~~l~~~~~ll 60 (69)
T TIGR00122 14 FSGEKLGEALGMSR---T----AVNKHIQTLREWGVDVLTV------GKGYRLPPPIPLL 60 (69)
T ss_pred cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCeEEec------CCceEecCccccC
Confidence 36789999999943 7 8999999999999865443 2446665544444
No 81
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=84.10 E-value=1.4 Score=25.88 Aligned_cols=34 Identities=15% Similarity=0.234 Sum_probs=29.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|+.|||+.+++.+ . -++|=|..|...|++....
T Consensus 15 ~s~~ela~~~~VS~---~----TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 15 VSVKELAEEFGVSE---M----TIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred EEHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEEc
Confidence 47899999999955 7 8999999999999987654
No 82
>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=83.79 E-value=1.5 Score=29.33 Aligned_cols=34 Identities=15% Similarity=0.159 Sum_probs=29.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
||...||+++++.- . +-+++||.|...|++....
T Consensus 60 ITp~~lserlkI~~---S----lAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 60 ITPSVLSERLKING---S----LARKALRELESKGLIKPVS 93 (105)
T ss_dssp ECHHHHHHHHCCSC---H----HHHHHHHHHHHCCSSEEEE
T ss_pred eeHHHHHHhHhhHH---H----HHHHHHHHHHHCCCEEEEe
Confidence 58899999999944 7 8899999999999997654
No 83
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=83.51 E-value=1.2 Score=26.95 Aligned_cols=33 Identities=15% Similarity=0.147 Sum_probs=27.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+..|||+.+|++ .. ..+++|..|...|.+...+
T Consensus 17 ~T~eiA~~~gls---~~----~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 17 KTREIADALGLS---IY----QARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp EHHHHHHHHTS----HH----HHHHHHHHHHHCTSEEEES
T ss_pred CHHHHHHHhCCC---HH----HHHHHHHHHHHCCCEEEec
Confidence 568999999994 36 8999999999999887654
No 84
>PF13730 HTH_36: Helix-turn-helix domain
Probab=83.16 E-value=1.9 Score=24.58 Aligned_cols=29 Identities=21% Similarity=0.212 Sum_probs=25.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcc
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFF 37 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf 37 (128)
|.+.||+.+|+. .. .+.|.++.|...|++
T Consensus 27 S~~~la~~~g~s---~~----Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVS---RR----TVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcC---HH----HHHHHHHHHHHCcCC
Confidence 678999999994 47 899999999998864
No 85
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=82.20 E-value=2 Score=34.98 Aligned_cols=34 Identities=12% Similarity=0.233 Sum_probs=29.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
.|.+||++++++++ . .++++|..|...|++.+.+
T Consensus 311 ~t~~~La~~l~~~~---~----~v~~iL~~L~~agLI~~~~ 344 (412)
T PRK04214 311 LDVDEIRRLEPMGY---D----ELGELLCELARIGLLRRGE 344 (412)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHHHHHhCCCeEecC
Confidence 47899999999955 7 8999999999999998654
No 86
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=82.04 E-value=2 Score=30.99 Aligned_cols=43 Identities=19% Similarity=0.234 Sum_probs=35.6
Q ss_pred CHHHHHHhC--CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 2 TLNELINAL--PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 2 S~~eLA~~~--~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
...+||.++ +++. . -++.-|.+|...|++...+ ++.|..|.-+
T Consensus 41 d~~~iak~l~p~is~---~----ev~~sL~~L~~~gli~k~~------~g~y~~t~~~ 85 (171)
T PF14394_consen 41 DPEWIAKRLRPKISA---E----EVRDSLEFLEKLGLIKKDG------DGKYVQTDKS 85 (171)
T ss_pred CHHHHHHHhcCCCCH---H----HHHHHHHHHHHCCCeEECC------CCcEEEecce
Confidence 467899999 6633 5 7889999999999998776 4789999876
No 87
>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=81.36 E-value=2.5 Score=30.87 Aligned_cols=33 Identities=18% Similarity=0.320 Sum_probs=28.3
Q ss_pred CHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.+|+..+ |+++ . .|+|.++.|+..|++....
T Consensus 72 SN~~La~r~~G~s~---~----tlrR~l~~LveaGLI~rrD 105 (177)
T PF03428_consen 72 SNAQLAERLNGMSE---R----TLRRHLARLVEAGLIVRRD 105 (177)
T ss_pred CHHHHHHHHcCCCH---H----HHHHHHHHHHHCCCeeecc
Confidence 567899999 8955 7 8999999999999987654
No 88
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=81.33 E-value=2 Score=28.71 Aligned_cols=34 Identities=12% Similarity=0.024 Sum_probs=28.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|...||++.|++- . .-+++||.|...|++....
T Consensus 60 VTpy~la~r~gI~~---S----vAr~vLR~LeeeGvv~lvs 93 (107)
T COG4901 60 VTPYVLASRYGING---S----VARIVLRHLEEEGVVQLVS 93 (107)
T ss_pred ecHHHHHHHhccch---H----HHHHHHHHHHhCCceeeec
Confidence 57889999999944 7 8899999999999987543
No 89
>PRK00215 LexA repressor; Validated
Probab=81.30 E-value=2.4 Score=30.91 Aligned_cols=34 Identities=24% Similarity=0.349 Sum_probs=29.4
Q ss_pred CCHHHHHHhCCC-CCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPF-HPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~-~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|+.|||+.+|+ +. . .+.|+|+.|...|++....
T Consensus 24 ~s~~ela~~~~~~~~---~----tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 24 PSRREIADALGLRSP---S----AVHEHLKALERKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHhCCCCh---H----HHHHHHHHHHHCCCEEeCC
Confidence 378899999999 65 6 8999999999999997654
No 90
>PRK05638 threonine synthase; Validated
Probab=81.17 E-value=2.8 Score=34.49 Aligned_cols=55 Identities=25% Similarity=0.210 Sum_probs=39.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
++..||++.++.+. ... .+++.|+.|...|++..... ++....|.+|+.++.+..
T Consensus 385 ~~~~el~~~l~~~~-s~~----~v~~hL~~Le~~GLV~~~~~--~g~~~~Y~Lt~~g~~~l~ 439 (442)
T PRK05638 385 MYGYEIWKALGKPL-KYQ----AVYQHIKELEELGLIEEAYR--KGRRVYYKLTEKGRRLLE 439 (442)
T ss_pred ccHHHHHHHHcccC-Ccc----hHHHHHHHHHHCCCEEEeec--CCCcEEEEECcHHHHHHH
Confidence 35789999998211 346 89999999999999965321 121346999999987754
No 91
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=80.57 E-value=2.3 Score=30.91 Aligned_cols=34 Identities=12% Similarity=0.165 Sum_probs=29.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|.+|||..+|++ .. .++|+|..|...|++....
T Consensus 37 ~tdeeLA~~Lgi~---~~----~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 37 VTDEEIAEQTGIK---LN----TVRKILYKLYDARLADYKR 70 (178)
T ss_pred cCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCeEEee
Confidence 5789999999994 48 9999999999999998443
No 92
>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=80.16 E-value=3.5 Score=23.43 Aligned_cols=33 Identities=21% Similarity=0.161 Sum_probs=26.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|..|||+.+++ ... .++|-|..|-..|+.-+.
T Consensus 16 it~~eLa~~l~v---S~r----Ti~~~i~~L~~~~~~I~~ 48 (55)
T PF08279_consen 16 ITAKELAEELGV---SRR----TIRRDIKELREWGIPIES 48 (55)
T ss_dssp BEHHHHHHHCTS----HH----HHHHHHHHHHHTT-EEEE
T ss_pred cCHHHHHHHhCC---CHH----HHHHHHHHHHHCCCeEEe
Confidence 478999999999 447 899999999999944443
No 93
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=80.04 E-value=2.4 Score=29.70 Aligned_cols=33 Identities=21% Similarity=0.234 Sum_probs=28.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
.|+.|||+.+|= |.. .|.|=||.|...||+.-.
T Consensus 79 ~Si~ElAe~vgR---dv~----nvhr~Ls~l~~~GlI~fe 111 (144)
T COG4190 79 ASINELAELVGR---DVK----NVHRTLSTLADLGLIFFE 111 (144)
T ss_pred ccHHHHHHHhCc---chH----HHHHHHHHHHhcCeEEEe
Confidence 478999999998 458 999999999999977543
No 94
>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=79.78 E-value=3 Score=30.27 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=28.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|..|||+.++++ ... .++|.|+.|...|++....
T Consensus 27 ~~~ela~~~~~~--s~~----tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 27 SIREIARAVGLR--SPS----AAEEHLKALERKGYIERDP 60 (199)
T ss_pred cHHHHHHHhCCC--ChH----HHHHHHHHHHHCCCEecCC
Confidence 678999999995 037 8999999999999997553
No 95
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=79.37 E-value=1.6 Score=23.64 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=18.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|++|||..+|++ +. .+.|+.+...
T Consensus 9 ~~l~~iA~~~g~S---~~----~f~r~Fk~~~ 33 (42)
T PF00165_consen 9 LTLEDIAEQAGFS---PS----YFSRLFKKET 33 (42)
T ss_dssp --HHHHHHHHTS----HH----HHHHHHHHHT
T ss_pred CCHHHHHHHHCCC---HH----HHHHHHHHHH
Confidence 4789999999994 47 8999888643
No 96
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=79.36 E-value=3.3 Score=28.65 Aligned_cols=34 Identities=21% Similarity=0.301 Sum_probs=28.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|+.|++..+|++ -. .+.+.+|.|+..|-+...+
T Consensus 27 iTi~ql~~~TGas---R~----Tvk~~lreLVa~G~l~~~G 60 (127)
T PF06163_consen 27 ITIKQLVAKTGAS---RN----TVKRYLRELVARGDLYRHG 60 (127)
T ss_pred ccHHHHHHHHCCC---HH----HHHHHHHHHHHcCCeEeCC
Confidence 5899999999994 47 8999999999999776553
No 97
>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=78.99 E-value=3.5 Score=26.83 Aligned_cols=41 Identities=22% Similarity=0.291 Sum_probs=30.2
Q ss_pred hHHHHHHHHHhcCcceeec-cCCCC-cccceechHhhhhhhcC
Q 045905 23 YVYRFMWILVHSGFFAQQN-FGQND-QERSYVATNASKLLLKD 63 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~~-~~~~~-~~~~y~~T~~s~~L~~~ 63 (128)
.|+++|+-|...|++.... ..+.+ ....|.+|+.|+.+...
T Consensus 41 tlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~ 83 (100)
T TIGR03433 41 SLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAA 83 (100)
T ss_pred cHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence 8999999999999987631 11111 13579999999988654
No 98
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=78.86 E-value=2.7 Score=28.42 Aligned_cols=34 Identities=21% Similarity=0.250 Sum_probs=30.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|++|||..+.+.+ . ..+++|+-|...|.+.=.+
T Consensus 20 vtl~elA~~l~cS~---R----n~r~lLkkm~~~gWi~W~p 53 (115)
T PF12793_consen 20 VTLDELAELLFCSR---R----NARTLLKKMQEEGWITWQP 53 (115)
T ss_pred eeHHHHHHHhCCCH---H----HHHHHHHHHHHCCCeeeeC
Confidence 58999999999955 7 8999999999999998654
No 99
>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=78.75 E-value=3 Score=29.71 Aligned_cols=33 Identities=21% Similarity=0.247 Sum_probs=28.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|-+|||..+|+ +.. .++|+|..|.-.|+....
T Consensus 29 ~tdEeLa~~Lgi---~~~----~VRk~L~~L~e~~Lv~~~ 61 (158)
T TIGR00373 29 FTDEEISLELGI---KLN----EVRKALYALYDAGLADYK 61 (158)
T ss_pred CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCceee
Confidence 477999999999 448 899999999999999643
No 100
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=78.68 E-value=1.8 Score=24.02 Aligned_cols=22 Identities=23% Similarity=0.194 Sum_probs=15.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|||..+|.++ . .++|.++
T Consensus 21 ~s~~~IA~~lg~s~---s----TV~relk 42 (44)
T PF13936_consen 21 MSIREIAKRLGRSR---S----TVSRELK 42 (44)
T ss_dssp --HHHHHHHTT--H---H----HHHHHHH
T ss_pred CCHHHHHHHHCcCc---H----HHHHHHh
Confidence 47899999999954 7 7888775
No 101
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=78.64 E-value=3.3 Score=30.42 Aligned_cols=34 Identities=24% Similarity=0.299 Sum_probs=29.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|-.+||+.+|+.+ . .|.|+|+.|...|++.-..
T Consensus 185 lt~~~iA~~lG~sr---~----tvsR~l~~l~~~g~I~~~~ 218 (235)
T PRK11161 185 MTRGDIGNYLGLTV---E----TISRLLGRFQKSGMLAVKG 218 (235)
T ss_pred ccHHHHHHHhCCcH---H----HHHHHHHHHHHCCCEEecC
Confidence 46689999999944 7 9999999999999998654
No 102
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=78.54 E-value=3.8 Score=24.21 Aligned_cols=45 Identities=13% Similarity=0.127 Sum_probs=30.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+.+++.++.|.+- . +.+.+.+.-+...|++..+. +++.+|+.|++
T Consensus 22 ~~~~~~~~~g~~~---~---~~~~~~l~~l~~~Gll~~~~-------~~l~lT~~G~l 66 (66)
T PF06969_consen 22 DLSEFEQRFGIDF---A---EEFQKELEELQEDGLLEIDG-------GRLRLTEKGRL 66 (66)
T ss_dssp EHHHHHHHTT--T---H---HH-HHHHHHHHHTTSEEE-S-------SEEEE-TTTGG
T ss_pred CHHHHHHHHCcCH---H---HHHHHHHHHHHHCCCEEEeC-------CEEEECcccCc
Confidence 5678888888732 2 25577788889999998764 78999998863
No 103
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=78.41 E-value=2.6 Score=30.22 Aligned_cols=34 Identities=18% Similarity=0.252 Sum_probs=29.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|-.|||+.+|+.+ . .+.|+|+.|...|++.-..
T Consensus 169 ~t~~~lA~~lG~tr---~----tvsR~l~~l~~~gii~~~~ 202 (211)
T PRK11753 169 ITRQEIGRIVGCSR---E----MVGRVLKMLEDQGLISAHG 202 (211)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHHHHHHCCCEEecC
Confidence 36689999999955 7 9999999999999997553
No 104
>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=78.17 E-value=3.7 Score=24.89 Aligned_cols=49 Identities=12% Similarity=0.097 Sum_probs=32.1
Q ss_pred CCHHHHHHhCCCCCCC--chhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIK--AQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~--~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
++..+|+..+.....+ .. .|+|.||.|-..|+.. ... ...+.+|+.|.-
T Consensus 14 ~g~~~l~~~L~~~g~~~se~----avRrrLr~me~~Glt~-~~g-----~~G~~iT~~G~~ 64 (66)
T PF08461_consen 14 LGRKQLAEELKLRGEELSEE----AVRRRLRAMERDGLTR-KVG-----RQGRIITEKGLD 64 (66)
T ss_pred CCHHHHHHHHHhcChhhhHH----HHHHHHHHHHHCCCcc-ccC-----CcccccCHHHHh
Confidence 3556777777653222 25 8999999999999444 321 234668887753
No 105
>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=78.02 E-value=2.7 Score=29.66 Aligned_cols=34 Identities=9% Similarity=0.109 Sum_probs=29.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|-.|||..+|+.+ . .+.|+|+.|...|++.-..
T Consensus 144 ~t~~~iA~~lG~tr---e----tvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 144 LSHQAIAEAIGSTR---V----TITRLLGDLRKKKLISIHK 177 (193)
T ss_pred CCHHHHHHHhCCcH---H----HHHHHHHHHHHCCCEEecC
Confidence 46789999999944 7 9999999999999997553
No 106
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=77.99 E-value=3 Score=28.66 Aligned_cols=33 Identities=21% Similarity=0.249 Sum_probs=27.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|..|||+++|+++ . .+.+.++-|...||+.--
T Consensus 23 ~~~~eia~~lglS~---~----~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 23 ISNAELAERVGLSP---S----TVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCceeeE
Confidence 47899999999955 7 888889999999988643
No 107
>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=77.68 E-value=4.4 Score=22.15 Aligned_cols=44 Identities=16% Similarity=0.242 Sum_probs=28.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
+|..|+|+.+|+++ . -+|.....|++.... .+++...|....+-
T Consensus 1 ~~~~e~a~~~gv~~---~--------tlr~~~~~g~l~~~~--~~~~~~~y~~~~v~ 44 (49)
T cd04761 1 YTIGELAKLTGVSP---S--------TLRYYERIGLLSPAR--TEGGYRLYSDADLE 44 (49)
T ss_pred CcHHHHHHHHCcCH---H--------HHHHHHHCCCCCCCc--CCCCCEEeCHHHHH
Confidence 57899999999954 3 466778889876221 11124567665554
No 108
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=77.41 E-value=3.2 Score=29.01 Aligned_cols=31 Identities=13% Similarity=0.164 Sum_probs=26.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|..|||+++|+++ . .+.|=++-|...|++.
T Consensus 24 ~s~~eiA~~lglS~---~----tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 24 TPYAELAKQFGVSP---G----TIHVRVEKMKQAGIIT 54 (153)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCee
Confidence 57899999999955 7 7888888899999886
No 109
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=77.27 E-value=2.8 Score=30.92 Aligned_cols=34 Identities=18% Similarity=0.247 Sum_probs=29.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|..|||+++++.+ . .++.-++.|+..|++.+..
T Consensus 179 ~s~~eIA~~l~iS~---~----Tv~~~~~~~~~~~~~~~~~ 212 (239)
T PRK10430 179 FSTDELANAVNISR---V----SCRKYLIWLVNCHILFTSI 212 (239)
T ss_pred cCHHHHHHHhCchH---H----HHHHHHHHHHhCCEEEEEe
Confidence 37889999999944 7 8999999999999997654
No 110
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=77.16 E-value=2.3 Score=28.00 Aligned_cols=38 Identities=24% Similarity=0.462 Sum_probs=28.2
Q ss_pred hHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 23 YVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
...+++..|+..|++.... ++....|.+|+.|+.|.+.
T Consensus 47 ~~~~yi~~L~~~Gli~~~~---~~~~~~y~lT~KG~~fle~ 84 (95)
T COG3432 47 RAQKYIEMLVEKGLIIKQD---NGRRKVYELTEKGKRFLEK 84 (95)
T ss_pred HHHHHHHHHHhCCCEEecc---CCccceEEEChhHHHHHHH
Confidence 7889999999999554433 1112379999999988653
No 111
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=77.13 E-value=4.3 Score=24.00 Aligned_cols=48 Identities=13% Similarity=0.131 Sum_probs=30.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+|+.|+|+.+|+++ . . +|.....|++..... ++++.+.|..+.+-++.
T Consensus 1 ~s~~eva~~~gvs~---~----t----lr~~~~~gli~~~~~-~~~g~r~y~~~dl~~l~ 48 (70)
T smart00422 1 YTIGEVAKLAGVSV---R----T----LRYYERIGLLPPPIR-TEGGYRLYSDEDLERLR 48 (70)
T ss_pred CCHHHHHHHHCcCH---H----H----HHHHHHCCCCCCCcc-CCCCCEecCHHHHHHHH
Confidence 57899999999955 4 4 455556898864311 11124578877776443
No 112
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=76.75 E-value=4 Score=30.18 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=28.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|-.|||+.+|+.+ . .|.|+|+.|...|++...
T Consensus 180 lt~~~IA~~lGisr---e----tlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 180 MSRRDIADYLGLTI---E----TVSRALSQLQDRGLIGLS 212 (230)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCcEEec
Confidence 36689999999954 7 999999999999999754
No 113
>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=76.52 E-value=2.6 Score=22.84 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=20.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|..|+|+.+|+++ . .|+++++ .|.+.
T Consensus 2 lt~~e~a~~lgis~---~----ti~~~~~----~g~i~ 28 (49)
T TIGR01764 2 LTVEEAAEYLGVSK---D----TVYRLIH----EGELP 28 (49)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHH----cCCCC
Confidence 58899999999944 6 6777665 46554
No 114
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=76.42 E-value=4.7 Score=25.59 Aligned_cols=34 Identities=12% Similarity=0.088 Sum_probs=29.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+++.|||.++++++ + .++=+|-.|+.+|-+....
T Consensus 17 ~s~~~Ls~~~~~p~---~----~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 17 MEAAQISQTLNTPQ---P----MINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred ccHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEeec
Confidence 47899999999966 8 9999999999999887554
No 115
>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=75.94 E-value=24 Score=24.72 Aligned_cols=44 Identities=23% Similarity=0.234 Sum_probs=31.8
Q ss_pred CchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhhhcC
Q 045905 16 KAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLLLKD 63 (128)
Q Consensus 16 ~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L~~~ 63 (128)
++. .|+++|+-|...|++...... +.+ ...+|.+|+.|+.....
T Consensus 56 ~~G----tLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~ 101 (138)
T TIGR02719 56 DQG----NVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSM 101 (138)
T ss_pred CcC----hHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHH
Confidence 557 899999999999999753221 112 13569999999887544
No 116
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=75.92 E-value=4.6 Score=26.19 Aligned_cols=47 Identities=13% Similarity=0.194 Sum_probs=32.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+++.|+|+.+|+++ +.+|+-...|++......+. +.+.|....+-++
T Consensus 1 m~I~eva~~~gvs~-----------~tlR~Ye~~GLl~p~~r~~~-g~r~Y~~~dv~~l 47 (95)
T cd04780 1 MRMSELSKRSGVSV-----------ATIKYYLREGLLPEGRRLAP-NQAEYSEAHVERL 47 (95)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCcCCCC-CCeecCHHHHHHH
Confidence 58899999999943 46888889999976432221 1356777666543
No 117
>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=75.78 E-value=2.8 Score=25.58 Aligned_cols=41 Identities=15% Similarity=0.131 Sum_probs=30.6
Q ss_pred CchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhh
Q 045905 16 KAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLL 60 (128)
Q Consensus 16 ~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L 60 (128)
++. .|++.|+-|...|++...... .++ ....|.+|+.|+..
T Consensus 30 ~~g----~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~ 72 (75)
T PF03551_consen 30 SPG----SLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREE 72 (75)
T ss_dssp THH----HHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHH
T ss_pred Chh----HHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHH
Confidence 557 899999999999999765432 111 23579999999754
No 118
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=75.37 E-value=4 Score=27.90 Aligned_cols=41 Identities=20% Similarity=0.231 Sum_probs=28.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+..+|++.+++ + .-.+||+. =+.|-|...+ .++|+||+.|+
T Consensus 75 ~~~~l~~~~~~-----~----~A~~IL~~-N~YGWFeRv~------rGvY~LT~~G~ 115 (118)
T PF09929_consen 75 RPADLRKATGV-----P----KATSILRD-NHYGWFERVE------RGVYALTPAGR 115 (118)
T ss_pred CHHHHHHhcCC-----C----hHHHHHHh-Ccccceeeec------cceEecCcchh
Confidence 45677777666 3 34466664 3578998776 58999999986
No 119
>PRK09462 fur ferric uptake regulator; Provisional
Probab=74.97 E-value=5.1 Score=27.83 Aligned_cols=48 Identities=21% Similarity=0.286 Sum_probs=32.9
Q ss_pred CCHHHHHHhCCC-CC-CCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905 1 MTLNELINALPF-HP-IKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT 54 (128)
Q Consensus 1 ~S~~eLA~~~~~-~~-~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T 54 (128)
+|+.||-.++.- .| .+.. .+||.|..|+..|++......+ +..+|.++
T Consensus 34 ~sa~eI~~~l~~~~~~i~~a----TVYR~L~~L~e~Gli~~~~~~~--~~~~y~~~ 83 (148)
T PRK09462 34 VSAEDLYKRLIDMGEEIGLA----TVYRVLNQFDDAGIVTRHNFEG--GKSVFELT 83 (148)
T ss_pred CCHHHHHHHHHhhCCCCCHH----HHHHHHHHHHHCCCEEEEEcCC--CcEEEEeC
Confidence 477888777742 12 2567 8999999999999998764311 13467664
No 120
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=74.77 E-value=4.9 Score=27.38 Aligned_cols=46 Identities=11% Similarity=0.068 Sum_probs=38.7
Q ss_pred HHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 5 ELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 5 eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
+||+.+++ +.+ -|--++.++...|+....+ |-..+|+.|+.+++..
T Consensus 2 ~La~~l~~---eiD----dL~p~~eAaelLgf~~~~~-------Gdi~LT~~G~~f~~a~ 47 (120)
T PF09821_consen 2 QLADELHL---EID----DLLPIVEAAELLGFAEVEE-------GDIRLTPLGRRFAEAD 47 (120)
T ss_pred chHHHhCC---cHH----HHHHHHHHHHHcCCeeecC-------CcEEeccchHHHHHCC
Confidence 57888888 447 8999999999999997654 6799999999999764
No 121
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=74.76 E-value=4 Score=29.10 Aligned_cols=33 Identities=21% Similarity=0.209 Sum_probs=28.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|-.|||..+|+.+ . .+.|+|+-|...|++...
T Consensus 150 ~t~~~iA~~lG~tr---e----tvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 150 ATHDELAAAVGSVR---E----TVTKVIGELSREGYIRSG 182 (202)
T ss_pred CCHHHHHHHhCccH---H----HHHHHHHHHHHCCCEEcC
Confidence 46789999999954 7 999999999999999744
No 122
>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=74.72 E-value=1.9 Score=27.05 Aligned_cols=30 Identities=20% Similarity=0.062 Sum_probs=22.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFF 37 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf 37 (128)
+|..|||+.+++++ . .+...++.+-..|++
T Consensus 33 lS~kEIAe~LGIS~---~----TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 33 KTASEIAEELGRTE---Q----TVRNHLKGETKAGGL 62 (73)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHhcCcccchH
Confidence 57899999999955 6 788888766666654
No 123
>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=74.68 E-value=4.9 Score=26.57 Aligned_cols=33 Identities=9% Similarity=0.181 Sum_probs=29.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|.++|++.+++++ . .+.+.+..|+.+||+...
T Consensus 55 Is~sq~~e~tg~~~---~----~V~~al~~Li~~~vI~~~ 87 (100)
T PF04492_consen 55 ISNSQIAEMTGLSR---D----HVSKALNELIRRGVIIRD 87 (100)
T ss_pred eeHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeC
Confidence 57899999999955 7 899999999999999655
No 124
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=74.64 E-value=4.7 Score=28.90 Aligned_cols=37 Identities=24% Similarity=0.387 Sum_probs=28.7
Q ss_pred CCHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|+.||.+++.- +..+.. .+||.|+.|+..||+.+-.
T Consensus 42 lSa~eI~~~L~~~~~~is~a----TVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 42 ISAYDLLDLLREAEPQAKPP----TVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred CCHHHHHHHHHhhCCCCCcc----hHHHHHHHHHHCCCEEEEe
Confidence 477888877763 122557 8999999999999998775
No 125
>PHA00738 putative HTH transcription regulator
Probab=74.45 E-value=6.1 Score=26.61 Aligned_cols=48 Identities=17% Similarity=0.156 Sum_probs=36.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+++.||++.+++ ..+ .+.+-|+.|-..|++..... |....|.+.+-..
T Consensus 27 ~~V~eLae~l~l---SQp----tVS~HLKvLreAGLV~srK~---Gr~vyY~Ln~~~~ 74 (108)
T PHA00738 27 LSASLISHTLLL---SYT----TVLRHLKILNEQGYIELYKE---GRTLYAKIRENSK 74 (108)
T ss_pred ccHHHHHHhhCC---CHH----HHHHHHHHHHHCCceEEEEE---CCEEEEEECCCcc
Confidence 357899999998 447 89999999999999986652 2235688877654
No 126
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=74.10 E-value=4.1 Score=28.82 Aligned_cols=31 Identities=19% Similarity=0.253 Sum_probs=26.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|..|||+++|+++ . .+.|=++-|...|++.
T Consensus 29 ~s~~eiA~~lglS~---~----tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 29 ISNVELSKRVGLSP---T----PCLERVRRLERQGFIQ 59 (164)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeE
Confidence 58899999999955 7 7788888889999986
No 127
>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=73.63 E-value=2.1 Score=26.59 Aligned_cols=28 Identities=32% Similarity=0.434 Sum_probs=20.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSG 35 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~g 35 (128)
+|+.|||+.+++.+ . .+.|+.+-|--.|
T Consensus 35 ~si~elA~~~~vS~---s----ti~Rf~kkLG~~g 62 (77)
T PF01418_consen 35 MSISELAEKAGVSP---S----TIVRFCKKLGFSG 62 (77)
T ss_dssp --HHHHHHHCTS-H---H----HHHHHHHHCTTTC
T ss_pred ccHHHHHHHcCCCH---H----HHHHHHHHhCCCC
Confidence 47899999999944 7 8888888765444
No 128
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=73.44 E-value=7.1 Score=25.49 Aligned_cols=52 Identities=17% Similarity=0.205 Sum_probs=37.5
Q ss_pred HHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccC--CC--------C----cccceechHhhhhhhc
Q 045905 4 NELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG--QN--------D----QERSYVATNASKLLLK 62 (128)
Q Consensus 4 ~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~--~~--------~----~~~~y~~T~~s~~L~~ 62 (128)
.-||..++++ .+ .+.++++-|..+|++.+.... .. . -..+|.+|..|+.|+.
T Consensus 25 k~ia~~l~~~---~~----~v~~~l~~Le~~GLler~~g~~iK~~~~k~K~~~e~~~hHtYY~LTr~G~~llR 90 (92)
T PF10007_consen 25 KSIARRLKIP---LE----EVREALEKLEEMGLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTREGELLLR 90 (92)
T ss_pred HHHHHHHCCC---HH----HHHHHHHHHHHCCCeEEecCcccchhhhhcccchhhhcCCceeeecHhHHHHHh
Confidence 3478888884 37 899999999999999877532 00 0 0246889988887764
No 129
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=73.40 E-value=6.4 Score=27.15 Aligned_cols=33 Identities=24% Similarity=0.324 Sum_probs=29.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|..|||..++++| . -+.|..+.|...|++.-..
T Consensus 37 SvRelA~~~~VNp---n----Tv~raY~eLE~eG~i~t~r 69 (125)
T COG1725 37 SVRELAKDLGVNP---N----TVQRAYQELEREGIVETKR 69 (125)
T ss_pred cHHHHHHHhCCCH---H----HHHHHHHHHHHCCCEEEec
Confidence 7889999999966 8 8999999999999987554
No 130
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=73.35 E-value=3.8 Score=24.40 Aligned_cols=27 Identities=26% Similarity=0.374 Sum_probs=21.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHS 34 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~ 34 (128)
+|+++||+.+++++ . .|.|+++.....
T Consensus 2 ~~~~~la~~~~~s~---~----~l~~~f~~~~~~ 28 (84)
T smart00342 2 LTLEDLAEALGMSP---R----HLQRLFKKETGT 28 (84)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHHHHhCc
Confidence 58999999999944 7 888988876533
No 131
>PF12728 HTH_17: Helix-turn-helix domain
Probab=72.76 E-value=3.5 Score=23.09 Aligned_cols=22 Identities=27% Similarity=0.459 Sum_probs=17.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|+|+.+|+++ . .++++++
T Consensus 2 lt~~e~a~~l~is~---~----tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISR---S----TVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHH
Confidence 58999999999944 6 6777765
No 132
>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=72.42 E-value=4.1 Score=26.44 Aligned_cols=33 Identities=15% Similarity=0.241 Sum_probs=26.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+++++|+++++++ .. .++-.+..|+..|.+-.+
T Consensus 66 v~v~~I~~~l~~~---~~----~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 66 VHVDEIAQQLGMS---EN----EVRKALDFLSNEGHIYST 98 (102)
T ss_dssp EEHHHHHHHSTS----HH----HHHHHHHHHHHTTSEEES
T ss_pred ccHHHHHHHhCcC---HH----HHHHHHHHHHhCCeEecc
Confidence 4688999999884 47 899999999999977543
No 133
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=71.91 E-value=4.5 Score=34.37 Aligned_cols=30 Identities=17% Similarity=0.377 Sum_probs=24.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSG 35 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~g 35 (128)
.|++|||++++.+. + .|.++.|||+|++.+
T Consensus 479 ~~~~~~~~~~~~~~-~----~~~~~~i~~~~~~n~ 508 (528)
T PRK14096 479 LSIEEIAAALGAPE-Q----VETIYKILRHLAANN 508 (528)
T ss_pred CCHHHHHHHcCCCc-c----HHHHHHHHHHHhcCC
Confidence 37899999999843 3 449999999999873
No 134
>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=70.56 E-value=3.9 Score=22.55 Aligned_cols=14 Identities=21% Similarity=0.261 Sum_probs=10.5
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|+.|||+.+|+++
T Consensus 18 ~s~~~la~~lglS~ 31 (42)
T PF13404_consen 18 RSYAELAEELGLSE 31 (42)
T ss_dssp S-HHHHHHHHTS-H
T ss_pred ccHHHHHHHHCcCH
Confidence 47899999999943
No 135
>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=70.41 E-value=5.8 Score=22.37 Aligned_cols=14 Identities=21% Similarity=0.332 Sum_probs=10.2
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|..|||+.+|+++
T Consensus 27 ~s~~eIa~~l~~s~ 40 (54)
T PF08281_consen 27 MSYAEIAEILGISE 40 (54)
T ss_dssp --HHHHHHHCTS-H
T ss_pred cCHHHHHHHHCcCH
Confidence 47899999999955
No 136
>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=70.04 E-value=4.4 Score=21.69 Aligned_cols=46 Identities=17% Similarity=0.263 Sum_probs=27.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|..|+|+.+|+++ . .|++..+ .|.+..... +++...|....+-++
T Consensus 1 ~s~~e~a~~lgvs~---~----tl~~~~~----~g~~~~~~~--~~~~~~~~~~ei~~~ 46 (49)
T cd04762 1 LTTKEAAELLGVSP---S----TLRRWVK----EGKLKAIRT--PGGHRRFPEEDLERL 46 (49)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHH----cCCCCceeC--CCCceecCHHHHHHH
Confidence 57899999999944 5 5666555 576643221 111345666555444
No 137
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=69.26 E-value=8.8 Score=24.76 Aligned_cols=40 Identities=23% Similarity=0.179 Sum_probs=29.7
Q ss_pred hHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 23 YVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
.+.|++|.|+..|++.+.... ..-.+..+|+.++-+..+.
T Consensus 58 ~~~~li~~Li~~g~L~~~~~~--~~~~~l~~~~~~~~~l~g~ 97 (106)
T PF09382_consen 58 DWERLIRQLILEGYLSEDNGG--FAYPYLKLTPKGKELLNGK 97 (106)
T ss_dssp HHHHHHHHHHHTTSEEEEECC--CCTEEEEE-GGGHHHHCTT
T ss_pred HHHHHHHHHHHcCCceecCCc--ccccEEEECHHHHHHHCCC
Confidence 799999999999999766510 0124789999999887654
No 138
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=68.29 E-value=7.5 Score=30.40 Aligned_cols=33 Identities=12% Similarity=0.081 Sum_probs=27.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|..|||++++++. . .+.|.++.|...|+....
T Consensus 19 ~s~~~LA~~lgvsr---~----tV~~~l~~L~~~G~~i~~ 51 (319)
T PRK11886 19 HSGEQLGEELGISR---A----AIWKHIQTLEEWGLDIFS 51 (319)
T ss_pred cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCceEE
Confidence 36789999999944 7 899999999999995443
No 139
>PRK12423 LexA repressor; Provisional
Probab=68.01 E-value=7.8 Score=28.39 Aligned_cols=33 Identities=18% Similarity=0.300 Sum_probs=28.0
Q ss_pred CHHHHHHhCCC-CCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPF-HPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~-~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|..|||+++|+ .+ . .+++-|+.|...|++....
T Consensus 27 s~~eia~~~g~~s~---~----~v~~~l~~L~~~G~l~~~~ 60 (202)
T PRK12423 27 SLAEIAQAFGFASR---S----VARKHVQALAEAGLIEVVP 60 (202)
T ss_pred CHHHHHHHhCCCCh---H----HHHHHHHHHHHCCCEEecC
Confidence 78999999995 34 6 7899999999999997654
No 140
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=67.77 E-value=7.1 Score=28.52 Aligned_cols=33 Identities=27% Similarity=0.391 Sum_probs=28.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|=+|||..+|+ +.. .++|+|+.|...|++....
T Consensus 34 tDeela~~l~i---~~~----~vrriL~~L~e~~li~~~k 66 (176)
T COG1675 34 TDEELAELLGI---KKN----EVRRILYALYEDGLISYRK 66 (176)
T ss_pred ChHHHHHHhCc---cHH----HHHHHHHHHHhCCceEEEe
Confidence 55799999999 558 8999999999999998554
No 141
>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=66.94 E-value=8.3 Score=25.10 Aligned_cols=33 Identities=21% Similarity=0.414 Sum_probs=25.3
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+=+|||..+++++ . .++++|..|...|++....
T Consensus 29 ~de~la~~~~l~~---~----~vRkiL~~L~~~~lv~~~~ 61 (105)
T PF02002_consen 29 TDEDLAKKLGLKP---K----EVRKILYKLYEDGLVSYRR 61 (105)
T ss_dssp -HHHHHHTT-S-H---H----HHHHHHHHHHHHSS-EEEE
T ss_pred CHHHHHHHhCCCH---H----HHHHHHHHHHHCCCeEEEE
Confidence 5589999999944 8 8999999999999996553
No 142
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=66.27 E-value=11 Score=31.75 Aligned_cols=52 Identities=15% Similarity=0.129 Sum_probs=41.7
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
+..|||+.+|+ +.. .+.+.+.-|.+.|++..... ....|.||.-|+..++++
T Consensus 23 ~~~~la~~~~~---~~~----~v~~~~~~L~~kg~v~~~~~----~~~~~~LT~eG~~~~~~G 74 (494)
T PTZ00326 23 NSLALAESLNI---DHQ----KVVGAIKSLESANYITTEMK----KSNTWTLTEEGEDYLKNG 74 (494)
T ss_pred CHHHHHHHcCC---CHH----HHHHHHHHHHhCCCEEEEEE----EEEEEEECHHHHHHHHcC
Confidence 57899999999 447 89999999999998865432 136899999999777654
No 143
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=66.26 E-value=11 Score=31.75 Aligned_cols=52 Identities=12% Similarity=0.104 Sum_probs=41.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
+..+||+.+|+ +.. .+.+.+.-|.+.|++.-... ....|.||.-|+..++++
T Consensus 20 ~~~~la~~~g~---~~~----~v~~~~~~L~~kg~v~~~~~----~~~~~~LT~eG~~~l~~G 71 (492)
T PLN02853 20 DSGQFAASHGL---DHN----EVVGVIKSLHGFRYVDAQDI----KRETWVLTEEGKKYAAEG 71 (492)
T ss_pred CHHHHHHHcCC---CHH----HHHHHHHHHHhCCCEEEEEE----EEEEEEECHHHHHHHHcC
Confidence 67899999999 447 89999999999998865432 146899999998777653
No 144
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=65.89 E-value=2.9 Score=23.23 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=16.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSG 35 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~g 35 (128)
.|..+||+.+|+++ . .++|+++---..|
T Consensus 18 ~s~~~ia~~lgvs~---~----Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 18 WSIREIAKRLGVSR---S----TVYRWIKRYREEG 45 (50)
T ss_dssp --HHHHHHHHTS-H---H----HHHHHHT------
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHccccc
Confidence 37889999999954 7 8999887644433
No 145
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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 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=64.88 E-value=11 Score=23.96 Aligned_cols=46 Identities=13% Similarity=0.315 Sum_probs=31.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
.|..|+|..+|+++ +.+|+....|++.... ++++.+.|....+-++
T Consensus 2 ~~i~e~A~~~gvs~-----------~tLr~ye~~Gli~p~r--~~~g~R~y~~~dv~~l 47 (91)
T cd04766 2 YVISVAAELSGMHP-----------QTLRLYERLGLLSPSR--TDGGTRRYSERDIERL 47 (91)
T ss_pred cCHHHHHHHHCcCH-----------HHHHHHHHCCCcCCCc--CCCCCeeECHHHHHHH
Confidence 47899999999954 4577778889997432 1122467877776643
No 146
>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=64.08 E-value=4 Score=23.40 Aligned_cols=27 Identities=19% Similarity=0.322 Sum_probs=18.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHh-cCcc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVH-SGFF 37 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~-~gvf 37 (128)
+++.|||..+|+++ . .|++.|.. .|+.
T Consensus 4 i~V~elAk~l~v~~---~-------~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 4 IRVSELAKELGVPS---K-------EIIKKLFKELGIM 31 (54)
T ss_dssp E-TTHHHHHHSSSH---H-------HHHHHH-HHHTS-
T ss_pred eEHHHHHHHHCcCH---H-------HHHHHHHHhCCcC
Confidence 47889999999933 4 67777744 7887
No 147
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=64.03 E-value=7.8 Score=29.43 Aligned_cols=34 Identities=24% Similarity=0.266 Sum_probs=29.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++..|||+.+++++ . -++|-|+.|...|++....
T Consensus 20 ~~~~ela~~l~vS~---~----TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 20 VTVEKVIERLGISP---A----TARRDINKLDESGKLKKVR 53 (251)
T ss_pred cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEec
Confidence 47899999999944 7 8999999999999997543
No 148
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=63.68 E-value=21 Score=24.93 Aligned_cols=41 Identities=15% Similarity=0.277 Sum_probs=31.1
Q ss_pred CchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 16 KAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 16 ~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
++. .||++|+-|...|++..... . .....|.+|+.|+....
T Consensus 76 s~G----tIYp~L~RLE~~GlI~s~~~-~-~~RK~Y~ITe~Gre~L~ 116 (135)
T PRK09416 76 NEG----SLYTLLHRLEQNRFIQSSWD-H-EGAKYYQLTDKGNKMLR 116 (135)
T ss_pred CCc----cHHHHHHHHHHCCCeEEeec-C-CCceEEEECHHHHHHHH
Confidence 557 89999999999999975431 1 11467999999987654
No 149
>PF13518 HTH_28: Helix-turn-helix domain
Probab=63.33 E-value=10 Score=20.90 Aligned_cols=28 Identities=18% Similarity=0.366 Sum_probs=23.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
|+.++|..+|+++ . .|+|.++..-..|+
T Consensus 14 s~~~~a~~~gis~---~----tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 14 SVREIAREFGISR---S----TVYRWIKRYREGGI 41 (52)
T ss_pred CHHHHHHHHCCCH---h----HHHHHHHHHHhcCH
Confidence 7889999999944 7 89999988776664
No 150
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=63.05 E-value=13 Score=27.24 Aligned_cols=34 Identities=12% Similarity=0.073 Sum_probs=28.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++..|||+.+|++- . .++--|+.|...|++...+
T Consensus 31 L~e~eLae~lgVSR---t----pVREAL~~L~~eGlv~~~~ 64 (224)
T PRK11534 31 LRMSLLTSRYALGV---G----PLREALSQLVAERLVTVVN 64 (224)
T ss_pred CCHHHHHHHHCCCh---H----HHHHHHHHHHHCCCEEEeC
Confidence 35679999999943 6 8999999999999997654
No 151
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=62.90 E-value=14 Score=24.43 Aligned_cols=47 Identities=11% Similarity=0.187 Sum_probs=32.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|..|+|+.+|+++ +-||+--..|++......+ ++-+.|....+-++
T Consensus 1 ~~i~e~a~~~gvs~-----------~tlr~ye~~gll~~~~r~~-~gyR~Y~~~~l~~l 47 (113)
T cd01109 1 YTIKEVAEKTGLSA-----------DTLRYYEKEGLLPPVKRDE-NGIRDFTEEDLEWL 47 (113)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCCccCCHHHHHHH
Confidence 57899999999954 5688888999995432211 12467877776643
No 152
>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=62.88 E-value=12 Score=23.84 Aligned_cols=46 Identities=15% Similarity=0.278 Sum_probs=30.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|..|+|+.+|+++ . -+|+....|++.... ++++.+.|....+-.+
T Consensus 1 ~~~~eva~~~gi~~---~--------tlr~~~~~Gll~~~~--~~~g~r~y~~~dv~~l 46 (100)
T cd00592 1 YTIGEVAKLLGVSV---R--------TLRYYEEKGLLPPER--SENGYRLYSEEDLERL 46 (100)
T ss_pred CCHHHHHHHHCcCH---H--------HHHHHHHCCCcCCCc--CCCCCcccCHHHHHHH
Confidence 57899999999954 4 356667789986322 1122456877776643
No 153
>COG3703 ChaC Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]
Probab=62.84 E-value=11 Score=27.83 Aligned_cols=33 Identities=15% Similarity=0.195 Sum_probs=27.2
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ 39 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e 39 (128)
+..||.++|...++.+ .|.+++.+|..+||=..
T Consensus 138 A~~ia~a~G~sG~n~e----YL~~t~~hL~~~gi~d~ 170 (190)
T COG3703 138 AAIIAAAVGLSGPNAE----YLFNTLQHLRKLGIRDH 170 (190)
T ss_pred HHHHHHHhCCCCCcHH----HHHHHHHHHHhcCCcch
Confidence 4678888888776777 99999999999998653
No 154
>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=62.51 E-value=11 Score=28.88 Aligned_cols=32 Identities=22% Similarity=0.254 Sum_probs=27.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHH-HHHhcCcceee
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMW-ILVHSGFFAQQ 40 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR-~L~~~gvf~e~ 40 (128)
++++||+.+|.++ . .+.++++ .|+..|++..+
T Consensus 257 ~~~~ia~~lg~~~---~----~~~~~~e~~Li~~~li~~~ 289 (305)
T TIGR00635 257 GLKTLAAALGEDA---D----TIEDVYEPYLLQIGFLQRT 289 (305)
T ss_pred cHHHHHHHhCCCc---c----hHHHhhhHHHHHcCCcccC
Confidence 6789999999955 7 8889999 79999999633
No 155
>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=62.33 E-value=13 Score=28.83 Aligned_cols=50 Identities=18% Similarity=0.250 Sum_probs=37.4
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
+-+|.+.+++++ . .++-.|.-|+..|.+..... |...+|.+|+.++...+
T Consensus 23 Li~l~~~~gi~~---~----~vr~al~RL~~~G~l~~~~~---grr~~Y~LT~~g~~~l~ 72 (280)
T TIGR02277 23 LIEFLAGLGINE---R----LVRTAVSRLVAQGWLQSERK---GRRSFYSLTDKGRRRFA 72 (280)
T ss_pred HHHHHHhcCCCc---c----hHHHHHHHHHHCCCEEeeec---CCCCEEEECHHHHHHHH
Confidence 456677778844 7 89999999999999975431 11368999999986653
No 156
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=62.19 E-value=12 Score=27.44 Aligned_cols=33 Identities=6% Similarity=0.159 Sum_probs=28.2
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.|||+.+|+.+ . .|.|+|+-|...|++.-..
T Consensus 171 t~~~lA~~lG~sr---e----tvsR~L~~L~~~G~I~~~~ 203 (226)
T PRK10402 171 KHTQAAEYLGVSY---R----HLLYVLAQFIQDGYLKKSK 203 (226)
T ss_pred hHHHHHHHHCCcH---H----HHHHHHHHHHHCCCEEeeC
Confidence 4579999999955 7 9999999999999997553
No 157
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=62.14 E-value=7.8 Score=24.71 Aligned_cols=31 Identities=13% Similarity=0.172 Sum_probs=23.8
Q ss_pred HHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 28 MWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 28 LR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
+-+|...|++..+. .+.|.+|+.|+-+....
T Consensus 61 ~~~L~~aGli~~~~------rG~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 61 RSYLKKAGLIERPK------RGIWRITEKGRKALAEH 91 (92)
T ss_pred HHHHHHCCCccCCC------CCceEECHhHHHHHhhC
Confidence 56778889986544 58999999999776543
No 158
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=62.04 E-value=6 Score=22.32 Aligned_cols=12 Identities=8% Similarity=0.230 Sum_probs=9.7
Q ss_pred CHHHHHHhCCCC
Q 045905 2 TLNELINALPFH 13 (128)
Q Consensus 2 S~~eLA~~~~~~ 13 (128)
|+.|||..+|++
T Consensus 1 Ti~dIA~~agvS 12 (46)
T PF00356_consen 1 TIKDIAREAGVS 12 (46)
T ss_dssp CHHHHHHHHTSS
T ss_pred CHHHHHHHHCcC
Confidence 678899998883
No 159
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. 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
Probab=62.00 E-value=14 Score=25.08 Aligned_cols=47 Identities=13% Similarity=0.231 Sum_probs=33.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|..|+|+.+|+++ +-+|+--..|++......+ ++-+.|....+-++
T Consensus 1 m~I~e~a~~~gvs~-----------~tlRyYe~~GLl~~~~r~~-~g~R~Y~~~~~~~l 47 (127)
T cd01108 1 MNIGEAAKLTGLSA-----------KMIRYYEEIGLIPPPSRSD-NGYRVYNQRDIEEL 47 (127)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCceecCHHHHHHH
Confidence 58899999999954 4588888999997443212 22467888777653
No 160
>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=61.12 E-value=15 Score=26.63 Aligned_cols=33 Identities=12% Similarity=0.138 Sum_probs=28.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+-.+||+.+|++. . .++.-|+.|...|++...+
T Consensus 36 ~e~~La~~lgVSR---t----pVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 36 NESDIAARLGVSR---G----PVREAFRALEEAGLVRNEK 68 (212)
T ss_pred cHHHHHHHhCCCh---H----HHHHHHHHHHHCCCEEEec
Confidence 5579999999944 7 8999999999999997554
No 161
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=61.02 E-value=2.5 Score=32.72 Aligned_cols=50 Identities=12% Similarity=0.126 Sum_probs=32.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH------HHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI------LVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~------L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|+.|||++.|+.. . -+.|+|+- -+..+|+..-+ +-.|.++...+.|...
T Consensus 2 ~ti~dIA~~aGVS~---~----TVSrvLn~~~~Vs~~tr~kV~~~a~------elgY~pn~~a~~l~~~ 57 (346)
T PRK10401 2 ITIRDVARQAGVSV---A----TVSRVLNNSALVSADTREAVMKAVS------ELGYRPNANAQALATQ 57 (346)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHCCCCCCCHHHHHHHHHHHH------HHCCCCCHHHHHhhcC
Confidence 58899999999944 6 77787763 22222332221 2348888888888754
No 162
>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=60.95 E-value=4.3 Score=22.85 Aligned_cols=22 Identities=18% Similarity=0.194 Sum_probs=15.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|||+++|+++ . .+.|+++
T Consensus 10 ls~~~la~~~gis~---~----~i~~~~~ 31 (55)
T PF01381_consen 10 LSQKELAEKLGISR---S----TISRIEN 31 (55)
T ss_dssp S-HHHHHHHHTS-H---H----HHHHHHT
T ss_pred CCHHHHHHHhCCCc---c----hhHHHhc
Confidence 57889999999844 6 7777765
No 163
>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=60.79 E-value=11 Score=29.02 Aligned_cols=34 Identities=6% Similarity=0.186 Sum_probs=28.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++..+||+++|+.+ . .+++-+|.|...|+..-..
T Consensus 199 lse~eLAerlGVSR---s----~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 199 LVASKIADRVGITR---S----VIVNALRKLESAGVIESRS 232 (251)
T ss_pred ccHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecc
Confidence 46789999999955 7 8999999999999997543
No 164
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=60.70 E-value=11 Score=26.00 Aligned_cols=47 Identities=21% Similarity=0.294 Sum_probs=34.1
Q ss_pred CCHHHHHHhCCCCCC-CchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905 1 MTLNELINALPFHPI-KAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA 56 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~-~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~ 56 (128)
+|+.||-+.++.+.. ... .+.-||+-|+..|++....+ ++.|.-+|+
T Consensus 21 ~t~~eI~~~l~~~~ews~s----TV~TLl~RL~KKg~l~~~kd-----gr~~~y~pL 68 (123)
T COG3682 21 ATVREIIEELPADREWSYS----TVKTLLNRLVKKGLLTRKKD-----GRAFRYSPL 68 (123)
T ss_pred ccHHHHHHHHhhcccccHH----HHHHHHHHHHhccchhhhhc-----CCeeeeecc
Confidence 467788887776431 334 68899999999999987763 466776665
No 165
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=60.59 E-value=11 Score=22.16 Aligned_cols=47 Identities=17% Similarity=0.280 Sum_probs=30.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+|..|+|+.+|+++ +.+|+-...|++..... +++.+.|....+-++.
T Consensus 1 yti~eva~~~gvs~-----------~tlr~y~~~gll~~~~~--~~g~r~y~~~dv~~l~ 47 (69)
T PF13411_consen 1 YTIKEVAKLLGVSP-----------STLRYYEREGLLPPPRD--ENGYRYYSEEDVERLR 47 (69)
T ss_dssp EEHHHHHHHTTTTH-----------HHHHHHHHTTSSTTBES--TTSSEEE-HHHHHHHH
T ss_pred CcHHHHHHHHCcCH-----------HHHHHHHHhcCcccccc--cCceeeccHHHHHHHH
Confidence 47899999999944 45777777898765441 1224678777776544
No 166
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=59.49 E-value=11 Score=27.37 Aligned_cols=33 Identities=12% Similarity=0.122 Sum_probs=28.7
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|..|||+++++.+ . -+++-+.+|+..|.....-
T Consensus 179 s~~eIa~~l~iS~---~----Tv~~~~~~~~~~~~~~~~~ 211 (225)
T PRK10046 179 TAETVAQALTISR---T----TARRYLEYCASRHLIIAEI 211 (225)
T ss_pred CHHHHHHHhCccH---H----HHHHHHHHHHhCCeEEEEe
Confidence 6789999999944 7 8999999999999998653
No 167
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=59.15 E-value=13 Score=28.10 Aligned_cols=33 Identities=27% Similarity=0.400 Sum_probs=28.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
.|++|||+++|+ ... ..+|-|-+|++.|++...
T Consensus 174 ~Taeela~~~gi---SRv----TaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 174 LTAEELAQALGI---SRV----TARRYLEYLVSNGILEAE 206 (224)
T ss_pred cCHHHHHHHhCc---cHH----HHHHHHHHHHhcCeeeEE
Confidence 388999999999 446 899999999999988644
No 168
>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=58.82 E-value=13 Score=23.38 Aligned_cols=34 Identities=21% Similarity=0.285 Sum_probs=21.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|++||...++-..-++. .+..|+..|...||=-
T Consensus 22 lT~~eI~~~L~~~~~~~e----~id~i~~~L~~~gI~V 55 (82)
T PF03979_consen 22 LTYDEINDALPEDDLDPE----QIDEIYDTLEDEGIEV 55 (82)
T ss_dssp -BHHHHHHH-S-S---HH----HHHHHHHHHHTT----
T ss_pred CCHHHHHHHcCccCCCHH----HHHHHHHHHHHCCCEE
Confidence 588999999984322556 9999999999999654
No 169
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=58.51 E-value=6.2 Score=24.34 Aligned_cols=23 Identities=13% Similarity=0.297 Sum_probs=16.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRF 27 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~Rl 27 (128)
++++||+..||++... |++|.+|
T Consensus 45 a~~~el~~~CgL~~aE----AeLl~~L 67 (70)
T PF10975_consen 45 ASVEELMEECGLSRAE----AELLLSL 67 (70)
T ss_pred CCHHHHHHHcCCCHHH----HHHHHHH
Confidence 4789999999996533 3477665
No 170
>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=57.77 E-value=9.3 Score=20.55 Aligned_cols=26 Identities=23% Similarity=0.419 Sum_probs=19.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
|..|+|+.+|+++ +-||+.-..|++.
T Consensus 1 ti~e~A~~~gvs~-----------~tlR~ye~~Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGVSP-----------RTLRYYEREGLLP 26 (38)
T ss_dssp EHHHHHHHHTS-H-----------HHHHHHHHTTSS-
T ss_pred CHHHHHHHHCCCH-----------HHHHHHHHCCCCC
Confidence 4689999999843 5688888899984
No 171
>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=57.72 E-value=18 Score=28.06 Aligned_cols=45 Identities=18% Similarity=0.146 Sum_probs=34.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
...+||.+|+.+- ... -++-.|.+|...|++...+ +|.|..|..+
T Consensus 139 ~~~~ia~~l~p~i-s~~----ev~~sL~~L~~~glikk~~------~g~y~~t~~~ 183 (271)
T TIGR02147 139 DPEELAKRCFPKI-SAE----QVKESLDLLERLGLIKKNE------DGFYKQTDKA 183 (271)
T ss_pred CHHHHHHHhCCCC-CHH----HHHHHHHHHHHCCCeeECC------CCcEEeecce
Confidence 4678999988321 234 6888999999999998665 5789999876
No 172
>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=57.68 E-value=9 Score=24.70 Aligned_cols=24 Identities=13% Similarity=0.044 Sum_probs=19.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
+|..|||..+|++. . .++|+.|.|
T Consensus 51 ~S~~eIA~~LgISr---s----TIyRi~R~~ 74 (88)
T TIGR02531 51 KTYSDIEAETGAST---A----TISRVKRCL 74 (88)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHhc
Confidence 47899999999944 7 899988753
No 173
>PRK13824 replication initiation protein RepC; Provisional
Probab=57.60 E-value=15 Score=30.14 Aligned_cols=33 Identities=15% Similarity=0.191 Sum_probs=27.1
Q ss_pred CHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.+|+.++ |+++ . .|+|.++.|+..|++.-..
T Consensus 84 SN~~La~r~~Gms~---~----tlrRhla~LveaGLI~rrD 117 (404)
T PRK13824 84 SNAQLSLRAHGMAG---A----TLRRHLAALVEAGLIIRRD 117 (404)
T ss_pred hHHHHHHHHcCCCH---H----HHHHHHHHHHHCCCeEeec
Confidence 456899985 8855 7 8999999999999887654
No 174
>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=57.21 E-value=20 Score=23.58 Aligned_cols=48 Identities=19% Similarity=0.252 Sum_probs=32.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+|..|+|+.+|+++ +.+|+-...|++..... .+++-+.|....+-++.
T Consensus 1 ~~i~eva~~~gvs~-----------~tlR~ye~~Gll~p~~~-~~~g~R~Y~~~dl~~l~ 48 (108)
T cd04773 1 MTIGELAHLLGVPP-----------STLRHWEKEGLLSPDRE-PETGYRVYDPSDVRDAR 48 (108)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCcC-CCCCceeeCHHHHHHHH
Confidence 58899999999955 45777788899864321 11123568887776543
No 175
>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=57.16 E-value=19 Score=21.26 Aligned_cols=46 Identities=13% Similarity=0.284 Sum_probs=28.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhc-CcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHS-GFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~-gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
.+..|+|+.+|+++ . . ||+.... |++.... .+++.+.|....+-++
T Consensus 1 ~~i~e~A~~~gVs~---~----t----lr~ye~~~gl~~~~r--~~~g~R~yt~~di~~l 47 (68)
T cd04763 1 YTIGEVALLTGIKP---H----V----LRAWEREFGLLKPQR--SDGGHRLFNDADIDRI 47 (68)
T ss_pred CCHHHHHHHHCcCH---H----H----HHHHHHhcCCCCCCc--CCCCCcccCHHHHHHH
Confidence 47899999999954 4 3 4555543 7774322 1122466877766543
No 176
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=57.05 E-value=24 Score=26.89 Aligned_cols=34 Identities=15% Similarity=0.203 Sum_probs=29.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++++|||+.+++.+ . -+||=|+.|...|++....
T Consensus 20 v~v~eLa~~~~VS~---~----TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 20 VSVEELAELFGVSE---M----TIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred EEHHHHHHHhCCCH---H----HHHHhHHHHHHCCcEEEEe
Confidence 47899999999954 7 8999999999999998754
No 177
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=57.03 E-value=24 Score=25.85 Aligned_cols=48 Identities=13% Similarity=0.041 Sum_probs=34.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC-CCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ-NDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~-~~~~~~y~~T~~s~ 58 (128)
+|-.||++..|++ -+.+++.|...|++.+....+ .|.+..|..|+--.
T Consensus 105 iTr~eI~~irGv~----------~~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 105 ITRIEIDEIRGVN----------SDGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred cCHHHHHHHHCCC----------HHHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 5778999999982 258899999999998754322 12245687787643
No 178
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=56.46 E-value=8.9 Score=29.10 Aligned_cols=29 Identities=24% Similarity=0.295 Sum_probs=24.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
+|+.|||+++++++ . .+-|+.|-|--.|+
T Consensus 31 ~si~elA~~~~vS~---a----Tv~Rf~kklG~~Gf 59 (278)
T PRK11557 31 LSSQQLANEAGVSQ---S----SVVKFAQKLGYKGF 59 (278)
T ss_pred cCHHHHHHHhCCCH---H----HHHHHHHHcCCCCH
Confidence 58999999999955 7 89999998876664
No 179
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=56.35 E-value=18 Score=24.40 Aligned_cols=47 Identities=11% Similarity=0.243 Sum_probs=33.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
|++.|+|+.+|+++ +-+|+--..|++......+ ++-+.|....+-++
T Consensus 1 m~I~e~a~~~gvs~-----------~tlRyYe~~GLl~p~~r~~-~gyR~Y~~~~l~~l 47 (127)
T TIGR02044 1 MNIGQVAKLTGLSS-----------KMIRYYEEKGLIPPPLRSE-GGYRTYTQQHLDEL 47 (127)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCCeecCHHHHHHH
Confidence 68899999999944 5689999999997543222 22466777776643
No 180
>PRK13749 transcriptional regulator MerD; Provisional
Probab=56.21 E-value=19 Score=24.56 Aligned_cols=47 Identities=9% Similarity=0.041 Sum_probs=34.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|+.|+|.++|+++ +-+|+--..|++.....++ ++-+.|....+-++
T Consensus 4 ~tIgelA~~~gvS~-----------~tiR~YE~~GLl~p~~r~~-~gyR~Y~~~~l~rL 50 (121)
T PRK13749 4 YTVSRLALDAGVSV-----------HIVRDYLLRGLLRPVACTT-GGYGLFDDAALQRL 50 (121)
T ss_pred CcHHHHHHHHCCCH-----------HHHHHHHHCCCCCCCCcCC-CCCccCCHHHHHHH
Confidence 47899999999943 5689999999997654322 22567888777654
No 181
>PRK09492 treR trehalose repressor; Provisional
Probab=56.15 E-value=3 Score=31.71 Aligned_cols=50 Identities=10% Similarity=0.120 Sum_probs=31.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH------HHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI------LVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~------L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|+.|||+++|++. . -+.|+|.- -+...|+..-+ +-.|.++...+.|...
T Consensus 5 ~ti~dIA~~agVS~---~----TVSrvLn~~~~vs~~tr~rV~~~a~------elgY~pn~~a~~l~~~ 60 (315)
T PRK09492 5 LTIKDIARLSGVGK---S----TVSRVLNNESGVSEETRERVEAVIN------QHGFSPSKSARAMRGQ 60 (315)
T ss_pred CcHHHHHHHhCCCH---H----HHhHHhCCCCCCCHHHHHHHHHHHH------HHCCCcCHHHHHhhcC
Confidence 48999999999944 6 67777763 11222222111 2348888888877644
No 182
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=56.02 E-value=20 Score=22.57 Aligned_cols=44 Identities=20% Similarity=0.419 Sum_probs=30.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|+.|++..+++++ . +++.|+..|++...... ....|....+.+
T Consensus 1 is~~e~~~~~~i~~---~--------~l~~lve~Gli~p~~~~---~~~~f~~~~l~r 44 (84)
T PF13591_consen 1 ISLEEFCEACGIEP---E--------FLRELVEEGLIEPEGEE---EEWYFSEEDLAR 44 (84)
T ss_pred CCHHHHHHHHCcCH---H--------HHHHHHHCCCeeecCCC---CeeeECHHHHHH
Confidence 68999999999954 4 46777888999765421 123466555554
No 183
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=56.00 E-value=19 Score=23.75 Aligned_cols=48 Identities=6% Similarity=0.020 Sum_probs=34.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
.|..|+|+.+|+++ +-+|+--..|++......+ ++-+.|....+-++.
T Consensus 1 y~Ige~A~~~gvs~-----------~tlR~ye~~GLl~p~~r~~-~g~R~Y~~~~l~~l~ 48 (107)
T cd01111 1 YSISQLALDAGVSV-----------HIVRDYLLRGLLHPVARTE-GGYGLFDDCALQRLR 48 (107)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCCeecCHHHHHHHH
Confidence 47899999999954 4589999999997543222 225678888777654
No 184
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=55.97 E-value=12 Score=24.19 Aligned_cols=48 Identities=13% Similarity=0.110 Sum_probs=32.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|++|||+.+++++ . .|.|+++-...+.+..-- ..+.+..+.++|..+
T Consensus 22 ~~~~~lA~~~~~S~---~----~l~r~f~~~~g~s~~~~i--------~~~Rl~~a~~~L~~~ 69 (107)
T PRK10219 22 LNIDVVAKKSGYSK---W----YLQRMFRTVTHQTLGDYI--------RQRRLLLAAVELRTT 69 (107)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHCcCHHHHH--------HHHHHHHHHHHHHcc
Confidence 47899999999954 7 899998876544444322 246666666666653
No 185
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=55.71 E-value=11 Score=25.37 Aligned_cols=48 Identities=13% Similarity=0.052 Sum_probs=33.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|++|||+.+|+++ . .|.|+++.-+.+.+-.-- ..+.+..+..+|...
T Consensus 26 ~sl~~lA~~~g~S~---~----~l~r~Fk~~~G~s~~~~l--------~~~Rl~~A~~~L~~t 73 (127)
T PRK11511 26 LSLEKVSERSGYSK---W----HLQRMFKKETGHSLGQYI--------RSRKMTEIAQKLKES 73 (127)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHCcCHHHHH--------HHHHHHHHHHHHHcC
Confidence 48899999999955 7 899999876655544332 246666666666643
No 186
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=55.67 E-value=17 Score=30.22 Aligned_cols=31 Identities=16% Similarity=0.163 Sum_probs=24.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
.|+.|||+.+++ ..+ .+.|.|+.| .|++...
T Consensus 14 ~~~~eL~~~l~~---sq~----~~s~~L~~L--~~~V~~~ 44 (442)
T PRK09775 14 LSAAELAARLGV---SQA----TLSRLLAAL--GDQVVRF 44 (442)
T ss_pred CCHHHHHHHhCC---CHH----HHHHHHHHh--hcceeEe
Confidence 478999999999 557 788999998 5665443
No 187
>PF02981 FokI_N: Restriction endonuclease FokI, recognition domain; InterPro: IPR004234 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions (IPR004233 from INTERPRO), respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=55.48 E-value=13 Score=26.21 Aligned_cols=33 Identities=21% Similarity=0.269 Sum_probs=27.1
Q ss_pred HHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 25 YRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 25 ~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
+-+||-.+++|++..+.. .+.|..|.+|+.++.
T Consensus 110 d~flrwAvslgfl~~~~~-----~Dtf~IT~lG~~~~~ 142 (145)
T PF02981_consen 110 DGFLRWAVSLGFLDYDRE-----TDTFSITELGKKYVK 142 (145)
T ss_dssp HHHHHHHHHTTSEEEETT-----TTEEEE-HHHHHHHH
T ss_pred cceeeeeeeeCceeeccC-----CCEEEeehhHHHHhh
Confidence 467999999999988763 578999999998875
No 188
>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=55.44 E-value=11 Score=20.90 Aligned_cols=23 Identities=26% Similarity=0.304 Sum_probs=16.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|..|||..+|++. . .++++++-
T Consensus 21 ~t~~eIa~~lg~s~---~----~V~~~~~~ 43 (50)
T PF04545_consen 21 LTLEEIAERLGISR---S----TVRRILKR 43 (50)
T ss_dssp -SHHHHHHHHTSCH---H----HHHHHHHH
T ss_pred CCHHHHHHHHCCcH---H----HHHHHHHH
Confidence 48899999999944 6 55555543
No 189
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=55.31 E-value=20 Score=24.32 Aligned_cols=46 Identities=13% Similarity=0.224 Sum_probs=33.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+++.|+|..+|+++ +-+|+=-..|++......+ ++-+.|....+-+
T Consensus 1 m~I~e~a~~~gvs~-----------~tlR~Ye~~GLl~~~~r~~-~gyR~Y~~~~l~~ 46 (127)
T TIGR02047 1 MKIGELAQKTGVSV-----------ETIRFYEKQGLLPPPARTD-NNYRVYTVGHVER 46 (127)
T ss_pred CcHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCCCcCCHHHHHH
Confidence 57899999999944 5689999999997543212 2246788777664
No 190
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=54.84 E-value=17 Score=29.02 Aligned_cols=34 Identities=18% Similarity=0.167 Sum_probs=29.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|=+|||+++|+ ... .+.|+|..+-..|++.-.-
T Consensus 27 ltQ~eIA~~Lgi---SR~----~v~rlL~~Ar~~GiV~I~i 60 (321)
T COG2390 27 LTQSEIAERLGI---SRA----TVSRLLAKAREEGIVKISI 60 (321)
T ss_pred CCHHHHHHHhCC---CHH----HHHHHHHHHHHCCeEEEEe
Confidence 467899999999 347 8999999999999997653
No 191
>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=54.31 E-value=8.6 Score=25.48 Aligned_cols=48 Identities=27% Similarity=0.410 Sum_probs=31.7
Q ss_pred CHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905 2 TLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN 55 (128)
Q Consensus 2 S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~ 55 (128)
|+.||-..+.- +..+.. .+||.|..|...|++......+ +..+|.+..
T Consensus 25 ta~ei~~~l~~~~~~is~~----TVYR~L~~L~e~Gli~~~~~~~--~~~~Y~~~~ 74 (120)
T PF01475_consen 25 TAEEIYDKLRKKGPRISLA----TVYRTLDLLEEAGLIRKIEFGD--GESRYELST 74 (120)
T ss_dssp EHHHHHHHHHHTTTT--HH----HHHHHHHHHHHTTSEEEEEETT--SEEEEEESS
T ss_pred CHHHHHHHhhhccCCcCHH----HHHHHHHHHHHCCeEEEEEcCC--CcceEeecC
Confidence 56677776642 111456 7999999999999998765321 134677665
No 192
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=54.30 E-value=13 Score=20.65 Aligned_cols=22 Identities=14% Similarity=0.081 Sum_probs=18.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
|..+||..+|++. . .+.|++..
T Consensus 29 s~~~vA~~~~vs~---~----TV~ri~~~ 50 (52)
T PF13542_consen 29 SFKDVARELGVSW---S----TVRRIFDR 50 (52)
T ss_pred CHHHHHHHHCCCH---H----HHHHHHHh
Confidence 7889999999944 7 78888764
No 193
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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=54.16 E-value=21 Score=23.04 Aligned_cols=46 Identities=17% Similarity=0.306 Sum_probs=31.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|+.|+|+.+|+++ +.||+....|++.... ++++.+.|....+-++
T Consensus 2 ~~i~eva~~~gVs~-----------~tLR~ye~~Gli~p~r--~~~g~R~Ys~~dv~~l 47 (98)
T cd01279 2 YPISVAAELLGIHP-----------QTLRVYDRLGLVSPAR--TNGGGRRYSNNDLELL 47 (98)
T ss_pred cCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCc--CCCCCeeECHHHHHHH
Confidence 47899999999954 3466777789885422 1223567888877653
No 194
>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=54.13 E-value=11 Score=22.78 Aligned_cols=30 Identities=13% Similarity=0.026 Sum_probs=21.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
|..|||+.+|+++ . .++.+|+.....-.+.
T Consensus 22 t~eEiA~~lgis~---~----~v~~~l~~~~~~~Sl~ 51 (78)
T PF04539_consen 22 TDEEIAEELGISV---E----EVRELLQASRRPVSLD 51 (78)
T ss_dssp BHHHHHHHHTS-H---H----HHHHHHHHHSCCEESS
T ss_pred CHHHHHHHHcccH---H----HHHHHHHhCCCCeEEe
Confidence 6789999999944 7 8889998755444443
No 195
>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=54.05 E-value=21 Score=21.91 Aligned_cols=45 Identities=20% Similarity=0.236 Sum_probs=27.6
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
+-+|.+.+|++ +. .++=-|--|+..|++..... |..-.|.+|+-+
T Consensus 26 Li~ll~~~Gv~---e~----avR~alsRl~~~G~L~~~r~---Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 26 LIRLLAAFGVS---ES----AVRTALSRLVRRGWLESERR---GRRSYYRLTERG 70 (70)
T ss_dssp HHHHHCCTT-----HH----HHHHHHHHHHHTTSEEEECC---CTEEEEEE-HHH
T ss_pred HHHHHHHcCCC---hH----HHHHHHHHHHHcCceeeeec---CccceEeeCCCC
Confidence 34566777773 36 66666677788899986652 112369999853
No 196
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=53.81 E-value=10 Score=28.71 Aligned_cols=29 Identities=24% Similarity=0.288 Sum_probs=24.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
+|+.|||+++++.+ . .+-|+.|.|--.|+
T Consensus 35 ~si~~lA~~~~vS~---a----Tv~Rf~kklG~~gf 63 (284)
T PRK11302 35 SSIATLAKMANVSE---P----TVNRFCRSLDTKGF 63 (284)
T ss_pred cCHHHHHHHhCCCH---H----HHHHHHHHcCCCCH
Confidence 58899999999955 7 89999998876664
No 197
>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=53.53 E-value=21 Score=21.73 Aligned_cols=36 Identities=22% Similarity=0.463 Sum_probs=27.8
Q ss_pred CCHHHHHHhC---CCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINAL---PFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~---~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+++.++|+.+ +... ... .||-++-.|.+.|++.-..
T Consensus 25 i~l~~ia~~l~~~~~k~-~~R----RlYDI~NVLealgli~K~~ 63 (71)
T PF02319_consen 25 ISLNEIADKLISENVKT-QRR----RLYDIINVLEALGLIEKQS 63 (71)
T ss_dssp EEHHHHHHHCHHHCCHH-HCH----HHHHHHHHHHHCTSEEEEE
T ss_pred ccHHHHHHHHccccccc-ccc----hhhHHHHHHHHhCceeecC
Confidence 3678999999 7611 226 7999999999999997643
No 198
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=53.15 E-value=8.7 Score=29.60 Aligned_cols=29 Identities=31% Similarity=0.466 Sum_probs=24.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
+|..|||+++|+++ . .+-|+.|-|-..|+
T Consensus 37 ~si~elA~~a~VS~---a----Tv~Rf~~kLGf~Gf 65 (281)
T COG1737 37 LSIAELAERAGVSP---A----TVVRFARKLGFEGF 65 (281)
T ss_pred HHHHHHHHHhCCCH---H----HHHHHHHHcCCCCH
Confidence 47899999999955 7 89999998887774
No 199
>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=52.81 E-value=14 Score=24.80 Aligned_cols=28 Identities=32% Similarity=0.454 Sum_probs=18.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|+.|||+.+|+++ . .|.| +|-.+|+-.
T Consensus 72 ~tl~Ela~~l~Vs~---~----ti~~---~Lkrlg~t~ 99 (119)
T PF01710_consen 72 ATLRELAERLGVSP---S----TIWR---ALKRLGITR 99 (119)
T ss_pred cCHHHHHHHcCCCH---H----HHHH---HHHHcCchh
Confidence 57899999999833 5 5554 444566554
No 200
>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=52.79 E-value=35 Score=29.26 Aligned_cols=54 Identities=11% Similarity=0.002 Sum_probs=36.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcH
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTV 68 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~ 68 (128)
++.||++.++.+ .. .+.++||.|+..|.+..-. ++.|-+.-+-.++..+..-++
T Consensus 490 ~~~~~~~~~~~~---~~----~~~~~l~~l~~~g~~~~~~------~~~~~~~~~~~~~~~~~~~~~ 543 (581)
T TIGR00475 490 WVREFAEEVNGD---EK----VMLKRVRKAGHRGGETLIV------KDRLLKKYINELKEEGGTFNV 543 (581)
T ss_pred CHHHHHhhhCCC---HH----HHHHHHHHHHhCCCEEEEe------CCeEHHHHHHHHHhcCCcCcH
Confidence 467889888884 37 8899999999999666554 345655555555544433333
No 201
>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=52.55 E-value=25 Score=20.63 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=27.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+|..|+|+.+|+++ . . ||+....|.+.... ++++.+.|....+-++.
T Consensus 1 ~~i~evA~~~gvs~---~----t----lR~~~~~g~l~~~~--~~~g~R~y~~~~l~~l~ 47 (67)
T cd04764 1 YTIKEVSEIIGVKP---H----T----LRYYEKEFNLYIPR--TENGRRYYTDEDIELLK 47 (67)
T ss_pred CCHHHHHHHHCcCH---H----H----HHHHHHhcCCCCCC--CCCCceeeCHHHHHHHH
Confidence 47899999999955 4 3 55555543332211 12224667777665443
No 202
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=52.12 E-value=17 Score=27.61 Aligned_cols=34 Identities=18% Similarity=0.262 Sum_probs=29.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+++.|||+.+++++ . -+||=|..|...|++...-
T Consensus 20 ~~~~ela~~l~vS~---~----TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 20 VSTEELVEHFSVSP---Q----TIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred EeHHHHHHHhCCCH---H----HHHHHHHHHHHCCCEEEec
Confidence 47899999999944 7 8999999999999987653
No 203
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=52.03 E-value=27 Score=22.55 Aligned_cols=46 Identities=11% Similarity=0.155 Sum_probs=30.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|..|+|+.+|+++ . -+|+-...|++..... ++++-+.|....+-+
T Consensus 1 ~ti~eva~~~gvs~---~--------tlR~ye~~Gll~~~~~-~~~g~R~y~~~di~~ 46 (103)
T cd01106 1 YTVGEVAKLTGVSV---R--------TLHYYDEIGLLKPSRR-TENGYRLYTEEDLER 46 (103)
T ss_pred CCHHHHHHHHCcCH---H--------HHHHHHHCCCCCCCcc-CCCCceeeCHHHHHH
Confidence 47899999999955 3 4677778899854321 111246688777654
No 204
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=52.03 E-value=18 Score=19.70 Aligned_cols=14 Identities=21% Similarity=0.280 Sum_probs=11.6
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|..|||..+++++
T Consensus 19 ~s~~eia~~l~is~ 32 (58)
T smart00421 19 LTNKEIAERLGISE 32 (58)
T ss_pred CCHHHHHHHHCCCH
Confidence 47889999999954
No 205
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=51.52 E-value=18 Score=26.45 Aligned_cols=28 Identities=21% Similarity=0.235 Sum_probs=24.7
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
|-.|||+.+|+.+ . .+.|+++.|...|+
T Consensus 175 t~~~iA~~lG~tr---e----tvsR~l~~L~~~gl 202 (236)
T PRK09392 175 EKRVLASYLGMTP---E----NLSRAFAALASHGV 202 (236)
T ss_pred CHHHHHHHhCCCh---h----HHHHHHHHHHhCCe
Confidence 4578999999955 7 99999999999997
No 206
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=51.47 E-value=26 Score=26.21 Aligned_cols=33 Identities=15% Similarity=0.138 Sum_probs=27.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.|||+++|+ ... .++.-|+.|...|++....
T Consensus 28 sE~eLae~~gV---SRt----pVREAL~~Le~~GlV~~~~ 60 (253)
T PRK10421 28 AERQLAMQLGV---SRN----SLREALAKLVSEGVLLSRR 60 (253)
T ss_pred CHHHHHHHhCC---CHH----HHHHHHHHHHHCCCEEEeC
Confidence 45799999999 347 8999999999999997554
No 207
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 su
Probab=51.42 E-value=25 Score=24.13 Aligned_cols=46 Identities=13% Similarity=0.160 Sum_probs=32.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
|++.|+|+.+|+++ +-||+=-..|++......+ ++-+.|..+.+-+
T Consensus 1 m~Ige~a~~~gvs~-----------~tLRyYE~~GLl~p~~r~~-~gyR~Y~~~~v~~ 46 (131)
T cd04786 1 MKIGELAKRSGMAA-----------SRIRFYEAEGLLSSVERSA-NGYRDYPPETVWV 46 (131)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCCeecCHHHHHH
Confidence 68899999999954 4689999999997543222 1235677776664
No 208
>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=51.34 E-value=51 Score=21.66 Aligned_cols=37 Identities=27% Similarity=0.381 Sum_probs=27.9
Q ss_pred CCHHHHHHhCCCC-CCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFH-PIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~-~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|+.||.+.++-+ .-... .+.-+|+-|+..|++....
T Consensus 18 ~t~~eI~~~l~~~~~~~~s----Tv~t~L~rL~~Kg~l~~~~ 55 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYS----TVQTLLNRLVEKGFLTREK 55 (115)
T ss_dssp EEHHHHHHHHCTTSS--HH----HHHHHHHHHHHTTSEEEEE
T ss_pred CCHHHHHHHHHhccccchh----HHHHHHHHHHhCCceeEee
Confidence 3678888888753 11456 7999999999999998765
No 209
>PRK05660 HemN family oxidoreductase; Provisional
Probab=51.13 E-value=26 Score=28.19 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=35.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+..++.++.|.+ .. .....++.|...|++.... +++.+|+.|++|.+.
T Consensus 323 ~~~~~~~~~g~~---~~----~~~~~l~~l~~~gl~~~~~-------~~~~lt~~G~~~~d~ 370 (378)
T PRK05660 323 PRADFEAYTGLP---ES----VIRPQLDEALAQGYLTETA-------DHWQITEHGKLFLND 370 (378)
T ss_pred CHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEEeC-------CEEEECcchhHHHHH
Confidence 445666666662 24 4556889999999987653 689999999988754
No 210
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=51.06 E-value=26 Score=23.31 Aligned_cols=46 Identities=17% Similarity=0.277 Sum_probs=32.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|..|+|+.+|+++ +.+|+--..|++......+ ++-+.|....+-+
T Consensus 1 ~~I~eva~~~gvs~-----------~tLRyYe~~GLl~p~~r~~-~gyR~Y~~~~i~~ 46 (123)
T cd04770 1 MKIGELAKAAGVSP-----------DTIRYYERIGLLPPPQRSE-NGYRLYGEADLAR 46 (123)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCCCC-CCCccCCHHHHHH
Confidence 58899999999954 4579999999997433211 1235677766654
No 211
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=50.77 E-value=25 Score=22.84 Aligned_cols=45 Identities=13% Similarity=0.183 Sum_probs=31.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
++..|+|+.+|+++ +-+|+--..|++..... + ++-+.|....+-+
T Consensus 2 ~~i~eva~~~gvs~-----------~tlR~ye~~Gll~~~r~-~-~g~R~Y~~~~l~~ 46 (102)
T cd04789 2 YTISELAEKAGISR-----------STLLYYEKLGLITGTRN-A-NGYRLYPDSDLQR 46 (102)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCcC-C-CCCeeCCHHHHHH
Confidence 57899999999955 45788888999974321 2 2246787777664
No 212
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=50.47 E-value=25 Score=23.83 Aligned_cols=47 Identities=9% Similarity=0.068 Sum_probs=33.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|+.|+|.++|+++ +-+|+--..|++......+ ++-+.|....+-++
T Consensus 4 ~tI~elA~~~gvs~-----------~tlR~Ye~~GLL~p~~r~~-~gyR~Y~~~~l~rL 50 (120)
T TIGR02054 4 YTISRLAEDAGVSV-----------HVVRDYLLRGLLHPVRRTT-SGYGIFDDASLQRL 50 (120)
T ss_pred CcHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCccCC-CCCeeCCHHHHHHH
Confidence 47899999999954 4589999999997543222 22467888777653
No 213
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=50.36 E-value=26 Score=28.68 Aligned_cols=48 Identities=13% Similarity=0.135 Sum_probs=35.7
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
..+++.++.|.+ .. .+...+..|...|++..+. +++.+|+.|+.|.+.
T Consensus 363 ~~~~~~~~~g~~---~~----~~~~~l~~l~~~gll~~~~-------~~l~lT~~G~~~~d~ 410 (430)
T PRK08208 363 DLADYRQRFGSD---PL----RDFPELELLIDRGWLEQNG-------GRLRLTEEGLALSDA 410 (430)
T ss_pred CHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEEEC-------CEEEECcchhhHHHH
Confidence 345666666763 24 4567888999999998764 679999999998764
No 214
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=50.22 E-value=17 Score=27.91 Aligned_cols=34 Identities=12% Similarity=0.111 Sum_probs=29.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|+.|||+.+++++ . -++|=|..|...|++....
T Consensus 32 vtv~eLa~~l~VS~---~----TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 32 VQVNDLSALYGVST---V----TIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred EeHHHHHHHHCCCH---H----HHHHHHHHHHhCCCeEEEe
Confidence 47899999999944 7 8999999999999998654
No 215
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=49.87 E-value=6.1 Score=30.35 Aligned_cols=53 Identities=13% Similarity=0.092 Sum_probs=31.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC--C-CcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ--N-DQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~--~-~~~~~y~~T~~s~~L~~~ 63 (128)
+|+.|||++.|++. . -+.|.|. ..+-+++..... . -++--|.++..++.|...
T Consensus 7 ~Ti~dIA~~agVS~---~----TVSr~Ln---~~~~vs~~tr~~V~~~a~elgY~p~~~a~~l~~~ 62 (342)
T PRK10014 7 ITIHDVALAAGVSV---S----TVSLVLS---GKGRISTATGERVNQAIEELGFVRNRQASALRGG 62 (342)
T ss_pred CcHHHHHHHhCCCH---H----HHHHHHC---CCCCCCHHHHHHHHHHHHHhCCCcCHHHHhhccC
Confidence 48999999999944 6 6777775 333333322100 0 001238888888777643
No 216
>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=49.77 E-value=14 Score=22.01 Aligned_cols=31 Identities=19% Similarity=0.388 Sum_probs=24.4
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ 39 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e 39 (128)
|+.+|++.+++++ . .++.-|-.|...|++.-
T Consensus 29 tl~~i~~~t~l~~---~----~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 29 TLREIVRRTGLSP---K----QVKKALVVLIQHNLVQY 59 (62)
T ss_dssp EHHHHHHHHT--H---H----HHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHhCCCH---H----HHHHHHHHHHHcCCeee
Confidence 6789999999854 7 88999999999998753
No 217
>PRK11642 exoribonuclease R; Provisional
Probab=49.76 E-value=24 Score=31.65 Aligned_cols=37 Identities=14% Similarity=0.109 Sum_probs=29.6
Q ss_pred CCHHHHHHhCCCCCC-CchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPI-KAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~-~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++..||+++++++.. +.. .|.++|+.|...|++....
T Consensus 35 ~~~~~L~~~l~l~~~~~~~----~l~~~L~~L~~~g~l~~~~ 72 (813)
T PRK11642 35 ASREELAVELNIEGEEQLE----ALRRRLRAMERDGQLVFTR 72 (813)
T ss_pred CCHHHHHHHhCCCChHHHH----HHHHHHHHHHHCCCEEEcC
Confidence 478999999999542 234 7999999999999887544
No 218
>PRK09954 putative kinase; Provisional
Probab=49.35 E-value=19 Score=28.37 Aligned_cols=31 Identities=19% Similarity=0.241 Sum_probs=26.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|..|||..+++.. . .+.+.|+-|...|+..
T Consensus 18 ~s~~~la~~l~~s~---~----~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 18 IQQNEIADILQISR---S----RVAAHIMDLMRKGRIK 48 (362)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCcC
Confidence 57899999999944 7 8999999999999874
No 219
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=49.23 E-value=27 Score=25.69 Aligned_cols=34 Identities=18% Similarity=0.159 Sum_probs=28.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++-.+||+.+|++. . .++.-|+-|+..|++.-.+
T Consensus 40 l~e~~La~~~gvSr---t----PVReAL~rL~~eGlv~~~p 73 (230)
T COG1802 40 LSEEELAEELGVSR---T----PVREALRRLEAEGLVEIEP 73 (230)
T ss_pred ccHHHHHHHhCCCC---c----cHHHHHHHHHHCCCeEecC
Confidence 46689999999954 6 8999999999999997664
No 220
>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=49.22 E-value=31 Score=23.38 Aligned_cols=35 Identities=14% Similarity=0.146 Sum_probs=28.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF 42 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~ 42 (128)
.|++|||+.+++|. . .++=|+--|+..|.+....+
T Consensus 56 ~SVAEiAA~L~lPl---g----VvrVLvsDL~~~G~v~v~~p 90 (114)
T PF05331_consen 56 LSVAEIAARLGLPL---G----VVRVLVSDLADAGLVRVRAP 90 (114)
T ss_pred ccHHHHHHhhCCCc---h----hhhhhHHHHHhCCCEEEeCC
Confidence 48899999999966 5 67777888999998876653
No 221
>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=49.19 E-value=31 Score=21.36 Aligned_cols=35 Identities=17% Similarity=0.293 Sum_probs=26.2
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+.+|+...+++|-... .++.+++-|...||+....
T Consensus 25 Y~~lc~~~~~~pls~~----r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 25 YEELCESLGVDPLSYR----RFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHHHHTTS----HH----HHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHcCCCCCCHH----HHHHHHHHHHhCCCeEEEe
Confidence 5688999999775666 8999999999999997554
No 222
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of 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 C-terminal domains are often unrelated and bind specific coactivator molecules. They 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.
Probab=49.10 E-value=30 Score=22.19 Aligned_cols=47 Identities=17% Similarity=0.244 Sum_probs=32.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
++..|+|..+|+++ +-+|+--..|++......+ ++-+.|....+-++
T Consensus 1 m~i~eva~~~gvs~-----------~tlR~ye~~Gll~p~~r~~-~gyR~Y~~~~l~~l 47 (96)
T cd04788 1 WKIGELARRTGLSV-----------RTLHHYDHIGLLSPSQRTE-GGHRLYDRADIRRL 47 (96)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCccCC-CCceeeCHHHHHHH
Confidence 57899999999954 4588888999997542211 22466877766543
No 223
>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=49.07 E-value=30 Score=25.49 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=27.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|=.|||++.|+ ... -++|-|+.|+..|++....
T Consensus 26 sE~eLa~~~gV---SR~----TVR~Al~~L~~eGli~r~~ 58 (233)
T TIGR02404 26 SEHELMDQYGA---SRE----TVRKALNLLTEAGYIQKIQ 58 (233)
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEeC
Confidence 44689999999 447 8999999999999997665
No 224
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=48.98 E-value=29 Score=27.66 Aligned_cols=45 Identities=13% Similarity=0.107 Sum_probs=32.8
Q ss_pred CCHHHHHHh--CCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINA--LPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~--~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
++..+||+. ++++| . -+||-|..|-..|++..... ...+-+|..|
T Consensus 26 v~s~~l~~~~~l~~S~---a----TIR~dm~~Le~~G~l~~~h~-----sagrIPT~kG 72 (339)
T PRK00082 26 VGSKTLSKRYGLGVSS---A----TIRNDMADLEELGLLEKPHT-----SSGRIPTDKG 72 (339)
T ss_pred cCHHHHHHHhCCCCCh---H----HHHHHHHHHHhCCCcCCCcC-----CCCCCcCHHH
Confidence 367899977 67744 7 89999999999999975432 2335566666
No 225
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=48.96 E-value=32 Score=25.67 Aligned_cols=33 Identities=12% Similarity=0.141 Sum_probs=28.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.|||+++|+ ... .++--|+.|...|++....
T Consensus 36 sE~eLa~~lgV---SRt----pVREAL~~L~~eGlv~~~~ 68 (254)
T PRK09464 36 PERELAKQFDV---SRP----SLREAIQRLEAKGLLLRRQ 68 (254)
T ss_pred CHHHHHHHhCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 45789999999 447 8999999999999997654
No 226
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are 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 C-terminal domains are often unrelated and bind specific coactivator molecules. They 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.
Probab=48.91 E-value=31 Score=22.16 Aligned_cols=47 Identities=15% Similarity=0.219 Sum_probs=32.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
.|..|+|+.+|+++ +-+|+--..|++......+ ++-+.|....+-++
T Consensus 1 ~~i~eva~~~gvs~-----------~tlR~ye~~Gll~p~~~~~-~gyR~Y~~~~~~~l 47 (97)
T cd04782 1 FTTGEFAKLCGISK-----------QTLFHYDKIGLFKPEIVKE-NGYRYYTLEQFEQL 47 (97)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCccCC-CCCccCCHHHHHHH
Confidence 47899999999954 4588888999996542211 22467877776554
No 227
>PRK00118 putative DNA-binding protein; Validated
Probab=48.61 E-value=15 Score=24.41 Aligned_cols=14 Identities=14% Similarity=0.294 Sum_probs=12.1
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|..|||+.+|+++
T Consensus 34 ~S~~EIAe~lGIS~ 47 (104)
T PRK00118 34 YSLGEIAEEFNVSR 47 (104)
T ss_pred CCHHHHHHHHCcCH
Confidence 48899999999965
No 228
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=48.48 E-value=11 Score=27.45 Aligned_cols=32 Identities=16% Similarity=-0.046 Sum_probs=27.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ 39 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e 39 (128)
++..|||+.++++. . -+||=|+.|...|++..
T Consensus 22 ~~~~~La~~~~vS~---~----TiRRDl~~L~~~g~~~r 53 (185)
T PRK04424 22 ITDEELAEKFGVSI---Q----TIRLDRMELGIPELRER 53 (185)
T ss_pred EEHHHHHHHHCcCH---H----HHHHHHHHHhcchHHHH
Confidence 46889999999944 7 89999999999998754
No 229
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=48.33 E-value=31 Score=25.16 Aligned_cols=33 Identities=15% Similarity=0.063 Sum_probs=27.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+-.+||+.+|++- . .++--|+.|...|++...+
T Consensus 36 ~e~~La~~lgVSR---t----pVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 36 ITKNLAEQLGMSI---T----PVREALLRLVSVNALSVAP 68 (221)
T ss_pred CHHHHHHHHCCCc---h----hHHHHHHHHHHCCCEEecC
Confidence 4578999999944 6 8999999999999997554
No 230
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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.
Probab=48.22 E-value=35 Score=22.33 Aligned_cols=48 Identities=15% Similarity=0.209 Sum_probs=33.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
++..|+|+.+|+++ +-+|+--..|++......++++-+.|....+-++
T Consensus 1 ~~i~eva~~~gis~-----------~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~~l 48 (108)
T cd01107 1 FTIGEFAKLSNLSI-----------KALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERL 48 (108)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHcCCCCCCcCCCCCCccccCHHHHHHH
Confidence 47899999999955 4588888999996533211112467887777653
No 231
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of 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 C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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.
Probab=48.20 E-value=29 Score=23.31 Aligned_cols=46 Identities=13% Similarity=0.177 Sum_probs=33.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+++.|+|+.+|+++ +-+|+=-..|++......+ ++-+.|....+-+
T Consensus 1 m~IgevA~~~gvs~-----------~tLRyYe~~GLl~p~~r~~-~gyR~Y~~~~l~~ 46 (127)
T cd04784 1 MKIGELAKKTGCSV-----------ETIRYYEKEGLLPAPARSA-NNYRLYDEEHLER 46 (127)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCCeecCHHHHHH
Confidence 57899999999954 5689999999997443222 2246788877764
No 232
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=48.03 E-value=32 Score=25.35 Aligned_cols=33 Identities=15% Similarity=0.211 Sum_probs=28.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.|||+++|+ ... .++.-|+.|...|++....
T Consensus 33 sE~eLae~~gV---SRt----~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 33 AERELSELIGV---TRT----TLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEeC
Confidence 45689999999 447 8999999999999997654
No 233
>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=47.82 E-value=39 Score=21.06 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=27.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
.|++||-+++|+ +.. .|-..|--|+..|+....
T Consensus 19 ~TLeeL~ekTgi---~k~----~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 19 CTLEELEEKTGI---SKN----TLLVYLSRLAKRGIIERK 51 (72)
T ss_pred CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCeeee
Confidence 489999999999 446 788888889999999765
No 234
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=47.74 E-value=28 Score=26.05 Aligned_cols=40 Identities=20% Similarity=0.259 Sum_probs=31.2
Q ss_pred HHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905 4 NELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN 55 (128)
Q Consensus 4 ~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~ 55 (128)
.|||++.+++ .. -++|-|+.|+..|++..... .|.|-..+
T Consensus 35 ~eLa~~f~VS---R~----TvRkAL~~L~~eGli~r~~G-----~GtfV~~~ 74 (236)
T COG2188 35 RELAEQFGVS---RM----TVRKALDELVEEGLIVRRQG-----KGTFVASP 74 (236)
T ss_pred HHHHHHHCCc---HH----HHHHHHHHHHHCCcEEEEec-----CeeEEcCc
Confidence 5899999994 47 89999999999999976542 45555554
No 235
>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=47.38 E-value=36 Score=25.08 Aligned_cols=33 Identities=15% Similarity=0.211 Sum_probs=28.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.+||+.+|+ ... .++--|+.|...|++...+
T Consensus 32 sE~~La~~lgV---SRt----pVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 32 AERELSELIGV---TRT----TLREVLQRLARDGWLTIQH 64 (235)
T ss_pred CHHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEEeC
Confidence 56799999999 446 8999999999999997654
No 236
>PHA02943 hypothetical protein; Provisional
Probab=47.32 E-value=33 Score=24.71 Aligned_cols=35 Identities=14% Similarity=0.220 Sum_probs=28.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF 42 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~ 42 (128)
.|.+|||+++|++- . ..+=+|+.|-..|.+.+...
T Consensus 25 ~TtseIAkaLGlS~---~----qa~~~LyvLErEG~VkrV~~ 59 (165)
T PHA02943 25 KTTSRIANKLGVSH---S----MARNALYQLAKEGMVLKVEI 59 (165)
T ss_pred ccHHHHHHHHCCCH---H----HHHHHHHHHHHcCceEEEee
Confidence 36889999999944 5 67778999999999887764
No 237
>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=47.32 E-value=35 Score=23.27 Aligned_cols=88 Identities=14% Similarity=0.225 Sum_probs=46.3
Q ss_pred CCHHHHHHhCCC-CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh--------hhhhhcC-CCCcHHH
Q 045905 1 MTLNELINALPF-HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA--------SKLLLKD-ITLTVRS 70 (128)
Q Consensus 1 ~S~~eLA~~~~~-~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~--------s~~L~~~-~~~s~~~ 70 (128)
+|+.||.+.++- .+-+.. .+.++|+-|...|++..... |....|.+.-- .+-+.+. -.+|+.+
T Consensus 19 ~t~~eI~~~l~~~~~~~~t----Tv~T~L~rL~~KG~v~~~k~---gr~~~Y~p~vs~ee~~~~~~~~~~~~~f~gs~~~ 91 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWSDS----TIKTLLGRLVDKGCLTTEKE---GRKFIYTALVSEDEAVENAAQELFSRICSRKVGA 91 (130)
T ss_pred CCHHHHHHHHhhccCCcHH----HHHHHHHHHHHCCceeeecC---CCcEEEEecCCHHHHHHHHHHHHHHHHHCCCHHH
Confidence 367787766532 111446 89999999999999975532 11224553211 1112111 1234555
Q ss_pred HHHHhcC--hhhHHHHHhHHHhhhcCC
Q 045905 71 FLQAVLD--PILTTPCQHVTTWFQNDD 95 (128)
Q Consensus 71 ~~~~~~~--~~~~~~~~~l~~~~~~g~ 95 (128)
++..+.+ ...-.-...|.+.+.+..
T Consensus 92 ll~~l~~~~~ls~eele~L~~li~~~~ 118 (130)
T TIGR02698 92 VIADLIEESPLSQTDIEKLEKLLSEKK 118 (130)
T ss_pred HHHHHHhcCCCCHHHHHHHHHHHHhcc
Confidence 5555433 233344566666666543
No 238
>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=47.26 E-value=7.5 Score=29.59 Aligned_cols=50 Identities=8% Similarity=0.106 Sum_probs=31.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH------HHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI------LVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~------L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|+.|||+.+|+.. . -+.|.|.- .+..+|+...+ +-.|.++...+.|...
T Consensus 2 ~ti~dIA~~agVS~---s----TVSr~Ln~~~~vs~~tr~rV~~~a~------~lgY~pn~~a~~l~~~ 57 (311)
T TIGR02405 2 LTIKDIARLAGVGK---S----TVSRVLNNEPKVSIETRERVEQVIQ------QSGFVPSKSARAMRGG 57 (311)
T ss_pred CcHHHHHHHhCCCH---H----HHHHHhCCCCCCCHHHHHHHHHHHH------HHCCCcCHHHHHhhcC
Confidence 58899999999944 6 77787752 12222222111 2348888888877654
No 239
>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=47.06 E-value=33 Score=25.15 Aligned_cols=33 Identities=18% Similarity=0.231 Sum_probs=27.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|=.|||++.|+ ... -++|-|..|+..|++....
T Consensus 34 sE~eLa~~~~V---SR~----TvR~Al~~L~~eGli~r~~ 66 (238)
T TIGR02325 34 AEMQLAERFGV---NRH----TVRRAIAALVERGLLRAEQ 66 (238)
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 44699999999 446 8999999999999997665
No 240
>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=47.00 E-value=34 Score=21.57 Aligned_cols=46 Identities=13% Similarity=0.266 Sum_probs=31.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|+.|+|+.+|+++ +-||+....|++..... ++++.+.|....+-+
T Consensus 2 ~ti~evA~~~gvs~-----------~tLR~ye~~Gll~p~r~-~~~g~R~Ys~~dv~~ 47 (88)
T cd01105 2 IGIGEVSKLTGVSP-----------RQLRYWEEKGLIKSIRS-DGGGQRKYSLADVDR 47 (88)
T ss_pred cCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCcc-CCCCceecCHHHHHH
Confidence 47899999999954 34778888898863321 111356788777653
No 241
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of 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 C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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.
Probab=47.00 E-value=32 Score=23.19 Aligned_cols=47 Identities=15% Similarity=0.196 Sum_probs=33.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|..|+|+.+|+++ +-+|+--..|++......+ ++-+.|....+-++
T Consensus 1 ~~I~e~a~~~gvs~-----------~tlR~Ye~~Gll~~~~r~~-~g~R~Y~~~~l~~l 47 (126)
T cd04785 1 LSIGELARRTGVNV-----------ETIRYYESIGLLPEPARTA-GGYRLYGAAHVERL 47 (126)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCccccCHHHHHHH
Confidence 58899999999954 4588999999997432211 22467877777653
No 242
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=46.91 E-value=17 Score=27.86 Aligned_cols=29 Identities=24% Similarity=0.358 Sum_probs=24.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
+|+.|||+++++.+ . .+-|+.|.|--.|+
T Consensus 47 ~si~~lA~~~~vS~---a----Ti~Rf~kkLGf~gf 75 (292)
T PRK11337 47 TALKDIAEALAVSE---A----MIVKVAKKLGFSGF 75 (292)
T ss_pred cCHHHHHHHhCCCh---H----HHHHHHHHcCCCCH
Confidence 57899999999955 7 89999998876664
No 243
>PRK04217 hypothetical protein; Provisional
Probab=46.86 E-value=20 Score=24.14 Aligned_cols=14 Identities=14% Similarity=0.071 Sum_probs=12.0
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|..|||+.+|++.
T Consensus 59 lS~~EIAk~LGIS~ 72 (110)
T PRK04217 59 LTQEEAGKRMGVSR 72 (110)
T ss_pred CCHHHHHHHHCcCH
Confidence 47899999999954
No 244
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=46.53 E-value=33 Score=23.86 Aligned_cols=50 Identities=22% Similarity=0.308 Sum_probs=31.8
Q ss_pred CHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 2 TLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 2 S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
|+.||=..+.- ++..++ -+||.|..|+..|++.+....+ +..+|.++.-+
T Consensus 38 sAeei~~~l~~~~p~isla----TVYr~L~~l~e~Glv~~~~~~~--~~~~y~~~~~~ 89 (145)
T COG0735 38 SAEELYEELREEGPGISLA----TVYRTLKLLEEAGLVHRLEFEG--GKTRYELNSEP 89 (145)
T ss_pred CHHHHHHHHHHhCCCCCHh----HHHHHHHHHHHCCCEEEEEeCC--CEEEEecCCCC
Confidence 44555444442 222557 8999999999999998776421 13457666554
No 245
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=46.37 E-value=36 Score=27.13 Aligned_cols=48 Identities=10% Similarity=0.070 Sum_probs=33.6
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
..++.+..|.+. . +.+...+..|...|++..+. +.+.+|+.|+++.+.
T Consensus 321 ~~~~~~~~~~~~---~---~~~~~~~~~l~~~gl~~~~~-------~~~~lt~~G~~~~~~ 368 (377)
T PRK08599 321 KARFEEKFGQSF---E---DVFGETIQELQEQGLLEEDD-------DHVRLTKKGKFLGNE 368 (377)
T ss_pred HHHHHHHHCcCH---H---HHHHHHHHHHHHCCCEEEEC-------CEEEECccHhHHHHH
Confidence 345555555521 2 24667788889999887653 679999999998764
No 246
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=46.31 E-value=17 Score=21.81 Aligned_cols=13 Identities=8% Similarity=0.138 Sum_probs=10.8
Q ss_pred CCHHHHHHhCCCC
Q 045905 1 MTLNELINALPFH 13 (128)
Q Consensus 1 ~S~~eLA~~~~~~ 13 (128)
+|..|||.++|+.
T Consensus 1 ~t~~~iA~~~gvS 13 (70)
T smart00354 1 ATIKDVARLAGVS 13 (70)
T ss_pred CCHHHHHHHHCCC
Confidence 4788999999983
No 247
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=46.22 E-value=35 Score=25.53 Aligned_cols=33 Identities=15% Similarity=0.174 Sum_probs=27.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.+||+++|++ .. .++--|+.|...|++....
T Consensus 35 sE~eLa~~~gVS---Rt----pVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 35 PEREIAEMLDVT---RT----VVREALIMLEIKGLVEVRR 67 (257)
T ss_pred CHHHHHHHhCCC---HH----HHHHHHHHHHHCCCEEEec
Confidence 457899999993 47 8999999999999997554
No 248
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=46.02 E-value=32 Score=24.68 Aligned_cols=46 Identities=11% Similarity=0.228 Sum_probs=31.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|+.|+|+.+|+++ +-+|+--..|++......++ +-+.|....+-+
T Consensus 2 ~~I~evA~~~gvs~-----------~tLRyYe~~GLl~p~~r~~~-gyR~Y~~~dl~r 47 (172)
T cd04790 2 LTISQLARQFGLSR-----------STLLYYERIGLLSPSARSES-NYRLYGERDLER 47 (172)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCccCCC-CCccCCHHHHHH
Confidence 57899999999944 45888889999975432111 235676665544
No 249
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=45.88 E-value=24 Score=25.07 Aligned_cols=28 Identities=18% Similarity=0.211 Sum_probs=18.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
+|+.|||+.+|+++ .-+-..|.|.++.|
T Consensus 148 ~s~~EIA~~lgis~---~tV~~~l~Rar~~L 175 (191)
T PRK12520 148 LETEEICQELQITA---TNAWVLLYRARMRL 175 (191)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHH
Confidence 58899999999965 32223455555544
No 250
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=45.81 E-value=38 Score=25.18 Aligned_cols=33 Identities=15% Similarity=0.172 Sum_probs=27.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.|||+.+|+ ... .++--|+.|...|++....
T Consensus 33 sE~eLa~~~gV---SRt----pVREAL~~L~~eGlV~~~~ 65 (251)
T PRK09990 33 SERRLCEKLGF---SRS----ALREGLTVLRGRGIIETAQ 65 (251)
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEeC
Confidence 45799999999 347 8999999999999997654
No 251
>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=45.80 E-value=18 Score=20.00 Aligned_cols=21 Identities=10% Similarity=0.154 Sum_probs=14.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFM 28 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlL 28 (128)
+|..|||..+|+++ . .+.++.
T Consensus 16 ltq~~lA~~~gvs~---~----~vs~~e 36 (58)
T TIGR03070 16 LTQADLADLAGVGL---R----FIRDVE 36 (58)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHH
Confidence 46788888888843 5 565554
No 252
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. 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.
Probab=45.65 E-value=34 Score=23.02 Aligned_cols=46 Identities=15% Similarity=0.237 Sum_probs=32.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
++..|+|+.+|+++ +-+|+--..|++......+ ++-+.|....+-+
T Consensus 1 m~I~e~a~~~gvs~-----------~tlR~Ye~~GLl~~~~r~~-~gyR~Y~~~~l~~ 46 (126)
T cd04783 1 LTIGELAKAAGVNV-----------ETIRYYQRRGLLPEPPRPE-GGYRRYPEETVTR 46 (126)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCCeecCHHHHHH
Confidence 57899999999954 3469999999997432211 2245677776665
No 253
>PRK15482 transcriptional regulator MurR; Provisional
Probab=45.59 E-value=19 Score=27.53 Aligned_cols=29 Identities=17% Similarity=0.304 Sum_probs=24.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
+|+.|||+++++++ . .+-|+.|.|--.|+
T Consensus 35 ~si~elA~~~~vS~---a----Tv~Rf~kkLGf~Gf 63 (285)
T PRK15482 35 VSSRKMAKQLGISQ---S----SIVKFAQKLGAQGF 63 (285)
T ss_pred cCHHHHHHHhCCCH---H----HHHHHHHHhCCCCH
Confidence 58899999999955 7 88899988876664
No 254
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=45.49 E-value=34 Score=23.54 Aligned_cols=48 Identities=13% Similarity=0.256 Sum_probs=34.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
|++.|+|+.+|+++ +-+|+--..|++......++ +-+.|....+.++.
T Consensus 1 m~Ige~a~~~gvs~-----------~tlRyYE~~GLl~p~~r~~~-gyR~Y~~~~l~~l~ 48 (135)
T PRK10227 1 MNISDVAKITGLTS-----------KAIRFYEEKGLVTPPMRSEN-GYRTYTQQHLNELT 48 (135)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCcccCCC-CcccCCHHHHHHHH
Confidence 67899999999944 45899999999976433222 24678887777543
No 255
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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, an
Probab=45.24 E-value=33 Score=22.85 Aligned_cols=45 Identities=11% Similarity=0.165 Sum_probs=33.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|+.|+|+.+|+++ +-+|+=-..|++..... + ++-+.|....+-+
T Consensus 1 m~IgevA~~~gvs~-----------~tlRyYe~~GLl~p~~~-~-~gyR~Y~~~~l~~ 45 (120)
T cd04781 1 LDIAEVARQSGLPA-----------STLRYYEEKGLIASIGR-R-GLRRQYDPQVLDR 45 (120)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCcC-C-CCceecCHHHHHH
Confidence 58899999999954 56899999999985432 1 2246788877764
No 256
>PRK03837 transcriptional regulator NanR; Provisional
Probab=45.20 E-value=41 Score=24.70 Aligned_cols=33 Identities=15% Similarity=0.132 Sum_probs=28.2
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+-.|||+++|+ ... .++--|+.|...|++....
T Consensus 39 ~E~~Lae~~gV---SRt----~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 39 SERELMAFFGV---GRP----AVREALQALKRKGLVQISH 71 (241)
T ss_pred CHHHHHHHhCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 56799999999 447 8999999999999997654
No 257
>PRK14999 histidine utilization repressor; Provisional
Probab=44.88 E-value=36 Score=25.25 Aligned_cols=33 Identities=18% Similarity=0.312 Sum_probs=27.7
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|=.|||++.|+ ... -++|-|..|+..|++....
T Consensus 38 sE~eLa~~~gV---SR~----TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 38 SEAELVAQYGF---SRM----TINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 44789999999 447 8999999999999997654
No 258
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=44.79 E-value=24 Score=26.03 Aligned_cols=30 Identities=17% Similarity=0.044 Sum_probs=20.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVH 33 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~ 33 (128)
+|+.|||+.+|+++ .-+-..|.|.++.|..
T Consensus 151 ~s~~EIAe~LgiS~---~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 151 MSYREIAAIADVPV---GTVMSRLARARRRLAA 180 (216)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHHH
Confidence 58899999999965 3333356666666653
No 259
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=44.79 E-value=52 Score=24.12 Aligned_cols=46 Identities=15% Similarity=0.140 Sum_probs=32.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC-CCcccceechHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ-NDQERSYVATNA 56 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~-~~~~~~y~~T~~ 56 (128)
+|-.||-+-=|+ ..+++++.|..+|++.+....+ .|.+..|+.|+.
T Consensus 107 iTR~eI~~iRGv----------~~~~~i~~L~e~glI~~~g~~~~~Grp~ly~tT~~ 153 (184)
T COG1386 107 VTRSEIEEIRGV----------AVSQVISTLLERGLIREVGRRDTPGRPYLYGTTEK 153 (184)
T ss_pred ccHHHHHHHhCc----------cHHHHHHHHHHCCCeEecCCCCCCCCceeeeccHH
Confidence 355667666666 4568999999999999886432 233456888775
No 260
>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=44.58 E-value=17 Score=21.87 Aligned_cols=14 Identities=14% Similarity=0.344 Sum_probs=11.7
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
|++.|||+++|+++
T Consensus 23 i~lkdIA~~Lgvs~ 36 (60)
T PF10668_consen 23 IKLKDIAEKLGVSE 36 (60)
T ss_pred ccHHHHHHHHCCCH
Confidence 57889999999954
No 261
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=44.52 E-value=35 Score=23.54 Aligned_cols=47 Identities=15% Similarity=0.249 Sum_probs=33.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+++.|+|+.+|+++ +-+|+--..|++......+ ++-+.|....+-++
T Consensus 2 ~~I~e~a~~~gvs~-----------~tlR~Ye~~GLl~p~~r~~-~gyR~Y~~~~l~~l 48 (140)
T PRK09514 2 YRIGELAKLAEVTP-----------DTLRFYEKQGLMDPEVRTE-GGYRLYTEQDLQRL 48 (140)
T ss_pred CcHHHHHHHHCcCH-----------HHHHHHHHCCCCCCcccCC-CCCeeeCHHHHHHH
Confidence 47899999999954 4588888999997543222 22467877777654
No 262
>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=44.44 E-value=15 Score=23.40 Aligned_cols=24 Identities=21% Similarity=0.236 Sum_probs=16.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
+|-.|||.++|-+ .. .+.+.|+.|
T Consensus 4 ~tq~eIA~~lGks---~s----~Vs~~l~Ll 27 (93)
T PF08535_consen 4 WTQEEIAKRLGKS---RS----WVSNHLALL 27 (93)
T ss_dssp --HHHHHHHTT-----HH----HHHHHHGGG
T ss_pred CCHHHHHHHHCCC---HH----HHHHHHHHH
Confidence 3678999999984 47 788888865
No 263
>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=44.35 E-value=31 Score=21.12 Aligned_cols=33 Identities=18% Similarity=0.285 Sum_probs=27.3
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+-.||+..++. |+. .+..+++.|...|++....
T Consensus 20 ~q~~L~~~~~~---D~r----~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 20 TQSDLSKLLGI---DPR----SIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred ehhHHHHHhCC---Cch----HHHHHHHHHHHCCCEEEEE
Confidence 45689999998 558 9999999999999886543
No 264
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=44.30 E-value=27 Score=24.77 Aligned_cols=29 Identities=14% Similarity=-0.081 Sum_probs=18.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|..|||+.+|+++. .+-..|.|.++.|-
T Consensus 148 ~s~~EIA~~lgis~~---tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 148 FAYKEIAEIMGTPIG---TVMSRLHRGRKQLR 176 (193)
T ss_pred CCHHHHHHHHCCCHH---HHHHHHHHHHHHHH
Confidence 588999999999663 22224555555543
No 265
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=44.28 E-value=38 Score=25.51 Aligned_cols=40 Identities=15% Similarity=0.119 Sum_probs=31.1
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT 54 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T 54 (128)
=.|||+++|+ .-. .|+--|+.|.+.|++.-... .|.|-.+
T Consensus 37 EreLae~fgV---SR~----~vREAl~~L~a~Glve~r~G-----~Gt~V~~ 76 (241)
T COG2186 37 ERELAERFGV---SRT----VVREALKRLEAKGLVEIRQG-----SGTFVRP 76 (241)
T ss_pred HHHHHHHHCC---CcH----HHHHHHHHHHHCCCeeecCC-----CceEecC
Confidence 3689999999 346 89999999999999976542 4566643
No 266
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=44.13 E-value=26 Score=28.86 Aligned_cols=50 Identities=14% Similarity=0.169 Sum_probs=33.5
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
.+.+.++.|++. .+.+ .....|+.|...|++..+. +++.+|+.|++|++.
T Consensus 384 ~~~~~~~~g~~~---~~~~-~~~~~l~~l~~~gl~~~~~-------~~~~lT~~G~~~~~~ 433 (453)
T PRK13347 384 LAAIAARHGFFA---RYFL-DELARLEPLAADGLVTIDG-------GGIRVTPEGRPLIRA 433 (453)
T ss_pred HHHHHHHHCCCH---HHHH-HHHHHHHHHHHCCCEEEEC-------CEEEECcchhHHHHH
Confidence 445666666522 2001 1245788999999988664 579999999998754
No 267
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=44.09 E-value=40 Score=25.04 Aligned_cols=33 Identities=15% Similarity=0.092 Sum_probs=27.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|=.|||+..|+ ... -+++-|..|+..|++....
T Consensus 31 sE~eL~~~~~V---SR~----TvR~Al~~L~~eGli~r~~ 63 (240)
T PRK09764 31 TESALQTEFGV---SRV----TVRQALRQLVEQQILESIQ 63 (240)
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 44799999999 447 8999999999999997654
No 268
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=44.06 E-value=23 Score=26.95 Aligned_cols=34 Identities=18% Similarity=0.207 Sum_probs=29.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+++.|||+.+++++ . -+||=|+.|...|++...-
T Consensus 20 v~v~eLa~~l~VS~---~----TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 20 TSVEELAQYFDTTG---T----TIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred EEHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEEE
Confidence 47899999999954 7 8999999999999887654
No 269
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=44.06 E-value=39 Score=22.84 Aligned_cols=44 Identities=16% Similarity=0.189 Sum_probs=32.1
Q ss_pred CchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhhhcC
Q 045905 16 KAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLLLKD 63 (128)
Q Consensus 16 ~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L~~~ 63 (128)
++. .||.+|+-|...|++...... +++ ....|.+|+.|+..+..
T Consensus 43 s~g----tiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~ 88 (138)
T COG1695 43 SPG----TIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAE 88 (138)
T ss_pred CCC----cHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHH
Confidence 557 899999999999999754221 111 13579999999877654
No 270
>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=43.88 E-value=63 Score=18.56 Aligned_cols=43 Identities=19% Similarity=0.190 Sum_probs=28.3
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
|+..-|+.+++.+ + .+.|-++.|- ...+|.... +.+.+|+.|+
T Consensus 15 s~~~AA~~l~is~---~----~vs~~i~~LE~~lg~~Lf~r~~-------~~~~lT~~G~ 60 (60)
T PF00126_consen 15 SISAAAEELGISQ---S----AVSRQIKQLEEELGVPLFERSG-------RGLRLTEAGE 60 (60)
T ss_dssp SHHHHHHHCTSSH---H----HHHHHHHHHHHHHTS-SEEECS-------SSEEE-HHHH
T ss_pred CHHHHHHHhhccc---h----HHHHHHHHHHHHhCCeEEEECC-------CCeeEChhhC
Confidence 5667788999944 6 6777776664 344776543 5699999874
No 271
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=43.53 E-value=19 Score=23.95 Aligned_cols=28 Identities=18% Similarity=0.117 Sum_probs=22.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVH 33 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~ 33 (128)
+|+.|||+..|.+- .+. .+.|+|+.|..
T Consensus 24 ~TYGdIA~laG~p~-~AR----qVG~il~~l~~ 51 (103)
T COG3695 24 STYGDIAKLAGLPR-AAR----QVGRILKHLPE 51 (103)
T ss_pred eeHHHHHHHhCCCh-hHH----HHHHHHhhCCC
Confidence 58899999999853 345 89999998653
No 272
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=43.48 E-value=40 Score=25.43 Aligned_cols=33 Identities=18% Similarity=0.171 Sum_probs=28.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
++..|||+.+++.+ . -++|-|..|...|.+...
T Consensus 19 ~~~~eLa~~l~VS~---~----TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 19 LTTEALAEQLNVSK---E----TIRRDLNELQTQGKILRN 51 (240)
T ss_pred CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEe
Confidence 47899999999944 7 899999999999887654
No 273
>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=43.46 E-value=16 Score=20.60 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=18.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
++..|+++.+|+ ... .++|+++ .|-|-
T Consensus 4 l~~~ev~~~~g~---s~~----ti~~~~k----~g~FP 30 (51)
T PF05930_consen 4 LRIKEVAELLGV---SRS----TIYRLIK----DGKFP 30 (51)
T ss_dssp E-HHHHHHHHSS----HH----HHHHHHH----HHH--
T ss_pred ccHHHHHHHHCC---CHH----HHHHHHh----cccCC
Confidence 467899999999 447 8999988 45564
No 274
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. 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.
Probab=43.32 E-value=43 Score=21.43 Aligned_cols=48 Identities=17% Similarity=0.220 Sum_probs=33.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+|+.|+|+.+|+++ +-+|+=-..|++......+ ++-+.|....+-++.
T Consensus 1 ~ti~eva~~~gvs~-----------~tLRyye~~Gll~p~~~~~-~gyR~Y~~~~l~~l~ 48 (96)
T cd04768 1 LTIGEFAKLAGVSI-----------RTLRHYDDIGLFKPAKIAE-NGYRYYSYAQLYQLQ 48 (96)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCccCC-CCeeeCCHHHHHHHH
Confidence 47899999999954 4588888899997643211 124678777776544
No 275
>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=43.29 E-value=24 Score=18.71 Aligned_cols=23 Identities=13% Similarity=0.161 Sum_probs=16.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|..+||+.+|++. . .++|.++.
T Consensus 27 ~~~~~ia~~~~~s~---~----~i~~~~~~ 49 (55)
T cd06171 27 LSYEEIAEILGISR---S----TVRQRLHR 49 (55)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHH
Confidence 46789999999844 6 66665543
No 276
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=43.24 E-value=39 Score=26.87 Aligned_cols=34 Identities=3% Similarity=0.009 Sum_probs=27.4
Q ss_pred hHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 23 YVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
.+.+.+..|...|++..+. +++.+|+.|..|.+.
T Consensus 334 ~~~~~l~~l~~~gl~~~~~-------~~~~lT~~G~~~~~~ 367 (374)
T PRK05799 334 VYGEVINKYIKLGLLIEKE-------GRIYLSERGIEVSNS 367 (374)
T ss_pred HHHHHHHHHHHCCCEEEEC-------CEEEEChhHHHHHHH
Confidence 4667788899999987653 689999999998764
No 277
>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=42.88 E-value=46 Score=23.77 Aligned_cols=34 Identities=18% Similarity=0.185 Sum_probs=26.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|++|||.+.|+.+ . .+---|-.+++.|.+....
T Consensus 7 ~T~eELA~~FGvtt---R----kvaStLa~~ta~Grl~Rv~ 40 (155)
T PF07789_consen 7 KTAEELAGKFGVTT---R----KVASTLAMVTATGRLIRVN 40 (155)
T ss_pred ccHHHHHHHhCcch---h----hhHHHHHHHHhcceeEEec
Confidence 58999999999944 5 5667788888999776554
No 278
>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=42.59 E-value=50 Score=20.22 Aligned_cols=35 Identities=14% Similarity=0.273 Sum_probs=28.2
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+.+|++..+++|-... .+..++.-|...||+....
T Consensus 32 Y~~~c~~~~~~~l~~~----~~~~~l~~L~~~gli~~~~ 66 (87)
T cd08768 32 YEELCEEIGVDPLTQR----RISDLLSELEMLGLLETEV 66 (87)
T ss_pred HHHHHHHcCCCCCcHH----HHHHHHHHHHHcCCeEEEE
Confidence 5678888888775666 7999999999999997554
No 279
>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=42.31 E-value=21 Score=27.00 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=18.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
|+..||+..++.| . .++|||+
T Consensus 31 t~~~Lae~F~vsp---e----~irrILk 51 (225)
T PF06413_consen 31 TVERLAESFKVSP---E----AIRRILK 51 (225)
T ss_pred CHHHHHhhCCCCH---H----HHHHHHh
Confidence 7788999999955 7 9999997
No 280
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=42.28 E-value=29 Score=24.70 Aligned_cols=28 Identities=11% Similarity=-0.001 Sum_probs=17.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
+|..|||+.+|+++ .-+-..|+|.++.|
T Consensus 153 ~s~~EIA~~lgis~---~tVk~~l~Rar~~L 180 (195)
T PRK12532 153 FSSDEIQQMCGIST---SNYHTIMHRARESL 180 (195)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHH
Confidence 58899999999965 32222455544444
No 281
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=42.07 E-value=42 Score=22.20 Aligned_cols=47 Identities=17% Similarity=0.203 Sum_probs=34.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+|+.|+|+.+|+++ +-||+=-..|++...... ++-+.|....+-++.
T Consensus 1 ~~ige~a~~~gvs~-----------~tLryYe~~GLi~p~~~~--~~yR~Y~~~d~~~l~ 47 (116)
T cd04769 1 MYIGELAQQTGVTI-----------KAIRLYEEKGLLPSPKRS--GNYRVYDAQHVECLR 47 (116)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCCC--CCceeeCHHHHHHHH
Confidence 68899999999954 568999999999754321 124678888887643
No 282
>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=41.77 E-value=45 Score=24.52 Aligned_cols=33 Identities=18% Similarity=0.274 Sum_probs=27.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|=.|||++.|+ ... -++|-|..|+..|++....
T Consensus 27 sE~eLa~~~~V---SR~----TVR~Al~~L~~eGli~r~~ 59 (230)
T TIGR02018 27 SEHELVAQYGC---SRM----TVNRALRELTDAGLLERRQ 59 (230)
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 45789999999 446 8999999999999997665
No 283
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=41.65 E-value=36 Score=26.86 Aligned_cols=33 Identities=24% Similarity=0.178 Sum_probs=27.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|=.|||+++|++ .. .+.|+|...-..||++-.
T Consensus 30 ~tQ~eIA~~lgiS---R~----~VsRlL~~Ar~~GiV~I~ 62 (318)
T PRK15418 30 LTQSEIGERLGLT---RL----KVSRLLEKGRQSGIIRVQ 62 (318)
T ss_pred CCHHHHHHHhCCC---HH----HHHHHHHHHHHcCcEEEE
Confidence 4668999999994 36 899999999999999754
No 284
>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=41.53 E-value=20 Score=21.85 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=23.1
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
++.++.+++.+ ++. .+.|+.|.|-.+||...=
T Consensus 18 ie~~~~~~~~~--~~e----~~~rf~~~L~~~Gv~~~L 49 (69)
T PF09269_consen 18 IERLVAMTNFD--DEE----SLRRFQRKLKKMGVEKAL 49 (69)
T ss_dssp HHHHHTTEEE---TGG----GHHHHHHHHHHTTHHHHH
T ss_pred HHHHHHhcCCC--CHH----HHHHHHHHHHHCCHHHHH
Confidence 34566666652 345 999999999999998653
No 285
>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=41.31 E-value=59 Score=25.47 Aligned_cols=61 Identities=13% Similarity=0.063 Sum_probs=35.6
Q ss_pred CCHHHHHHhCCCCCCCch--hhhhhHHHHH-HHHHhcCcceeeccCCC--C--cccceechHhhhhhh
Q 045905 1 MTLNELINALPFHPIKAQ--YVAQYVYRFM-WILVHSGFFAQQNFGQN--D--QERSYVATNASKLLL 61 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~--~~~~~L~RlL-R~L~~~gvf~e~~~~~~--~--~~~~y~~T~~s~~L~ 61 (128)
+|+++||..||+.+.+.. ---..+.|++ .+|..+|++.+...-|. + .+....+||..-.|.
T Consensus 96 ~sie~LA~ecGLst~s~~Gn~sitRasR~i~e~le~~Gli~~~~~~D~~~~~~~Pk~I~lT~~ff~l~ 163 (281)
T PF02387_consen 96 ASIEQLADECGLSTKSAAGNKSITRASRLISEFLEPLGLITCEKEWDPYNGNYIPKHIWLTPLFFMLL 163 (281)
T ss_pred ecHHHHHHHhCCcccCCCCCeeHHHHHHHHHHHHHhcCCeeeeeeechhhccccCeEEEECHHHHHHh
Confidence 578999999997332111 0011455555 45677999876543221 1 234567888877666
No 286
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=41.26 E-value=25 Score=26.66 Aligned_cols=55 Identities=7% Similarity=0.146 Sum_probs=37.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSF 71 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~ 71 (128)
+|+++||+++++++ . .|.|+.|--+.+.+..-- ..+.+..+..+|... ..++...
T Consensus 200 isl~~lA~~~~lS~---~----~l~r~Fk~~~G~tp~~~l--------~~~Rl~~A~~lL~~t-~~sI~eI 254 (290)
T PRK10572 200 FDIESVAQHVCLSP---S----RLAHLFRQQLGISVLRWR--------EDQRISRAKLLLQTT-RMPIATI 254 (290)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHCcCHHHHH--------HHHHHHHHHHHHHcC-CCCHHHH
Confidence 58999999999955 7 899999987766555432 246677777766542 2345444
No 287
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=41.16 E-value=34 Score=24.37 Aligned_cols=29 Identities=14% Similarity=0.004 Sum_probs=19.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|..|||+.+|+++ ..+-..|.|.++.|-
T Consensus 128 ~s~~EIA~~lgis~---~tV~~~l~Rar~~Lr 156 (182)
T PRK12511 128 LSYQEAAAVLGIPI---GTLMSRIGRARAALR 156 (182)
T ss_pred CCHHHHHHHhCcCH---HHHHHHHHHHHHHHH
Confidence 58899999999965 322234555555544
No 288
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=40.90 E-value=32 Score=24.48 Aligned_cols=29 Identities=10% Similarity=-0.048 Sum_probs=20.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|..|||+.+|+++ ..+-..|+|.++.|-
T Consensus 128 ~s~~EIA~~Lgis~---~tV~~~l~RAr~~Lr 156 (182)
T PRK12540 128 FSYEDAAAICGCAV---GTIKSRVNRARSKLS 156 (182)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHH
Confidence 47899999999965 323335666666654
No 289
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=40.75 E-value=30 Score=25.30 Aligned_cols=33 Identities=21% Similarity=0.163 Sum_probs=26.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|++||++.+|++- . .+.--||-|-..|++...
T Consensus 42 mtl~Ei~E~lg~Sk---s----~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 42 LTLDEIAEALGMSK---S----NVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred ccHHHHHHHHCCCc---c----hHHHHHHHHHhcchHHhh
Confidence 68999999999943 5 677788888888888654
No 290
>smart00753 PAM PCI/PINT associated module.
Probab=40.72 E-value=40 Score=20.69 Aligned_cols=33 Identities=15% Similarity=0.250 Sum_probs=27.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+++++||+.++++. + .+.+++.-++..|.+...
T Consensus 25 i~~~~i~~~~~l~~---~----~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00753 25 ISLSDLAKLLGLSV---P----EVEKLVSKAIRDGEISAK 57 (88)
T ss_pred eeHHHHHHHhCcCH---H----HHHHHHHHHHHCCCeEEE
Confidence 57899999999944 5 688999999999988654
No 291
>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=40.72 E-value=40 Score=20.69 Aligned_cols=33 Identities=15% Similarity=0.250 Sum_probs=27.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+++++||+.++++. + .+.+++.-++..|.+...
T Consensus 25 i~~~~i~~~~~l~~---~----~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00088 25 ISLSDLAKLLGLSV---P----EVEKLVSKAIRDGEISAK 57 (88)
T ss_pred eeHHHHHHHhCcCH---H----HHHHHHHHHHHCCCeEEE
Confidence 57899999999944 5 688999999999988654
No 292
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=40.61 E-value=46 Score=21.95 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=33.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
++..|+|..+|+++ +-+|+=-..|++.... .+++-+.|....+-++.
T Consensus 1 m~i~eva~~~gvs~-----------~tlR~Ye~~GLl~p~r--~~~g~R~Y~~~~~~~l~ 47 (112)
T cd01282 1 MRIGELAARTGVSV-----------RSLRYYEEQGLLVPER--SANGYRDYDEAAVDRVR 47 (112)
T ss_pred CCHHHHHHHHCCCH-----------HHHHHHHHCCCCCCCc--CCCCCeecCHHHHHHHH
Confidence 57899999999954 4588888899997432 12224678887776543
No 293
>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=40.45 E-value=17 Score=19.99 Aligned_cols=14 Identities=0% Similarity=0.171 Sum_probs=11.0
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|+.+||+++|++.
T Consensus 17 ~s~~~Ia~~~gvs~ 30 (47)
T PF00440_consen 17 VSIRDIARRAGVSK 30 (47)
T ss_dssp SSHHHHHHHHTSCH
T ss_pred CCHHHHHHHHccch
Confidence 47889999999843
No 294
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=40.44 E-value=25 Score=22.81 Aligned_cols=22 Identities=14% Similarity=0.294 Sum_probs=16.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|.++||+.+++++ . .|.++|-
T Consensus 24 ls~~~ia~dL~~s~---~----~le~vL~ 45 (89)
T PF10078_consen 24 LSLEQIAADLGTSP---E----HLEQVLN 45 (89)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHc
Confidence 47889999999844 6 6777765
No 295
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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 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 spe
Probab=40.12 E-value=44 Score=22.78 Aligned_cols=45 Identities=18% Similarity=0.384 Sum_probs=32.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+++.|+|+.+|+++ +-||+-...|++.... . ++.+.|....+-++
T Consensus 2 ysI~eVA~~~GVs~-----------~TLR~wE~~GLl~p~r--~-~G~R~Ys~~dv~rL 46 (120)
T cd04767 2 YPIGVVAELLNIHP-----------ETLRIWERHGLIKPAR--R-NGQRLYSNNDLKRL 46 (120)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCcC--C-CCcEEECHHHHHHH
Confidence 57899999999954 3577888889996532 1 23577888877653
No 296
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=40.03 E-value=31 Score=29.05 Aligned_cols=34 Identities=24% Similarity=0.312 Sum_probs=29.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|++|||+.+.|.+ . ..++||+.|...|.+.=.+
T Consensus 24 ~~l~~la~~l~cs~---R----~~~~~l~~~~~~gwl~w~~ 57 (552)
T PRK13626 24 TTLNELAELLNCSR---R----HMRTLLNTMQQRGWLTWQA 57 (552)
T ss_pred eeHHHHHHHhcCCh---h----HHHHHHHHHHHCCCeeeec
Confidence 58999999999955 7 8999999999999987554
No 297
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=40.03 E-value=17 Score=20.92 Aligned_cols=22 Identities=14% Similarity=0.155 Sum_probs=13.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..+||.++|+++ . .|.|++.
T Consensus 11 it~~~La~~~gis~---~----tl~~~~~ 32 (63)
T PF13443_consen 11 ITQKDLARKTGISR---S----TLSRILN 32 (63)
T ss_dssp --HHHHHHHHT--H---H----HHHHHHT
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHh
Confidence 46788899988833 6 6777765
No 298
>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=39.98 E-value=27 Score=22.68 Aligned_cols=29 Identities=14% Similarity=0.363 Sum_probs=21.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ 39 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e 39 (128)
+|+.|+|..+++.+ . .|.++|| ..|++..
T Consensus 25 ~ti~~~AK~L~i~~---~----~l~~~Lr---~~g~l~~ 53 (111)
T PF03374_consen 25 YTIREAAKLLGIGR---N----KLFQWLR---EKGWLYR 53 (111)
T ss_pred ccHHHHHHHhCCCH---H----HHHHHHH---hCCceEE
Confidence 57899999999944 6 5555555 5888765
No 299
>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=39.95 E-value=28 Score=26.14 Aligned_cols=59 Identities=14% Similarity=0.052 Sum_probs=40.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAV 75 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~ 75 (128)
+|+++||+.+++++ . .|.|+.+-.+.+.+..-- ..+.+..+.++|.... .|+......+
T Consensus 203 ~sl~~lA~~~~~S~---~----~l~r~Fk~~~G~t~~~yi--------~~~Rl~~A~~lL~~t~-~sI~eIA~~~ 261 (287)
T TIGR02297 203 LRLPEYADRLGISE---S----RLNDICRRFSALSPKRLI--------IERVMQEARRLLLFTQ-HSINQIAYDL 261 (287)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHhCCCHHHHH--------HHHHHHHHHHHHHcCC-CCHHHHHHHh
Confidence 58999999999955 7 899999987755543322 2467888888776432 3465554333
No 300
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=39.63 E-value=58 Score=18.81 Aligned_cols=36 Identities=17% Similarity=0.127 Sum_probs=25.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+-+||-+++..+.-+.. .+..+|..|+..|++....
T Consensus 19 ~keeLrsrl~~~~l~~k----~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 19 PKEELRSRLFKPRLPPK----LFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp EHHHHHHHCST-TS-HC----CHHHHHHHHHHTTSEEEES
T ss_pred CHHHHHHHHhhccCCHH----HHHHHHHHHHHCCCeeeEC
Confidence 34688888744222456 8999999999999998664
No 301
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=39.59 E-value=44 Score=23.30 Aligned_cols=47 Identities=11% Similarity=0.218 Sum_probs=32.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|+.|+|+.+|+++ +-||+--..|++......+ ++-+.|....+-++
T Consensus 8 ~~IgevAk~~Gvs~-----------~TLRyYE~~GLl~p~~r~~-~gyR~Y~~~~l~rl 54 (144)
T PRK13752 8 LTIGVFAKAAGVNV-----------ETIRFYQRKGLLPEPDKPY-GSIRRYGEADVTRV 54 (144)
T ss_pred ccHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCccCC-CCCeecCHHHHHHH
Confidence 47899999999944 5689999999997433211 22456777666543
No 302
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=39.11 E-value=53 Score=24.33 Aligned_cols=33 Identities=21% Similarity=0.172 Sum_probs=27.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|=.|||+..|+ .-. -++|-|..|+..|++....
T Consensus 35 sE~eLa~~~~V---SR~----TvR~Al~~L~~eGli~r~~ 67 (241)
T PRK11402 35 TENELCTQYNV---SRI----TIRKAISDLVADGVLIRWQ 67 (241)
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 34689999999 446 8999999999999997655
No 303
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=38.99 E-value=52 Score=24.55 Aligned_cols=32 Identities=9% Similarity=0.097 Sum_probs=27.2
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
-.|||+.+|+ ... .++--|+.|...|++....
T Consensus 35 E~eLae~~gV---SRt----pVREAL~~L~~eGlV~~~~ 66 (253)
T PRK11523 35 ERFIADEKNV---SRT----VVREAIIMLEVEGYVEVRK 66 (253)
T ss_pred HHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 4689999999 447 8999999999999997554
No 304
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=38.87 E-value=42 Score=21.89 Aligned_cols=30 Identities=13% Similarity=0.130 Sum_probs=22.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|..||+..+|+++ . ++.-|+..|++....
T Consensus 8 lt~~Elc~~~gi~~---~--------~l~eLve~GlIep~~ 37 (101)
T PRK10265 8 FTITEFCLHTGVSE---E--------ELNEIVGLGVIEPRE 37 (101)
T ss_pred eeHHHHHHHHCcCH---H--------HHHHHHHCCCeecCC
Confidence 47899999999954 5 455667789997543
No 305
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=38.75 E-value=57 Score=26.36 Aligned_cols=47 Identities=9% Similarity=0.064 Sum_probs=32.7
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
...+.++.|. +.. .+...+..|...|++..+. +++.+|+.|+.+.+.
T Consensus 341 ~~~f~~~~g~---~~~----~~~~~l~~l~~~gll~~~~-------~~~~LT~~G~~~~d~ 387 (394)
T PRK08898 341 AHLFQERTGL---PLA----AIEPQLAAAEQRGLLERDH-------TRIRPTPLGQRFLND 387 (394)
T ss_pred HHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEEC-------CEEEEChhHhHHHHH
Confidence 3445555555 223 4556778889999988654 579999999988754
No 306
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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 dissimil
Probab=38.72 E-value=57 Score=21.10 Aligned_cols=45 Identities=11% Similarity=0.179 Sum_probs=30.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+|..|+|+.+|+++ +-+|+--..|++.. .. ++++-+.|....+-+
T Consensus 2 ~~i~eva~~~gvs~-----------~tLR~ye~~Gll~~-~r-~~~g~R~Y~~~dl~~ 46 (102)
T cd04775 2 YTIGQMSRKFGVSR-----------STLLYYESIGLIPS-AR-SEANYRLYSEADLSR 46 (102)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCC-CC-CCCCCeeeCHHHHHH
Confidence 47899999999954 34689999999942 22 112235677776654
No 307
>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=38.71 E-value=33 Score=19.95 Aligned_cols=23 Identities=13% Similarity=0.057 Sum_probs=17.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
++..|-|..+|+.+ . .|.|+.|.
T Consensus 16 lp~~eAA~~Lgv~~---T----~LKr~CR~ 38 (52)
T PF02042_consen 16 LPIKEAAKELGVSV---T----TLKRRCRR 38 (52)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHHH
Confidence 35677888888843 6 88888884
No 308
>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=38.70 E-value=39 Score=18.37 Aligned_cols=14 Identities=21% Similarity=0.207 Sum_probs=11.6
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|..|||+.+++++
T Consensus 16 ~s~~eia~~l~~s~ 29 (57)
T cd06170 16 KTNKEIADILGISE 29 (57)
T ss_pred CCHHHHHHHHCCCH
Confidence 47889999999954
No 309
>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=38.61 E-value=39 Score=20.28 Aligned_cols=33 Identities=6% Similarity=0.171 Sum_probs=25.7
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+++.||.+.|+ -.. .+-.-||-|-+-||+....
T Consensus 6 vas~iAd~~Gi---TRS----vIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 6 VASKIADRVGI---TRS----VIVNALRKLESAGVIESRS 38 (61)
T ss_dssp -HHHHHHHHT-----HH----HHHHHHHHHHHTTSEEEEE
T ss_pred hHHHHHHHhCc---cHH----HHHHHHHHHHhcCceeecc
Confidence 57899999998 336 7889999999999997543
No 310
>cd04772 HTH_TioE_rpt1 First 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 contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=38.51 E-value=55 Score=21.13 Aligned_cols=46 Identities=15% Similarity=0.185 Sum_probs=31.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
.+..|+|+.+|+++ +-+|+--..|++.......+ +-+.|....+.+
T Consensus 1 y~i~e~A~~~gvs~-----------~tlR~Ye~~Gll~~~~r~~~-g~R~Y~~~~v~~ 46 (99)
T cd04772 1 YRTVDLARAIGLSP-----------QTVRNYESLGLIPPAERTAN-GYRIYTDKHIAA 46 (99)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHcCCCCCCCcCCC-CCeecCHHHHHH
Confidence 36889999999954 34788888999975432121 246788777764
No 311
>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=38.38 E-value=48 Score=21.96 Aligned_cols=27 Identities=22% Similarity=0.185 Sum_probs=15.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|++|||+.+|+. .+-+-+.+.|--..
T Consensus 34 lSlsEIAe~~~iS---RqaV~d~ikr~~~~ 60 (101)
T PF04297_consen 34 LSLSEIAEELGIS---RQAVYDSIKRAEKK 60 (101)
T ss_dssp --HHHHHHHCTS----HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCCC---HHHHHHHHHHHHHH
Confidence 4899999999993 35233445554333
No 312
>PRK09526 lacI lac repressor; Reviewed
Probab=38.20 E-value=12 Score=28.61 Aligned_cols=53 Identities=17% Similarity=0.137 Sum_probs=30.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccC---CCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG---QNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~---~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|+.|||++.|+.. . -+.|+|.- .+-+++.... +--.+--|.++...+.|...
T Consensus 6 ~ti~dIA~~aGVS~---~----TVSrvLn~---~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~ 61 (342)
T PRK09526 6 VTLYDVARYAGVSY---Q----TVSRVLNQ---ASHVSAKTREKVEAAMAELNYVPNRVAQQLAGK 61 (342)
T ss_pred CcHHHHHHHhCCCH---H----HHHHHhcC---CCCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcC
Confidence 48899999999944 6 67777763 2222222110 00002248888888777644
No 313
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=38.11 E-value=45 Score=26.15 Aligned_cols=47 Identities=19% Similarity=0.089 Sum_probs=36.3
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
-.|||..++-+| - .+|-.|..|-+.|++.-.+. ..|.|.+|--.--.
T Consensus 28 geeIA~~l~rnp---G----TVRNqmq~LkaLgLVegvpG----PkGGY~PT~kAYe~ 74 (294)
T COG2524 28 GEEIAEVLNRNP---G----TVRNQMQSLKALGLVEGVPG----PKGGYKPTSKAYEA 74 (294)
T ss_pred hHHHHHHHccCc---c----hHHHHHHHHHhcCccccccC----CCCCccccHHHHHH
Confidence 368999999855 8 99999999999999975542 14679888766433
No 314
>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=38.04 E-value=54 Score=26.13 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=28.0
Q ss_pred CCHHHHHHh--CCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINA--LPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~--~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++..+|++. +++.+ . -+||-|..|...|++....
T Consensus 22 v~s~~l~~~~~~~vS~---a----TiR~d~~~Le~~G~l~~~h 57 (337)
T TIGR00331 22 VGSKTLLEKYNLGLSS---A----TIRNDMADLEDLGFIEKPH 57 (337)
T ss_pred cCHHHHHhhcCCCCCh---H----HHHHHHHHHHHCCCccCCC
Confidence 467899999 66644 7 8999999999999997543
No 315
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=37.95 E-value=55 Score=18.41 Aligned_cols=32 Identities=16% Similarity=0.069 Sum_probs=23.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|-+||.+-+|.. .-.+-.+.|..+||.-...
T Consensus 3 LT~~El~elTG~k---------~~~~Q~~~L~~~Gi~~~~~ 34 (47)
T PF13986_consen 3 LTDEELQELTGYK---------RPSKQIRWLRRNGIPFVVR 34 (47)
T ss_pred CCHHHHHHHHCCC---------CHHHHHHHHHHCCCeeEEC
Confidence 5789999999982 2234577888889876554
No 316
>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=37.92 E-value=63 Score=18.83 Aligned_cols=31 Identities=19% Similarity=0.308 Sum_probs=18.7
Q ss_pred HHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcc
Q 045905 4 NELINALPFHPIKAQYVAQYVYRFMWILVHSGFF 37 (128)
Q Consensus 4 ~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf 37 (128)
..|+++.++++ ....+.+..+|..|...|++
T Consensus 37 ~~l~~~y~~~~---~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 37 DALAEEYDVDP---EEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp HHHHHHTT--H---HHHHHHHHHHHHHHHHTT--
T ss_pred HHHHHHcCCCH---HHHHHHHHHHHHHHHHCcCc
Confidence 34566666644 43445688889998888875
No 317
>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=37.79 E-value=34 Score=21.18 Aligned_cols=25 Identities=12% Similarity=-0.079 Sum_probs=16.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|+.+||+.+|.+. .+. .+.+.|+.
T Consensus 18 ~TYg~iA~~~g~p~-~~R----~Vg~al~~ 42 (79)
T cd06445 18 TTYGQIAKLAGTPK-AAR----AVGSALAR 42 (79)
T ss_pred CcHHHHHHHHCCCC-cHH----HHHHHHHh
Confidence 58999999999843 223 45555544
No 318
>COG3828 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.60 E-value=18 Score=27.13 Aligned_cols=44 Identities=14% Similarity=0.138 Sum_probs=32.3
Q ss_pred hhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchhhhhhccCC
Q 045905 78 PILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTISCAVSNGR 127 (128)
Q Consensus 78 ~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~~~~~~~~~ 127 (128)
+.--.-|++|..||++|. . |.-.||. .||+++.++++. +|-||+
T Consensus 64 ~I~ke~~q~i~aaiesG~-G-~aG~Hg~-~~D~fr~~~~yq---f~igGq 107 (239)
T COG3828 64 TIEKEEVQNITAAIESGV-G-FAGFHGG-MGDAFRNSVDYQ---FIIGGQ 107 (239)
T ss_pred cCcHHHHHHHHHHHHcCC-c-eeeeccc-cccccCCCcceE---EEeCCE
Confidence 455678999999999987 3 7777775 588887777654 555553
No 319
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=37.59 E-value=45 Score=21.28 Aligned_cols=17 Identities=18% Similarity=0.261 Sum_probs=11.5
Q ss_pred CHHHHHHhCCCCCCCch
Q 045905 2 TLNELINALPFHPIKAQ 18 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~ 18 (128)
++++||.++|+++.++.
T Consensus 58 ~aD~iA~~~g~~~~d~~ 74 (94)
T PF14490_consen 58 TADKIALKLGIEPDDPR 74 (94)
T ss_dssp HHHHHHHTTT--TT-HH
T ss_pred HHHHHHHHcCCCCCCHH
Confidence 47899999999775555
No 320
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. 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 winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.55 E-value=58 Score=20.94 Aligned_cols=47 Identities=13% Similarity=0.234 Sum_probs=30.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L 60 (128)
+++.|+|+.+|+++ . -+|+=...|++.... .+++-+.|....+-++.
T Consensus 1 ~~I~e~a~~~gvs~---~--------tLR~ye~~Gll~p~r--~~~g~R~Y~~~dv~~l~ 47 (96)
T cd04774 1 YKVDEVAKRLGLTK---R--------TLKYYEEIGLVSPER--SEGRYRLYSEEDLKRLE 47 (96)
T ss_pred CCHHHHHHHHCcCH---H--------HHHHHHHCCCCCCCc--CCCCCEEECHHHHHHHH
Confidence 57899999999954 3 355556679886322 12224678877776543
No 321
>PF14502 HTH_41: Helix-turn-helix domain
Probab=37.52 E-value=82 Score=18.05 Aligned_cols=33 Identities=12% Similarity=0.146 Sum_probs=27.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|++|+++++++. .- .+..-|++|-..|.+.-..
T Consensus 8 tI~e~~~~~~vs---~G----tiQ~Alk~Le~~gaI~Le~ 40 (48)
T PF14502_consen 8 TISEYSEKFGVS---RG----TIQNALKFLEENGAIKLES 40 (48)
T ss_pred CHHHHHHHhCcc---hh----HHHHHHHHHHHCCcEEeee
Confidence 789999999993 36 7899999999999887554
No 322
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=37.39 E-value=38 Score=24.15 Aligned_cols=29 Identities=14% Similarity=-0.036 Sum_probs=19.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|..|||+.+|+++ .-+-..|.|.++.|-
T Consensus 133 ~s~~EIA~~Lgis~---~tVk~~l~Rar~~Lr 161 (187)
T PRK12516 133 FAYEEAAEICGCAV---GTIKSRVNRARQRLQ 161 (187)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHH
Confidence 47899999999965 322335666665554
No 323
>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=37.38 E-value=36 Score=21.88 Aligned_cols=25 Identities=12% Similarity=0.048 Sum_probs=19.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|..||++.+|+.. . -+.|+=|.|-
T Consensus 50 ~syreIa~~tgvS~---a----TItRvsr~Lk 74 (87)
T PF01371_consen 50 KSYREIAEETGVSI---A----TITRVSRCLK 74 (87)
T ss_dssp SSHHHHHHHHTSTH---H----HHHHHHHHHH
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHHHHH
Confidence 47889999999933 6 6778777765
No 324
>PF13551 HTH_29: Winged helix-turn helix
Probab=37.29 E-value=33 Score=21.78 Aligned_cols=27 Identities=26% Similarity=0.421 Sum_probs=23.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSG 35 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~g 35 (128)
|..+||..+|+++ . .++|.++..-..|
T Consensus 14 ~~~~ia~~lg~s~---~----Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISR---R----TVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCH---H----HHHHHHHHHHccc
Confidence 4899999999954 8 9999999988887
No 325
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=36.66 E-value=23 Score=20.63 Aligned_cols=22 Identities=18% Similarity=0.197 Sum_probs=14.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|+|.++|+++ . .+.|+.+
T Consensus 15 ls~~~lA~~~g~s~---s----~v~~iE~ 36 (64)
T PF13560_consen 15 LSQAQLADRLGVSQ---S----TVSRIER 36 (64)
T ss_dssp S-HHHHHHHHTS-H---H----HHHHHHT
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHC
Confidence 57889999999843 6 6666654
No 326
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=36.44 E-value=40 Score=24.50 Aligned_cols=29 Identities=17% Similarity=0.075 Sum_probs=20.3
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
.|+.|||+.+|+++ ..+-..|.|.++.|-
T Consensus 155 ~s~~EIA~~Lgis~---~tV~~~l~RArk~Lr 183 (203)
T PRK09647 155 LSYEEIAATLGVKL---GTVRSRIHRGRQQLR 183 (203)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHH
Confidence 47899999999965 433345666666655
No 327
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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. This subgroup lacks one of the c
Probab=36.24 E-value=56 Score=22.19 Aligned_cols=46 Identities=22% Similarity=0.284 Sum_probs=31.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
|++.|+|+.+|+++ |-+|+=-..|++..... .+++-+.|....+-+
T Consensus 1 m~IgE~A~~~gvs~-----------~TLRyYE~~GLl~p~r~-~~~gyR~Y~~~~~~~ 46 (133)
T cd04787 1 MKVKELANAAGVTP-----------DTVRFYTRIGLLRPTRD-PVNGYRLYSEKDLSR 46 (133)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCcC-CCCCeeeCCHHHHHH
Confidence 67899999999944 45788899999975432 112235677666654
No 328
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=36.06 E-value=54 Score=21.46 Aligned_cols=45 Identities=13% Similarity=0.216 Sum_probs=31.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
+|..|+|+.+|+++ |-||+--..|++......+ ++-+.|..-.+-
T Consensus 1 ~~I~eva~~~gvs~-----------~tLRyYE~~GLl~p~~~~~-~gyR~Ys~~dl~ 45 (124)
T COG0789 1 YTIGEVAKLTGVSV-----------RTLRFYERKGLLSPERRDE-GGYRYYTPEDLE 45 (124)
T ss_pred CcHHHHHHHhCCCH-----------HHHHHHHHcCCCCCcccCC-CCceecCHHHHH
Confidence 57899999999954 6699999999997654322 224566665543
No 329
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=35.84 E-value=44 Score=23.25 Aligned_cols=29 Identities=17% Similarity=0.367 Sum_probs=23.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
+|=+|||..+|+ +.. .|+++|..|-..++
T Consensus 16 ~~dedLa~~l~i---~~n----~vRkiL~~L~ed~~ 44 (147)
T smart00531 16 VTEEDLAELLGI---KQK----QLRKILYLLYDEKL 44 (147)
T ss_pred cCHHHHHHHhCC---CHH----HHHHHHHHHHhhhc
Confidence 456899999999 448 89999999999444
No 330
>PHA01976 helix-turn-helix protein
Probab=35.82 E-value=31 Score=20.06 Aligned_cols=21 Identities=19% Similarity=0.264 Sum_probs=14.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFM 28 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlL 28 (128)
+|..|||.++|+++ . .+.++.
T Consensus 16 lt~~~lA~~~gvs~---~----~v~~~e 36 (67)
T PHA01976 16 WSAPELSRRAGVRH---S----LIYDFE 36 (67)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHH
Confidence 47788999988843 5 566554
No 331
>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=35.77 E-value=52 Score=28.85 Aligned_cols=37 Identities=16% Similarity=0.305 Sum_probs=29.4
Q ss_pred CCHHHHHHhCCCCCC-CchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPI-KAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~-~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++..||+.+++++.. +.. .|.++|+.|...|++....
T Consensus 19 ~~~~~l~~~l~~~~~~~~~----~l~~~l~~l~~~g~l~~~~ 56 (709)
T TIGR02063 19 ISLKELAKAFHLKGADEKK----ALRKRLRALEDDGLVKKNR 56 (709)
T ss_pred CCHHHHHHHhCCCChHHHH----HHHHHHHHHHHCCCEEEcC
Confidence 467899999998542 445 7999999999999986543
No 332
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=35.58 E-value=33 Score=26.19 Aligned_cols=47 Identities=13% Similarity=0.057 Sum_probs=32.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
+|+++||+.+++++ . .|.|+.+..+...+-.-- ...+++.+..+|..
T Consensus 22 ~~l~~lA~~~~~S~---~----~l~r~F~~~~g~s~~~yi--------~~~Rl~~A~~~L~~ 68 (289)
T PRK15121 22 LSLDNVAAKAGYSK---W----HLQRMFKDVTGHAIGAYI--------RARRLSKAAVALRL 68 (289)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHCcCHHHHH--------HHHHHHHHHHHHHc
Confidence 58899999999954 7 899998887655443322 34566666666654
No 333
>PRK13503 transcriptional activator RhaS; Provisional
Probab=35.50 E-value=36 Score=25.37 Aligned_cols=58 Identities=10% Similarity=-0.024 Sum_probs=38.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQA 74 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~ 74 (128)
+|+++||+.+++++ . .|.|+.+--+.+.+..-- ..+++..+.++|.... .++......
T Consensus 188 ~tl~~lA~~~~lS~---~----~l~r~Fk~~~G~S~~~yi--------~~~Rl~~A~~LL~~~~-~sI~eIA~~ 245 (278)
T PRK13503 188 VNWEALADQFSLSL---R----TLHRQLKQQTGLTPQRYL--------NRLRLLKARHLLRHSD-ASVTDIAYR 245 (278)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHhCcCHHHHH--------HHHHHHHHHHHHHcCC-CCHHHHHHH
Confidence 58999999999955 7 899999876655544432 2467777777776432 235544333
No 334
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=35.48 E-value=44 Score=25.76 Aligned_cols=33 Identities=27% Similarity=0.328 Sum_probs=28.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+-+||..++|.+. . -+.|++|-|-.+|+.....
T Consensus 212 ~Q~eL~r~lglsk---t----TvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 212 TQAELRRALGLSK---T----TVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred eHHHHHHhhCCCh---H----HHHHHHHHHHhCCceEEEE
Confidence 4579999999954 6 7999999999999997654
No 335
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=35.09 E-value=62 Score=21.97 Aligned_cols=47 Identities=13% Similarity=0.208 Sum_probs=32.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+++.|+|+.+|+++ +-+|+=-..|++......+ ++-+.|....+-++
T Consensus 2 ~~I~e~a~~~gvs~-----------~tlR~Ye~~GLl~p~~r~~-~gyR~Y~~~~l~~l 48 (131)
T TIGR02043 2 FQIGELAKLCGVTS-----------DTLRFYEKNGLIKPAGRTD-SGYRLYTDEDQKRL 48 (131)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCCcCC-CCceecCHHHHHHH
Confidence 47899999999954 4588888899997543211 22467887776653
No 336
>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=35.07 E-value=21 Score=20.58 Aligned_cols=14 Identities=36% Similarity=0.536 Sum_probs=10.3
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|..|||+.+|++|
T Consensus 29 vSS~~La~~~gi~~ 42 (50)
T PF06971_consen 29 VSSQELAEALGITP 42 (50)
T ss_dssp E-HHHHHHHHTS-H
T ss_pred ECHHHHHHHHCCCH
Confidence 46789999999954
No 337
>PRK10736 hypothetical protein; Provisional
Probab=35.01 E-value=55 Score=26.72 Aligned_cols=34 Identities=12% Similarity=0.031 Sum_probs=28.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++++||+.++++++ . .+..+|-.|--.|++.+..
T Consensus 322 ~~iD~L~~~~~l~~---~----~v~~~L~~LEl~G~v~~~~ 355 (374)
T PRK10736 322 TPVDVVAERAGQPV---P----EVVTQLLELELAGWIAAVP 355 (374)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHhCCcEEEcC
Confidence 36899999999954 7 7888888889999998775
No 338
>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=34.94 E-value=41 Score=24.20 Aligned_cols=25 Identities=16% Similarity=0.227 Sum_probs=19.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|.+|||+++|.+ .. .+.|.|+++-
T Consensus 121 ~s~~~iA~~lg~s---~~----~V~r~l~l~~ 145 (187)
T TIGR00180 121 MTQEDLAKKIGKS---RA----HITNLLRLLK 145 (187)
T ss_pred CCHHHHHHHHCcC---HH----HHHHHHHHHc
Confidence 3678899999994 47 8888888753
No 339
>PHA00542 putative Cro-like protein
Probab=34.90 E-value=34 Score=21.33 Aligned_cols=22 Identities=9% Similarity=0.131 Sum_probs=16.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|||+.+|++. . .+.|+.+
T Consensus 32 lTq~elA~~lgIs~---~----tIsr~e~ 53 (82)
T PHA00542 32 WSQEQIADATDVSQ---P----TICRIYS 53 (82)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHc
Confidence 47788999999843 6 6666665
No 340
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=34.85 E-value=61 Score=22.34 Aligned_cols=46 Identities=11% Similarity=0.216 Sum_probs=32.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+|+.|+|+.+|+++ +-+|+=-..|++.... ++++-+.|....+-++
T Consensus 2 ~~I~EvA~~~Gvs~-----------~tLRyYE~~GLl~p~r--~~~g~R~Y~~~dl~~l 47 (139)
T cd01110 2 LSVGEVAKRSGVAV-----------SALHFYEQKGLIASWR--NAGNQRRYPRDVLRRI 47 (139)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCCc--CCCCCeEECHHHHHHH
Confidence 58899999999954 4588888889996432 2222467877666543
No 341
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=34.72 E-value=48 Score=23.85 Aligned_cols=28 Identities=18% Similarity=-0.018 Sum_probs=17.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
+|+.|||+.+|+++ .-+-..|.|.++.|
T Consensus 150 ~s~~EIAe~lgis~---~tV~~~l~Rar~~L 177 (196)
T PRK12535 150 YTYEEAAKIADVRV---GTIRSRVARARADL 177 (196)
T ss_pred CCHHHHHHHhCCCH---HHHHHHHHHHHHHH
Confidence 47899999999965 32222455554443
No 342
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=34.37 E-value=25 Score=21.78 Aligned_cols=14 Identities=29% Similarity=0.323 Sum_probs=9.1
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|-.|+|+.+|++.
T Consensus 32 ltQ~e~A~~lgisq 45 (80)
T PF13744_consen 32 LTQAELAERLGISQ 45 (80)
T ss_dssp --HHHHHHHHTS-H
T ss_pred CCHHHHHHHHCCCh
Confidence 36678999999843
No 343
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=34.33 E-value=12 Score=28.71 Aligned_cols=53 Identities=13% Similarity=0.180 Sum_probs=30.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC--C-CcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ--N-DQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~--~-~~~~~y~~T~~s~~L~~~ 63 (128)
+|+.|||+++|+.. . -+.|+|+ ..+-+++..... . -.+--|.++...+.|...
T Consensus 2 ~Ti~dIA~~agVS~---~----TVSrvLn---~~~~vs~~tr~~V~~~a~elgY~pn~~a~~l~~~ 57 (341)
T PRK10703 2 ATIKDVAKRAGVST---T----TVSHVIN---KTRFVAEETRNAVWAAIKELHYSPSAVARSLKVN 57 (341)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHc---CCCCCCHHHHHHHHHHHHHHCCCcCHHHHHHhhC
Confidence 48999999999943 5 6777775 222232221100 0 002238888877777543
No 344
>PRK15340 transcriptional regulator InvF; Provisional
Probab=34.22 E-value=37 Score=25.57 Aligned_cols=31 Identities=10% Similarity=-0.138 Sum_probs=24.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
.|+++||+.+|+++ . .+.|+.+..+...+-.
T Consensus 126 ~sleeLA~~~gvS~---r----~f~RlFk~~~G~tpk~ 156 (216)
T PRK15340 126 NTMRMLGEDYGVSY---T----HFRRLCSRALGGKAKS 156 (216)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHCcCHHH
Confidence 37899999999955 7 8999999877666543
No 345
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.16 E-value=41 Score=21.93 Aligned_cols=23 Identities=13% Similarity=0.262 Sum_probs=17.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|..+||.+++..+ . .|.++|..
T Consensus 24 LS~~~iA~~Ln~t~---~----~lekil~~ 46 (97)
T COG4367 24 LSDEEIATALNWTE---V----KLEKILQV 46 (97)
T ss_pred ccHHHHHHHhCCCH---H----HHHHHHHH
Confidence 47788999999844 6 77787754
No 346
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=34.12 E-value=45 Score=23.77 Aligned_cols=29 Identities=14% Similarity=0.092 Sum_probs=19.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
.|+.|||+.+|+++ ..+-..|.|.++.|-
T Consensus 153 ~s~~eIA~~lgis~---~tV~~~l~Ra~~~Lr 181 (196)
T PRK12524 153 LSNPEIAEVMEIGV---EAVESLTARGKRALA 181 (196)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHHHHHHHHH
Confidence 47899999999965 433345666665553
No 347
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=34.06 E-value=59 Score=24.33 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=34.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.+ + .+.|-++-|= ..-+|.... +.+.+|+.|+.|...
T Consensus 17 s~s~AA~~L~isQ---~----avSr~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~ 67 (296)
T PRK09906 17 NFTKAAEKLHTAQ---P----SLSQQIKDLENCVGVPLLVRDK-------RKVALTAAGEVFLQD 67 (296)
T ss_pred CHHHHHHHhCCCC---c----HHHHHHHHHHHHhCCeeeeeCC-------CcceEcHhHHHHHHH
Confidence 5677889999954 5 6666666654 344776553 679999999999864
No 348
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=34.03 E-value=70 Score=23.70 Aligned_cols=32 Identities=16% Similarity=0.215 Sum_probs=27.0
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
=.|||+..|+ ... -++|-|..|+..|++....
T Consensus 38 E~eLa~~~~V---SR~----TVR~Al~~L~~eGli~r~~ 69 (241)
T PRK10079 38 EQQLAARYEV---NRH----TLRRAIDQLVEKGWVQRRQ 69 (241)
T ss_pred HHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 3689999999 446 8999999999999997655
No 349
>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=34.02 E-value=74 Score=19.77 Aligned_cols=30 Identities=13% Similarity=0.150 Sum_probs=21.3
Q ss_pred CHHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 2 TLNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 2 S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
|.++.-..+. . |.. .+.|+..+|...|++.
T Consensus 55 t~~~~~~~i~~~---d~~----~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 55 TKTDARKLIKGI---DVN----KIRRIYDFLERWGLIN 85 (86)
T ss_dssp -HHHHHHHTTSS---SHH----HHHHHHHHHHHTTSSS
T ss_pred cHHHHHHHcccc---CHH----HHHHHHHHHHHcCccC
Confidence 4445444444 3 667 9999999999999863
No 350
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=34.01 E-value=47 Score=19.72 Aligned_cols=32 Identities=13% Similarity=0.233 Sum_probs=17.3
Q ss_pred CCHHHHHHhC---CCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINAL---PFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~---~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|+.||+..+ |.+. ... .++|.|+ ..|+....
T Consensus 14 ~s~~~i~~~l~~~~~~v-S~~----TI~r~L~---~~g~~~~~ 48 (72)
T PF01498_consen 14 ISAREIAQELQEAGISV-SKS----TIRRRLR---EAGLKKRK 48 (72)
T ss_dssp --HHHHHHHT---T--S--HH----HHHHHHH---HT-EEEET
T ss_pred CCHHHHHHHHHHccCCc-CHH----HHHHHHH---HcCccccc
Confidence 4789999998 6543 334 5666665 56766544
No 351
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=33.99 E-value=43 Score=26.15 Aligned_cols=43 Identities=26% Similarity=0.274 Sum_probs=31.7
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHH-HHHhcCcceeeccCCCCcccceechHhhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMW-ILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR-~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+++.||+.+|.++ . .+.++++ +|+..|++..+. +.-..|+.+.
T Consensus 278 ~~~~~a~~lg~~~---~----~~~~~~e~~Li~~~li~~~~-------~gr~~~~~~~ 321 (328)
T PRK00080 278 GLDTLAAALGEER---D----TIEDVYEPYLIQQGFIQRTP-------RGRVATPKAY 321 (328)
T ss_pred eHHHHHHHHCCCc---c----hHHHHhhHHHHHcCCcccCC-------chHHHHHHHH
Confidence 6789999999954 6 7888899 999999996443 3344555554
No 352
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=33.91 E-value=46 Score=23.31 Aligned_cols=14 Identities=14% Similarity=0.164 Sum_probs=12.1
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|+.|||+.+|++.
T Consensus 134 ~s~~EIA~~lgis~ 147 (179)
T PRK12543 134 YSQEEIAQLLQIPI 147 (179)
T ss_pred CCHHHHHHHHCCCH
Confidence 47899999999965
No 353
>PRK00400 hisE phosphoribosyl-ATP pyrophosphatase; Validated
Probab=33.85 E-value=40 Score=22.49 Aligned_cols=19 Identities=21% Similarity=0.471 Sum_probs=16.6
Q ss_pred hhhhhHHHHHHHHHhcCcc
Q 045905 19 YVAQYVYRFMWILVHSGFF 37 (128)
Q Consensus 19 ~~~~~L~RlLR~L~~~gvf 37 (128)
+.||+||.+|-.|...||=
T Consensus 62 E~ADLlYHllVlL~~~gv~ 80 (105)
T PRK00400 62 EIADLLYHLLVLLAARGIS 80 (105)
T ss_pred HHHHHHHHHHHHHHHcCCC
Confidence 5688999999999999974
No 354
>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=33.84 E-value=42 Score=23.47 Aligned_cols=23 Identities=13% Similarity=0.348 Sum_probs=17.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|+.||++.+|+++ . .+.+++|-
T Consensus 47 ati~eV~e~tgVs~---~----~I~~~Ire 69 (137)
T TIGR03826 47 ATVSEIVEETGVSE---K----LILKFIRE 69 (137)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHc
Confidence 47899999999944 6 66666663
No 355
>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=33.83 E-value=69 Score=23.31 Aligned_cols=33 Identities=9% Similarity=0.083 Sum_probs=28.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|-.|||+++|++ .. .+++-|+.|...|++....
T Consensus 27 sE~eLa~~~~Vs---r~----Tvr~Al~~L~~eGli~~~~ 59 (231)
T TIGR03337 27 SERDLGERFNTT---RV----TIREALQQLEAEGLIYRED 59 (231)
T ss_pred CHHHHHHHHCCC---HH----HHHHHHHHHHHCCeEEEeC
Confidence 457999999994 47 8999999999999998765
No 356
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=33.24 E-value=56 Score=24.41 Aligned_cols=48 Identities=17% Similarity=0.110 Sum_probs=35.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.+ + .+.|-++.|- ...+|.... +.+.+|+.|+.|.+.
T Consensus 17 s~s~AA~~L~isq---p----avS~~I~~LE~~lG~~LF~R~~-------r~~~lT~~G~~l~~~ 67 (275)
T PRK03601 17 HFGRAAESLYLTQ---S----AVSFRIRQLENQLGVNLFTRHR-------NNIRLTAAGERLLPY 67 (275)
T ss_pred CHHHHHHHhCCCh---H----HHHHHHHHHHHHhCCceEEECC-------CceEECHhHHHHHHH
Confidence 4566788899844 5 6777777664 345887654 679999999998764
No 357
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=32.81 E-value=63 Score=20.43 Aligned_cols=45 Identities=16% Similarity=0.018 Sum_probs=30.1
Q ss_pred HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
.+.|++..+++ .. .+...|.-|+..+++...... -..|++|-.|-
T Consensus 27 ~~~I~~~s~l~---~~----~~~~~L~~L~~~kLv~~~~~~----Y~GYrLT~~GY 71 (82)
T PF09202_consen 27 LELIEKISGLS---EG----EVEKRLKRLVKLKLVSRRNKP----YDGYRLTFLGY 71 (82)
T ss_dssp HHHHHHHHT-----HH----HHHHHHHHHHHTTSEEEE-SS----S-EEEE-HHHH
T ss_pred HHHHHHHhCcC---HH----HHHHHHHHHHhcCCccccCCC----cceEEEeecch
Confidence 56778888883 36 788899999999999875320 13599998873
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=32.74 E-value=70 Score=18.80 Aligned_cols=25 Identities=20% Similarity=0.177 Sum_probs=18.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|+.-+|+.+++.+ . ...|+++-|.
T Consensus 14 Vsa~mva~~L~vT~---~----~A~~li~eLg 38 (54)
T PF11972_consen 14 VSAPMVAKELGVTP---Q----AAQRLIAELG 38 (54)
T ss_pred ccHHHHHHHhCCCH---H----HHHHHHHHhh
Confidence 47888999999955 6 6777776554
No 359
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=32.40 E-value=52 Score=23.56 Aligned_cols=29 Identities=14% Similarity=-0.041 Sum_probs=19.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|..|||+.+|+++ .-+-..|+|.++.|-
T Consensus 130 ~s~~EIA~~LgiS~---~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 130 FSYEEAAEMCGVAV---GTVKSRANRARARLA 158 (188)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHH
Confidence 47899999999965 323335666666654
No 360
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=32.39 E-value=70 Score=21.45 Aligned_cols=46 Identities=17% Similarity=0.267 Sum_probs=30.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
|+.|+|+.+|+++ . -+|+--..|++......+ ++-+.|....+-++
T Consensus 1 ~I~e~a~~~gvs~---~--------tlR~Ye~~GLl~~~~r~~-~g~R~Y~~~~l~~l 46 (124)
T TIGR02051 1 TIGELAKAAGVNV---E--------TIRYYERKGLLPEPDRPE-GGYRRYPEETVKRL 46 (124)
T ss_pred CHHHHHHHHCcCH---H--------HHHHHHHCCCCCCCccCC-CCCEeECHHHHHHH
Confidence 5789999999954 3 468888999996432211 22466777666543
No 361
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=32.34 E-value=71 Score=16.58 Aligned_cols=24 Identities=21% Similarity=0.169 Sum_probs=15.5
Q ss_pred HHHHHhCCCCCC--CchhhhhhHHHHHHHH
Q 045905 4 NELINALPFHPI--KAQYVAQYVYRFMWIL 31 (128)
Q Consensus 4 ~eLA~~~~~~~~--~~~~~~~~L~RlLR~L 31 (128)
.++..+.|++.+ +.+ .+.||..++
T Consensus 10 k~~l~~~gL~~~G~K~~----Li~Rl~~~l 35 (35)
T PF02037_consen 10 KEELKERGLSTSGKKAE----LIERLKEHL 35 (35)
T ss_dssp HHHHHHTTS-STSSHHH----HHHHHHHHH
T ss_pred HHHHHHCCCCCCCCHHH----HHHHHHHhC
Confidence 456667777544 555 899988764
No 362
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=32.30 E-value=70 Score=22.20 Aligned_cols=45 Identities=13% Similarity=0.182 Sum_probs=31.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+++.|+|+.+|+++ +-+|+=-..|++..... + ++-+.|....+-+
T Consensus 2 ~~IgevA~~~Gvs~-----------~tLRyYE~~GLl~~~r~-~-~g~R~Y~~~di~~ 46 (142)
T TIGR01950 2 LTVGELAKRSGVAV-----------SALHFYESKGLITSIRN-S-GNQRRYKRDVLRR 46 (142)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCccC-C-CCCEEECHHHHHH
Confidence 57899999999954 56899999999975321 2 2246677666543
No 363
>TIGR03188 histidine_hisI phosphoribosyl-ATP pyrophosphohydrolase. This enzyme, phosphoribosyl-ATP pyrophosphohydrolase, catalyses the second step in the histidine biosynthesis pathway. It often occurs as a fusion protein. This model a somewhat narrower scope than Pfam model pfam01503, as some paralogs that appear to be functionally distinct are excluded from this model.
Probab=31.93 E-value=46 Score=21.23 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=16.4
Q ss_pred hhhhhHHHHHHHHHhcCcc
Q 045905 19 YVAQYVYRFMWILVHSGFF 37 (128)
Q Consensus 19 ~~~~~L~RlLR~L~~~gvf 37 (128)
+.||.++.+|-.|...||=
T Consensus 58 E~ADLlYHllVlL~~~gi~ 76 (84)
T TIGR03188 58 EAADLLYHLLVLLAAQGVS 76 (84)
T ss_pred HHHHHHHHHHHHHHHcCCC
Confidence 5688999999999999873
No 364
>PRK13502 transcriptional activator RhaR; Provisional
Probab=31.73 E-value=38 Score=25.44 Aligned_cols=57 Identities=11% Similarity=0.043 Sum_probs=39.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQ 73 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~ 73 (128)
+++++||+.++++| . .|.|+.+--+...+-.-- ..+.+..+-++|... ..++.....
T Consensus 193 ~~~~~lA~~~~iS~---~----~L~r~fk~~~G~t~~~yi--------~~~Rl~~A~~lL~~t-~~sI~eIA~ 249 (282)
T PRK13502 193 FALDAFCQQEQCSE---R----VLRQQFRAQTGMTINQYL--------RQVRICHAQYLLQHS-PLMISEISM 249 (282)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHCcCHHHHH--------HHHHHHHHHHHHHcC-CCCHHHHHH
Confidence 47899999999955 7 899999976655444322 357888887788754 234554433
No 365
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=31.38 E-value=1.2e+02 Score=22.73 Aligned_cols=54 Identities=20% Similarity=0.124 Sum_probs=40.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
+|..|||.+++.++ + ...|.|-.|--.|......... +.....|.-+.-|....
T Consensus 20 ~t~~ela~~l~~S~---q----ta~R~l~~le~~~~I~R~~~~~---Gq~i~iTekG~~~L~~~ 73 (214)
T COG1339 20 VTSSELAKRLGVSS---Q----TAARKLKELEDEGYITRTISKR---GQLITITEKGIDLLYKE 73 (214)
T ss_pred ccHHHHHHHhCcCc---H----HHHHHHHhhccCCcEEEEecCC---CcEEEehHhHHHHHHHH
Confidence 47899999999954 7 8889999999889886443111 35688888888776543
No 366
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=31.36 E-value=54 Score=23.60 Aligned_cols=14 Identities=7% Similarity=0.418 Sum_probs=12.2
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|+.|||+.+|+++
T Consensus 156 ~s~~EIA~~lgis~ 169 (201)
T PRK12545 156 FEIDDICTELTLTA 169 (201)
T ss_pred CCHHHHHHHHCcCH
Confidence 47899999999965
No 367
>PRK09726 antitoxin HipB; Provisional
Probab=31.10 E-value=37 Score=21.31 Aligned_cols=22 Identities=18% Similarity=0.175 Sum_probs=14.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|||.++|+++ . .|.++.+
T Consensus 26 ltq~elA~~~gvs~---~----tis~~e~ 47 (88)
T PRK09726 26 WTQSELAKKIGIKQ---A----TISNFEN 47 (88)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHC
Confidence 46788999988843 5 5555544
No 368
>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=31.05 E-value=50 Score=20.38 Aligned_cols=30 Identities=20% Similarity=0.166 Sum_probs=24.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSG 35 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~g 35 (128)
+++.||.+.|....+.. .+.+++..|+.-+
T Consensus 3 AvD~la~~~g~~i~~~~----~~k~vsaalv~g~ 32 (93)
T PF11761_consen 3 AVDLLARELGWRIENRE----AVKRVSAALVNGE 32 (93)
T ss_pred CcchhhhhCCCEEcCHH----HHHHHHHHHHCCC
Confidence 57889999998655667 9999999999655
No 369
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=31.03 E-value=57 Score=22.68 Aligned_cols=30 Identities=17% Similarity=0.028 Sum_probs=19.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVH 33 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~ 33 (128)
.|..|||+.+|+++ ..+-..|.|.++.|..
T Consensus 117 ~s~~eIA~~lgis~---~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 117 LSQQEIAEKLGLSL---SGAKSRVQRGRKKLKE 146 (170)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHHH
Confidence 47899999999965 3222345565555543
No 370
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=31.02 E-value=41 Score=17.29 Aligned_cols=13 Identities=31% Similarity=0.365 Sum_probs=9.5
Q ss_pred CCHHHHHHhCCCC
Q 045905 1 MTLNELINALPFH 13 (128)
Q Consensus 1 ~S~~eLA~~~~~~ 13 (128)
+|..+||..++++
T Consensus 11 ~s~~~la~~~~i~ 23 (56)
T smart00530 11 LTQEELAEKLGVS 23 (56)
T ss_pred CCHHHHHHHhCCC
Confidence 4677888888873
No 371
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=30.91 E-value=52 Score=25.32 Aligned_cols=29 Identities=17% Similarity=-0.051 Sum_probs=20.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|+.|||+.+|+++ .-+-..|.|.++.|-
T Consensus 159 ~s~~EIA~~lgis~---~tV~~~l~Rar~~Lr 187 (324)
T TIGR02960 159 WRAAETAELLGTST---ASVNSALQRARATLD 187 (324)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHH
Confidence 58899999999965 333335677666665
No 372
>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=30.86 E-value=49 Score=22.57 Aligned_cols=31 Identities=16% Similarity=0.084 Sum_probs=22.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA 38 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~ 38 (128)
+|.+|+++..+. .+. .+..++..|...|+=.
T Consensus 48 Lt~~e~~~~~~p---~~~----~v~~V~~wL~~~G~~~ 78 (143)
T PF09286_consen 48 LTPEEFAALFAP---SPE----DVAAVKSWLKSHGLTV 78 (143)
T ss_dssp --HHHHHHHHS-----HH----HHHHHHHHHHHCT-EE
T ss_pred CCHHHHHHHHCC---CHH----HHHHHHHHHHHcCCce
Confidence 477899998886 336 8999999999999643
No 373
>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=30.76 E-value=35 Score=19.82 Aligned_cols=45 Identities=16% Similarity=0.220 Sum_probs=25.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
.|..|+|+.+|+++ . .|++--+. .|+..... ++++.+.|....+-
T Consensus 1 ~s~~eva~~~gvs~---~----tlr~w~~~---~g~~~~~r--~~~~~r~yt~~~v~ 45 (68)
T cd01104 1 YTIGAVARLTGVSP---D----TLRAWERR---YGLPAPQR--TDGGHRLYSEADVA 45 (68)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHh---CCCCCCCc--CCCCCeecCHHHHH
Confidence 47899999999955 5 55554431 35543211 11113567766654
No 374
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=30.76 E-value=52 Score=25.62 Aligned_cols=30 Identities=17% Similarity=0.027 Sum_probs=22.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVH 33 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~ 33 (128)
+|+.|||+.+|+++ ..+-..|+|.++.|-.
T Consensus 170 ~s~~EIA~~lgis~---~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 170 WSAAEVAELLDTSV---AAVNSALQRARATLAE 199 (339)
T ss_pred CCHHHHHHHhCCCH---HHHHHHHHHHHHHHhh
Confidence 58899999999966 3333467787777765
No 375
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=30.55 E-value=82 Score=20.37 Aligned_cols=46 Identities=13% Similarity=0.231 Sum_probs=28.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhc-CcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHS-GFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~-gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
.|+.|+|+.+|+++ . -||+.... |++.... .+++.+.|....+-++
T Consensus 1 yti~EvA~~~gVs~---~--------tLR~ye~~~gli~p~r--~~~g~R~Yt~~di~~l 47 (99)
T cd04765 1 FSIGEVAEILGLPP---H--------VLRYWETEFPQLKPVK--RAGGRRYYRPKDVELL 47 (99)
T ss_pred CCHHHHHHHHCcCH---H--------HHHHHHHHcCCCCCcC--CCCCCeeeCHHHHHHH
Confidence 47899999999954 3 36666655 6653222 1222567887777643
No 376
>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=30.42 E-value=45 Score=21.00 Aligned_cols=25 Identities=24% Similarity=0.091 Sum_probs=15.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|+.|||+.+|. |..+. .+.+.|+.
T Consensus 20 ~TYg~iA~~~g~-p~~ar----~Vg~al~~ 44 (85)
T PF01035_consen 20 TTYGEIARLLGR-PKAAR----AVGSALAR 44 (85)
T ss_dssp EEHHHHHHHTT--TTCHH----HHHHHHHT
T ss_pred EeHHHHHHHHhh-cccHH----HHHHHhcc
Confidence 478999999994 32334 45555543
No 377
>PRK13501 transcriptional activator RhaR; Provisional
Probab=30.39 E-value=49 Score=25.08 Aligned_cols=55 Identities=7% Similarity=0.015 Sum_probs=39.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSF 71 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~ 71 (128)
+|++|||+++++++ . .|.|+.+--+..-+..-- ..+.+..+.++|.... .++...
T Consensus 193 ~sl~~lA~~~~lS~---~----~l~r~Fk~~~G~T~~qyi--------~~~Ri~~A~~LL~~t~-~sI~eI 247 (290)
T PRK13501 193 FDMADFCHKNQLVE---R----SLKQLFRQQTGMSISHYL--------RQIRLCHAKCLLRGSE-HRISDI 247 (290)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHCcCHHHHH--------HHHHHHHHHHHHHcCC-CCHHHH
Confidence 58999999999955 8 899999987765555433 2478888888887543 235444
No 378
>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=30.13 E-value=52 Score=19.63 Aligned_cols=22 Identities=18% Similarity=0.261 Sum_probs=15.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|||.++|++. . .+.+++.
T Consensus 19 ~t~~~lA~~~gis~---~----tis~~~~ 40 (78)
T TIGR02607 19 LSIRALAKALGVSR---S----TLSRIVN 40 (78)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHc
Confidence 46788888888833 5 5666544
No 379
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=29.65 E-value=88 Score=23.19 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=33.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.. + .+.|-++.|= ...+|.... +.+.+|+.|+.|.+.
T Consensus 19 s~t~AA~~L~isq---p----avS~~I~~LE~~lg~~Lf~R~~-------r~~~lT~~G~~l~~~ 69 (290)
T PRK10837 19 STTQASVMLALSQ---S----AVSAALTDLEGQLGVQLFDRVG-------KRLVVNEHGRLLYPR 69 (290)
T ss_pred CHHHHHHHhCCCc---c----HHHHHHHHHHHHhCCccEeecC-------CeEEECHhHHHHHHH
Confidence 4566788899844 5 6666666654 345786553 679999999999754
No 380
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=29.45 E-value=75 Score=23.80 Aligned_cols=46 Identities=13% Similarity=0.177 Sum_probs=33.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
++..|||+.+|+++ |-+|+.-..|++...... ++-+.|....+.++
T Consensus 2 y~i~elA~~~Gvs~-----------~tIR~Ye~~GLL~p~r~~--~~~r~Y~~~~v~rL 47 (219)
T cd04778 2 YRIDDLARAAGTTV-----------RNVRAYQDRGLLPPPRRR--GRVAIYNDSHLARL 47 (219)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCcccC--CCCcccCHHHHHHH
Confidence 47899999999943 468999999999754321 12467888887654
No 381
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=29.43 E-value=58 Score=20.63 Aligned_cols=49 Identities=18% Similarity=0.125 Sum_probs=32.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI 64 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~ 64 (128)
+++++||..+|+.+ . .|.|+.+......+...- ..+.+..+-++|..+.
T Consensus 37 ~~l~~la~~~g~S~---~----~l~r~f~~~~g~s~~~~~--------~~~Rl~~A~~lL~~~~ 85 (127)
T COG2207 37 LTLEDLARRLGMSR---R----TLSRLFKKETGTSPSQYL--------RQLRLEEARRLLRSTD 85 (127)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHHHHCCCHHHHH--------HHHHHHHHHHHHHcCC
Confidence 47899999999954 7 888888866644443222 2356666666666543
No 382
>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=29.32 E-value=84 Score=18.88 Aligned_cols=26 Identities=19% Similarity=0.199 Sum_probs=17.8
Q ss_pred CCHHHHHHhCCC------CCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPF------HPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~------~~~~~~~~~~~L~RlLR~ 30 (128)
+|..||+..++. .|-+.. .|.+|||.
T Consensus 25 lTP~EL~~~lg~~~~~~~apl~Ra----~Ld~Lm~~ 56 (60)
T TIGR02216 25 LTPAELAAAIAGLQGAAAAPLDRA----ALDALLAA 56 (60)
T ss_pred CCHHHHHHHhCCccCCCCCCCCHH----HHHHHHHH
Confidence 578899999883 222445 68888874
No 383
>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=29.25 E-value=93 Score=18.85 Aligned_cols=30 Identities=20% Similarity=0.320 Sum_probs=22.6
Q ss_pred HHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905 4 NELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ 39 (128)
Q Consensus 4 ~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e 39 (128)
..+..+++.+ +++ .+.|+.|.|-.+||...
T Consensus 19 er~~~~~~~~--~~e----~~~~f~~~L~~~Gv~~~ 48 (69)
T TIGR03595 19 ERWVAKTPFN--NDE----NLRRFARKLKKLGVEDA 48 (69)
T ss_pred HHHHHHcCCC--CHH----HHHHHHHHHHHCCHHHH
Confidence 4566777762 335 89999999999998754
No 384
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=29.24 E-value=58 Score=24.46 Aligned_cols=29 Identities=10% Similarity=0.103 Sum_probs=20.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|+.|||+.+|+++ .-+...|.|-++.|-
T Consensus 133 ~S~~EIAe~LgiS~---~tVksrL~Rark~Lr 161 (228)
T PRK06704 133 YSIADIAKVCSVSE---GAVKASLFRSRNRLK 161 (228)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHHHHHHHHH
Confidence 48899999999965 333335677666664
No 385
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=29.21 E-value=47 Score=21.82 Aligned_cols=14 Identities=21% Similarity=0.268 Sum_probs=11.7
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|+.+||+++|+++
T Consensus 33 ~t~~~Ia~~agvs~ 46 (201)
T COG1309 33 TTVDEIAKAAGVSK 46 (201)
T ss_pred CCHHHHHHHhCCCc
Confidence 57899999999854
No 386
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=28.96 E-value=85 Score=22.18 Aligned_cols=45 Identities=11% Similarity=0.100 Sum_probs=31.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~ 58 (128)
+++.|+|+.+|+++ +-+|+--..|++..... . ++.+.|....+-+
T Consensus 12 ~~IgevAk~~gvs~-----------~TlRyYE~~GLi~~~r~-~-~g~R~Y~~~~i~~ 56 (154)
T PRK15002 12 LTPGEVAKRSGVAV-----------SALHFYESKGLITSIRN-S-GNQRRYKRDVLRY 56 (154)
T ss_pred ccHHHHHHHHCcCH-----------HHHHHHHHCCCCCCccC-C-CCCEEECHHHHHH
Confidence 57899999999944 56899999999975322 2 2246677666543
No 387
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=28.78 E-value=97 Score=21.34 Aligned_cols=46 Identities=15% Similarity=0.235 Sum_probs=32.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL 59 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~ 59 (128)
+++.|+|+.+|+++ |-+|+=...|++.... .+++-+.|....+-++
T Consensus 1 y~I~e~a~~~gvs~-----------~TLR~Ye~~GLl~p~r--~~~g~R~Y~~~~l~~l 46 (134)
T cd04779 1 YRIGQLAHLAGVSK-----------RTIDYYTNLGLLTPER--SDSNYRYYDETALDRL 46 (134)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCCCCcc--CCCCCeeECHHHHHHH
Confidence 47899999999954 4577888899997432 1122466888777654
No 388
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=28.73 E-value=51 Score=25.50 Aligned_cols=55 Identities=9% Similarity=0.175 Sum_probs=35.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSF 71 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~ 71 (128)
+|+++||+.+++++ . .|.|+.+--+...+..-- ..+++..+-++|... ..++...
T Consensus 208 ~tl~~lA~~~~~S~---~----~l~r~Fk~~~G~t~~~~l--------~~~Rl~~A~~lL~~~-~~si~eI 262 (302)
T PRK10371 208 LTINDVAEHVKLNA---N----YAMGIFQRVMQLTMKQYI--------TAMRINHVRALLSDT-DKSILDI 262 (302)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHhCCCHHHHH--------HHHHHHHHHHHHhcC-CCCHHHH
Confidence 47889999999944 7 888888875544444322 347777777777653 2335444
No 389
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=28.58 E-value=73 Score=24.04 Aligned_cols=48 Identities=19% Similarity=0.261 Sum_probs=33.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.. + .+.|-++.|= ..-+|.... +.+.+|+.|+.|...
T Consensus 20 s~s~AA~~L~isq---p----avS~~I~~LE~~lg~~Lf~R~~-------r~~~lT~~G~~l~~~ 70 (296)
T PRK11062 20 SVVGAAEALFLTP---Q----TITGQIKALEERLQGKLFKRKG-------RGLEPTELGELVFRY 70 (296)
T ss_pred CHHHHHHHhCCCh---H----HHHHHHHHHHHHcCccceeecC-------CceeECHhHHHHHHH
Confidence 5566789999844 5 6666666664 334776553 679999999988753
No 390
>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=28.48 E-value=21 Score=29.80 Aligned_cols=33 Identities=18% Similarity=0.181 Sum_probs=26.2
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+|++||++.+|++ .. .|.|.|..|+..|++...
T Consensus 535 ~t~~ei~~~~~~~---~~----~l~~~L~~l~~~~~l~~~ 567 (588)
T PF00888_consen 535 LTVEEISEKTGIS---EE----ELKRALKSLVKSKILILL 567 (588)
T ss_dssp EEHHHHHHHC------HH----HHHHHHHCCCTTTTCSEE
T ss_pred ccHHHHHHHHCcC---HH----HHHHHHHHHHhCCcceee
Confidence 4789999999994 47 899999999999999744
No 391
>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=28.31 E-value=51 Score=19.37 Aligned_cols=14 Identities=14% Similarity=0.266 Sum_probs=11.4
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
.+..|||+.+|+++
T Consensus 14 ~~~~eIA~~Lg~~~ 27 (58)
T PF06056_consen 14 WSIKEIAEELGVPR 27 (58)
T ss_pred CCHHHHHHHHCCCh
Confidence 36889999999954
No 392
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=28.27 E-value=1.8e+02 Score=27.76 Aligned_cols=55 Identities=9% Similarity=0.077 Sum_probs=37.0
Q ss_pred CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC-CCCcHHHHHHHhc
Q 045905 13 HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD-ITLTVRSFLQAVL 76 (128)
Q Consensus 13 ~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~-~~~s~~~~~~~~~ 76 (128)
+|++.. .+.+-++.|...|.+..... +....+|++|+.|..= -++.++-+++...
T Consensus 451 dpP~~~----~i~~al~~L~~LgAld~~~~-----~~~~~LT~lG~~la~LPldPrlakmLl~a~ 506 (1294)
T PRK11131 451 EAPDKR----NIQDGVRLLEELGAITTDEQ-----ASAYKLTPLGRQLAQLPVDPRLARMVLEAQ 506 (1294)
T ss_pred CCCCHH----HHHHHHHHHHHCCCCCcccc-----CCCccCcHHHHHHHhCCCChHHHHHHHHhh
Confidence 343666 89999999999999975431 2357899999999753 2233554544433
No 393
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=28.22 E-value=56 Score=21.93 Aligned_cols=34 Identities=18% Similarity=0.172 Sum_probs=26.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
||.+=|.+++.++- . +-++.||.|...|++....
T Consensus 61 it~svl~dRlkIng---s----LAr~alr~L~~kG~Ik~Vs 94 (110)
T KOG1767|consen 61 ITPSVLSDRLKING---S----LARAALRELSNKGVIKQVS 94 (110)
T ss_pred ecHHHhhhhhhhch---H----HHHHHHHHHHhcchHHHHh
Confidence 46667788888844 6 7889999999999987653
No 394
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=28.19 E-value=45 Score=28.73 Aligned_cols=29 Identities=17% Similarity=0.189 Sum_probs=24.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF 36 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv 36 (128)
+|+.|||+++++++ . .+.|+.|-|--.|+
T Consensus 375 ~si~eLA~~~~vS~---a----TV~Rf~kkLGf~Gf 403 (638)
T PRK14101 375 DPIVDIARKADVSQ---P----TVIRFCRSLGCQGL 403 (638)
T ss_pred ccHHHHHHHhCCCH---H----HHHHHHHHhCCCCH
Confidence 58999999999955 7 89999998876665
No 395
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=28.09 E-value=82 Score=23.88 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=35.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.. + .+.|-++.|- ..-+|.... +.+.+|+.|+.|...
T Consensus 17 S~s~AA~~L~isQ---~----avS~~I~~LE~~lg~~LF~R~~-------r~v~lT~~G~~l~~~ 67 (305)
T PRK11233 17 SLTQAAEVLHIAQ---P----ALSQQVATLEGELNQQLLIRTK-------RGVTPTEAGKILYTH 67 (305)
T ss_pred CHHHHHHHhCCCc---h----HHHHHHHHHHHHhCCceEEeCC-------CCceECHhHHHHHHH
Confidence 5677789999944 6 6777777664 344777653 679999999988754
No 396
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.08 E-value=68 Score=22.51 Aligned_cols=28 Identities=14% Similarity=0.097 Sum_probs=18.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
+|+.|||+.+|+++ .-+-..|.|.+..|
T Consensus 139 ~s~~EIA~~lgis~---~tVk~~l~Rar~~L 166 (185)
T PRK12542 139 LTYQEISSVMGITE---ANVRKQFERARKRV 166 (185)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHH
Confidence 47899999999965 32222455555554
No 397
>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=28.02 E-value=53 Score=16.97 Aligned_cols=14 Identities=29% Similarity=0.318 Sum_probs=9.5
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|..++|..+++++
T Consensus 13 ~s~~~~a~~~~~~~ 26 (58)
T cd00093 13 LTQEELAEKLGVSR 26 (58)
T ss_pred CCHHHHHHHHCCCH
Confidence 35677888887733
No 398
>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=27.89 E-value=88 Score=22.79 Aligned_cols=35 Identities=29% Similarity=0.297 Sum_probs=26.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|.+||.+++.-.- .+. .+..+|+.|...|++.+..
T Consensus 44 t~~eI~~~l~~~~-p~~----~v~~~L~~L~~~G~l~~~~ 78 (193)
T TIGR03882 44 TLDEIIAALAGRF-PAE----EVLYALDRLERRGYLVEDA 78 (193)
T ss_pred CHHHHHHHhhccC-CHH----HHHHHHHHHHHCCCEeccC
Confidence 7889988876521 124 7999999999999998754
No 399
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=27.81 E-value=50 Score=21.00 Aligned_cols=17 Identities=24% Similarity=0.249 Sum_probs=14.1
Q ss_pred hhhhHHHHHHHHHhcCc
Q 045905 20 VAQYVYRFMWILVHSGF 36 (128)
Q Consensus 20 ~~~~L~RlLR~L~~~gv 36 (128)
.+..|++||-.|+.+||
T Consensus 69 l~~~lr~i~~sLa~MGI 85 (85)
T PF14357_consen 69 LAGILRNIMDSLANMGI 85 (85)
T ss_pred HHHHHHHHHHHHHHCCC
Confidence 34479999999999997
No 400
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=27.72 E-value=59 Score=20.15 Aligned_cols=33 Identities=18% Similarity=0.381 Sum_probs=27.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
+++++||+.++++. . .+..++.-++..|.+...
T Consensus 61 i~~~~ia~~l~~~~---~----~vE~~l~~~I~~~~i~~~ 93 (105)
T PF01399_consen 61 ISISEIAKALQLSE---E----EVESILIDLISNGLIKAK 93 (105)
T ss_dssp EEHHHHHHHHTCCH---H----HHHHHHHHHHHTTSSEEE
T ss_pred cchHHHHHHhccch---H----HHHHHHHHHHHCCCEEEE
Confidence 46889999999944 6 888999999999988743
No 401
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=27.57 E-value=92 Score=23.15 Aligned_cols=47 Identities=21% Similarity=0.247 Sum_probs=33.2
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
|+..-|+++++.+ + .+.|-||.|= ...+|.... +.+.+|+.|+.|..
T Consensus 23 s~t~AA~~L~itq---~----avS~~i~~LE~~lg~~Lf~R~~-------r~~~lT~~G~~l~~ 72 (294)
T PRK09986 23 HFGRAAARLNISQ---P----PLSIHIKELEDQLGTPLFIRHS-------RSVVLTHAGKILME 72 (294)
T ss_pred CHHHHHHHhCCCC---C----HHHHHHHHHHHHhCCeeEeeCC-------CceeECHhHHHHHH
Confidence 4566788899855 5 5666666554 445787653 67999999998874
No 402
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=27.56 E-value=64 Score=24.07 Aligned_cols=29 Identities=17% Similarity=0.045 Sum_probs=19.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|+.|||+.+|+++ ..+-..|.|-++.|-
T Consensus 188 ~s~~EIA~~Lgis~---~tVk~~l~RAr~kLr 216 (233)
T PRK12538 188 MSNGEIAEVMDTTV---AAVESLLKRGRQQLR 216 (233)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHHHHHHHHH
Confidence 58899999999955 322234666666554
No 403
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=27.46 E-value=77 Score=23.06 Aligned_cols=29 Identities=3% Similarity=-0.043 Sum_probs=20.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
.|..|||+++++.+ .-+-..+.|||+-|-
T Consensus 153 ~snkeIA~~L~iS~---~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 153 QGTIQISDQMNIKA---KTVSSHKGNIKRKIK 181 (207)
T ss_pred CCHHHHHHHcCCCH---HHHHHHHHHHHHHhC
Confidence 47789999999955 323336778887664
No 404
>smart00351 PAX Paired Box domain.
Probab=27.46 E-value=78 Score=21.32 Aligned_cols=32 Identities=9% Similarity=0.062 Sum_probs=26.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ 39 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e 39 (128)
.|..+||.++|+++ . .++|+++--...|.+..
T Consensus 34 ~s~~~iA~~~gvs~---~----tV~kwi~r~~~~G~~~p 65 (125)
T smart00351 34 VRPCDISRQLCVSH---G----CVSKILGRYYETGSIRP 65 (125)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHHcCCcCC
Confidence 36789999999944 7 89999998888887764
No 405
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=27.40 E-value=1e+02 Score=25.37 Aligned_cols=49 Identities=12% Similarity=0.159 Sum_probs=34.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+.+.+.+..|++. . +.+...+..|...|++..+. +.+.+|+.|+.+.+.
T Consensus 360 d~~~f~~~~g~~~---~---~~~~~~l~~l~~~Gll~~~~-------~~l~lT~~G~~~~d~ 408 (433)
T PRK08629 360 SIKYFRETFGVNL---D---KALFKEMLLLKLIGAIKNDP-------GDLIVTDFGKYLGVV 408 (433)
T ss_pred CHHHHHHHHCCCH---H---HHHHHHHHHHHHCCCEEEEC-------CEEEECcchhHHHHH
Confidence 3455556666522 2 13667777888999988653 679999999998764
No 406
>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=27.40 E-value=43 Score=15.59 Aligned_cols=11 Identities=18% Similarity=0.329 Sum_probs=7.6
Q ss_pred CHHHHHHhCCC
Q 045905 2 TLNELINALPF 12 (128)
Q Consensus 2 S~~eLA~~~~~ 12 (128)
|..+||..+++
T Consensus 23 s~~~ia~~~~i 33 (42)
T cd00569 23 SVAEIARRLGV 33 (42)
T ss_pred CHHHHHHHHCC
Confidence 55677777776
No 407
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=26.96 E-value=74 Score=23.22 Aligned_cols=29 Identities=17% Similarity=0.185 Sum_probs=22.4
Q ss_pred hHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905 23 YVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS 57 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s 57 (128)
-...+|.-|+..|-|.... .|.|+++|-+
T Consensus 168 eae~lL~~lv~~gWl~~s~------~G~y~L~~Ra 196 (200)
T PF07574_consen 168 EAESLLDRLVEDGWLYRSR------EGFYSLGPRA 196 (200)
T ss_dssp HHHHHHHHHHHTTSE-EEE------TTEEEE-HHH
T ss_pred HHHHHHHHHHHCCCceeCC------CCEEEEChHH
Confidence 5678899999999996665 5899999865
No 408
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=26.92 E-value=96 Score=24.90 Aligned_cols=47 Identities=17% Similarity=0.132 Sum_probs=31.3
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+.+++.+..|.+. . ...+..|...|++..+. ++++.+|+.|+.|.+.
T Consensus 327 d~~~~~~~~g~~~---~------~~~l~~l~~~gl~~~~~------~~~~~lT~~G~~~~d~ 373 (380)
T PRK09057 327 DLARYAALSGRPL---D------PERLADLIEEGLIERDG------GSRLRATPAGRLVLDA 373 (380)
T ss_pred CHHHHHHHHCCCc---h------HHHHHHHHHCCCEEEcC------CCEEEECcchhHHHHH
Confidence 3455556656522 1 23577888899887553 2489999999988754
No 409
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=26.83 E-value=52 Score=24.92 Aligned_cols=23 Identities=13% Similarity=0.174 Sum_probs=18.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|+++||+++|+++ . .|.|+.+-
T Consensus 215 ls~~~lA~~~giS~---r----~L~r~Fk~ 237 (302)
T PRK09685 215 LRPEWIAGELGISV---R----SLYRLFAE 237 (302)
T ss_pred CCHHHHHHHHCCCH---H----HHHHHHHH
Confidence 58899999999944 6 77777763
No 410
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=26.83 E-value=1e+02 Score=24.80 Aligned_cols=33 Identities=24% Similarity=0.220 Sum_probs=27.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|..+||++++++ .. .+++-++.|...|++....
T Consensus 31 s~r~la~~~~vs---r~----tv~~a~~~L~~~g~i~~~~ 63 (431)
T PRK15481 31 PVRELASELGVN---RN----TVAAAYKRLVTAGLAQSQG 63 (431)
T ss_pred CHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEEeC
Confidence 568999999994 47 8999999999999987543
No 411
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=26.81 E-value=68 Score=24.56 Aligned_cols=31 Identities=16% Similarity=0.138 Sum_probs=22.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhc
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHS 34 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~ 34 (128)
+|+.|||+.+|+++ ..+-..|.|-.+.|-..
T Consensus 132 ~s~~EIA~~lg~s~---~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 132 VPFDEIASTLGRSP---AACRQLASRARKHVRAA 162 (293)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHHhh
Confidence 47899999999965 33334677777777653
No 412
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=26.38 E-value=77 Score=24.03 Aligned_cols=49 Identities=22% Similarity=0.144 Sum_probs=33.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.+ + .+.|-++.|= ...+|.... .+.+.+|+.|+.|.+.
T Consensus 18 s~s~AA~~L~isq---~----avSr~I~~LE~~lg~~LF~R~~------~~~~~lT~~G~~l~~~ 69 (309)
T PRK12682 18 NLTEAAKALHTSQ---P----GVSKAIIELEEELGIEIFIRHG------KRLKGLTEPGKAVLDV 69 (309)
T ss_pred CHHHHHHHhcCcc---H----HHHHHHHHHHHHhCCeeEEECC------CCcCccCHhHHHHHHH
Confidence 6777899999954 6 6667666664 344776543 2334899999998754
No 413
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=25.94 E-value=47 Score=25.52 Aligned_cols=35 Identities=17% Similarity=0.285 Sum_probs=25.5
Q ss_pred CHHHHH--HhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELI--NALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA--~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
|++||. +++.++ .|+. .+.|.|+.|-..|+..-.+
T Consensus 123 si~DL~~Gk~IAip-~d~~----n~~r~L~lL~~~Gli~l~~ 159 (271)
T PRK11063 123 SLDELQDGSQVAVP-NDPT----NLGRSLLLLQKVGLIKLKD 159 (271)
T ss_pred CHHHhcCCCEEEec-CCCc----cHHHHHHHHHHCCCEEecC
Confidence 566775 344443 2668 8999999999999987654
No 414
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=25.92 E-value=1.2e+02 Score=26.36 Aligned_cols=33 Identities=9% Similarity=0.014 Sum_probs=25.9
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
++.||+..+++ +.. ..+.+|+.|+..|.+..-.
T Consensus 508 ~~~~~~~~l~~---~~~----~~~~~l~~l~~~g~lv~l~ 540 (614)
T PRK10512 508 WVRDLAKETGT---DEQ----AMRLTLRQAAQQGIITAIV 540 (614)
T ss_pred CHHHHHHHhCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence 35788888888 346 7899999999999776554
No 415
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=25.82 E-value=79 Score=22.47 Aligned_cols=14 Identities=14% Similarity=0.268 Sum_probs=11.9
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
.|..|||+.+|+++
T Consensus 145 ~s~~EIA~~lgis~ 158 (188)
T PRK12517 145 FSGEEIAEILDLNK 158 (188)
T ss_pred CCHHHHHHHHCCCH
Confidence 47899999999955
No 416
>PRK13500 transcriptional activator RhaR; Provisional
Probab=25.60 E-value=63 Score=24.99 Aligned_cols=56 Identities=11% Similarity=0.061 Sum_probs=39.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFL 72 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~ 72 (128)
+|+++||+++++++ . .|.|+.+--+.+.+..-- ..+.+..+.++|.... .++....
T Consensus 223 isl~~lA~~~~iS~---~----~L~r~FK~~tG~T~~~yi--------~~~RL~~A~~LL~~t~-~sI~eIA 278 (312)
T PRK13500 223 FALDKFCDEASCSE---R----VLRQQFRQQTGMTINQYL--------RQVRVCHAQYLLQHSR-LLISDIS 278 (312)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHCcCHHHHH--------HHHHHHHHHHHHHcCC-CCHHHHH
Confidence 57899999999955 7 899999887655554432 3578888888887542 3455443
No 417
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=25.32 E-value=83 Score=23.57 Aligned_cols=48 Identities=19% Similarity=0.252 Sum_probs=34.6
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.+ + .+.|-++.|= ..-+|.... +.+.+|+.|+.|.+.
T Consensus 19 S~s~AA~~L~isq---~----avS~~I~~LE~~lg~~LF~R~~-------~~~~lT~~G~~l~~~ 69 (300)
T TIGR02424 19 SVKRAAEALHITQ---P----AVSKTLRELEEILGTPLFERDR-------RGIRLTRYGELFLRH 69 (300)
T ss_pred CHHHHHHHhCCCh---H----HHHHHHHHHHHHhCCeEEEEcC-------CCccccHhHHHHHHH
Confidence 5677789999844 5 6666666653 445787654 679999999998754
No 418
>PF04738 Lant_dehyd_C: Lantibiotic dehydratase, C terminus; InterPro: IPR006827 Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides []. They are produced by bacteria of the Firmicutes phylum, and include mutacin, subtilin, and nisin. Lantibiotic peptides contain thioether bridges termed lanthionines that are thought to be generated by dehydration of serine and threonine residues followed by addition of cysteine residues []. This family constitutes the C terminus of the enzyme proposed to catalyse the dehydration step [, ].
Probab=25.31 E-value=63 Score=26.45 Aligned_cols=36 Identities=28% Similarity=0.551 Sum_probs=24.8
Q ss_pred CCHHHHHHhCC--CCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905 1 MTLNELINALP--FHPIKAQYVAQYVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 1 ~S~~eLA~~~~--~~~~~~~~~~~~L~RlLR~L~~~gvf~e~ 40 (128)
||+.||++.+. .+..++. .+..+|+.|+..|++.-.
T Consensus 1 i~~~~l~~~L~~~~~~~~~~----~v~~~L~~Li~~~~L~~~ 38 (500)
T PF04738_consen 1 ISYSELIEQLAKEFPEAEAE----RVENYLRQLIEQGFLISE 38 (500)
T ss_pred ChHHHHHHHHHHhCCCCCHH----HHHHHHHHHHHCCEEEec
Confidence 45566665555 2222446 899999999999988644
No 419
>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=25.24 E-value=65 Score=21.09 Aligned_cols=25 Identities=20% Similarity=0.048 Sum_probs=18.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|-.|||+++|+.. . .+.|.=|.|.
T Consensus 56 ~tQrEIa~~lGiS~---a----tIsR~sn~lk 80 (94)
T TIGR01321 56 MSQREIASKLGVSI---A----TITRGSNNLK 80 (94)
T ss_pred CCHHHHHHHhCCCh---h----hhhHHHhhcc
Confidence 47789999999843 6 6777777654
No 420
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=25.19 E-value=1.7e+02 Score=21.39 Aligned_cols=46 Identities=15% Similarity=0.122 Sum_probs=30.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC-CCcccceechHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ-NDQERSYVATNA 56 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~-~~~~~~y~~T~~ 56 (128)
+|-.||-+-=|+ .-+.+++.|...|+..+....+ .|.+-.|+.|+.
T Consensus 102 ITr~eIe~IRGv----------~s~~~l~~L~ergLI~~~Gr~~~~Grp~ly~TT~~ 148 (186)
T TIGR00281 102 ITRARINEIRGV----------KSYQIVDDLVEKGLVVELGRKDTPGRSFIYETTPK 148 (186)
T ss_pred cCHHHHHHHcCC----------CHHHHHHHHHHCCCeEecCcCCCCCCCeeehhhHH
Confidence 455677776666 2357899999999998874322 222345777664
No 421
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=25.14 E-value=1.4e+02 Score=20.20 Aligned_cols=47 Identities=13% Similarity=-0.023 Sum_probs=37.4
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL 61 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~ 61 (128)
+..+||..++-+. . .+..-|-+|...|+....+ ++.|..+...+..-
T Consensus 55 ~~e~LA~~~~~~~---~----~V~~AL~~f~k~glIe~~e------d~~i~i~~~~~~~g 101 (121)
T PF09681_consen 55 TAEMLALEFDRPV---D----TVRLALAVFQKLGLIEIDE------DGVIYIPNWEKHQG 101 (121)
T ss_pred cHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEec------CCeEEeecHHHHhC
Confidence 5788999988743 7 8999999999999998765 47788887766553
No 422
>COG0140 HisI Phosphoribosyl-ATP pyrophosphohydrolase [Amino acid transport and metabolism]
Probab=24.89 E-value=72 Score=20.82 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=16.4
Q ss_pred hhhhhHHHHHHHHHhcCcc
Q 045905 19 YVAQYVYRFMWILVHSGFF 37 (128)
Q Consensus 19 ~~~~~L~RlLR~L~~~gvf 37 (128)
+.||++|.+|-.|+..||=
T Consensus 58 E~ADLlYH~lVlL~~~gv~ 76 (92)
T COG0140 58 EAADLLYHLLVLLAAQGLS 76 (92)
T ss_pred HHHHHHHHHHHHHHHcCCC
Confidence 5788999999999998863
No 423
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=24.85 E-value=93 Score=23.80 Aligned_cols=49 Identities=27% Similarity=0.192 Sum_probs=33.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.+ + .+.|-++.|= ..-+|.... .+...+|+.|+.|...
T Consensus 18 s~s~AA~~L~iSQ---~----avSr~I~~LE~~lg~~LF~R~~------~~~~~lT~~G~~l~~~ 69 (316)
T PRK12679 18 NLTEVANMLFTSQ---S----GVSRHIRELEDELGIEIFIRRG------KRLLGMTEPGKALLVI 69 (316)
T ss_pred CHHHHHHHhcCCc---h----HHHHHHHHHHHHhCCEEEEECC------CcccccCHhHHHHHHH
Confidence 5677789999855 5 6666666554 344776553 2336999999988643
No 424
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=24.85 E-value=81 Score=23.23 Aligned_cols=14 Identities=21% Similarity=0.344 Sum_probs=12.1
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
.|..|||+.+|+++
T Consensus 166 ~s~~EIAe~lgis~ 179 (231)
T PRK11922 166 LSVEETAQALGLPE 179 (231)
T ss_pred CCHHHHHHHHCcCH
Confidence 47899999999965
No 425
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=24.84 E-value=85 Score=23.29 Aligned_cols=29 Identities=17% Similarity=0.111 Sum_probs=20.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
.|..|||+++++++ .-+...+.|+|+-|-
T Consensus 149 kTnKEIAe~L~IS~---rTVkth~srImkKLg 177 (198)
T PRK15201 149 YHLSETAALLSLSE---EQTKSLRRSIMRKLH 177 (198)
T ss_pred CCHHHHHHHhCCCH---HHHHHHHHHHHHHhC
Confidence 47889999999955 434446777777654
No 426
>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=24.80 E-value=24 Score=25.20 Aligned_cols=22 Identities=23% Similarity=0.395 Sum_probs=0.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+|..|||..+|+++ . -+.|+++
T Consensus 50 Lt~~~iA~~lgl~~---S----TVSRav~ 71 (160)
T PF04552_consen 50 LTMKDIADELGLHE---S----TVSRAVK 71 (160)
T ss_dssp -----------------------------
T ss_pred CCHHHHHHHhCCCH---h----HHHHHHc
Confidence 47889999999976 6 6777766
No 427
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=24.55 E-value=57 Score=24.73 Aligned_cols=22 Identities=14% Similarity=0.078 Sum_probs=16.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
||+.|||+.+|++. . -+.|+|.
T Consensus 1 ~ti~dIA~~aGVS~---~----TVSrvLn 22 (328)
T PRK11303 1 MKLDEIARLAGVSR---T----TASYVIN 22 (328)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHc
Confidence 68999999999943 5 5666664
No 428
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=24.33 E-value=81 Score=23.73 Aligned_cols=48 Identities=10% Similarity=0.158 Sum_probs=35.1
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.. + .+.|-++.|= ...+|.... +.+.+|+.|+.|.+.
T Consensus 21 s~s~AA~~L~isQ---~----avS~~i~~LE~~lG~~LF~R~~-------r~~~lT~~G~~l~~~ 71 (302)
T PRK09791 21 SIRGASRMLNMSQ---P----ALTKSIQELEEGLAAQLFFRRS-------KGVTLTDAGESFYQH 71 (302)
T ss_pred CHHHHHHHhCCCh---H----HHHHHHHHHHHHhCCeEEEEcC-------CCceECccHHHHHHH
Confidence 5667789999844 6 6777777664 445787653 679999999998753
No 429
>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=24.20 E-value=95 Score=19.42 Aligned_cols=25 Identities=8% Similarity=-0.165 Sum_probs=16.4
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+|+.|||..+|.+. .+. .+.+.|+.
T Consensus 20 ~TYg~iA~~~g~p~-~~R----aVg~al~~ 44 (80)
T TIGR00589 20 KSYGQLAARIGNPK-AVR----AVGGANGR 44 (80)
T ss_pred CCHHHHHHHhCCCC-hHH----HHHHHHHh
Confidence 58999999999633 233 45555544
No 430
>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=24.13 E-value=40 Score=18.44 Aligned_cols=8 Identities=13% Similarity=0.198 Sum_probs=5.3
Q ss_pred HHHHhCCC
Q 045905 5 ELINALPF 12 (128)
Q Consensus 5 eLA~~~~~ 12 (128)
|||+++|+
T Consensus 2 ~lA~~~gv 9 (52)
T cd01392 2 DIARAAGV 9 (52)
T ss_pred cHHHHHCc
Confidence 56666666
No 431
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=24.09 E-value=88 Score=21.82 Aligned_cols=29 Identities=17% Similarity=0.099 Sum_probs=18.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|..|||+.+|++. ..+...+.|.++-|-
T Consensus 22 lTq~EIAe~LgiS~---stV~~~e~ra~kkLr 50 (137)
T TIGR00721 22 LSQKEIAKELKTTR---ANVSAIEKRAMENIE 50 (137)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHHhHHHHHH
Confidence 47899999999954 523334445555443
No 432
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=23.99 E-value=96 Score=20.04 Aligned_cols=42 Identities=5% Similarity=0.095 Sum_probs=29.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA 56 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~ 56 (128)
+++.|+|+.+|+++ |-+|+=-..|++.... .+ +.+.|.-..+
T Consensus 1 m~Ige~a~~~gvs~-----------~tlRyYe~~GLl~p~~--~~-g~r~Y~~~~~ 42 (107)
T cd04777 1 MKIGKFAKKNNITI-----------DTVRHYIDLGLLIPEK--KG-GQYFFDEKCQ 42 (107)
T ss_pred CCHHHHHHHHCcCH-----------HHHHHHHHCCCcCCcc--CC-CccccCHHHH
Confidence 57899999999943 5699999999996432 11 1345655544
No 433
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.92 E-value=99 Score=21.81 Aligned_cols=29 Identities=17% Similarity=0.036 Sum_probs=18.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
++++|||+.+|+++ ..+-..|.|.++.|-
T Consensus 123 ~~~~EIA~~lgis~---~tV~~~l~Rar~~Lr 151 (181)
T PRK09637 123 LSQKEIAEKLGLSL---SGAKSRVQRGRVKLK 151 (181)
T ss_pred CCHHHHHHHhCCCH---HHHHHHHHHHHHHHH
Confidence 47899999999965 311123555544443
No 434
>KOG3789 consensus Nitrogen permease regulator NLRG/NPR2 [Inorganic ion transport and metabolism]
Probab=23.61 E-value=51 Score=26.90 Aligned_cols=53 Identities=19% Similarity=0.203 Sum_probs=39.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+.+||+..++ ++. ++.|-+|.|.-.|+++-...-+ -...|.+|+.-+-|..+
T Consensus 219 sV~rIa~lanv---d~~----lv~~Ci~nl~YYgcVtL~~Ifq--ysNiY~~T~~v~~ll~d 271 (396)
T KOG3789|consen 219 SVQRIAALANV---DPS----LVARCIRNLLYYGCVTLVDIFQ--YSNIYAPTENVHNLLQD 271 (396)
T ss_pred HHHHHHHHhcC---CHH----HHHHHHHhhHhhhhhhhhhHHh--hhhhcccccchhhhhcC
Confidence 56789998888 558 9999999999999887654211 02479988888777655
No 435
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=23.42 E-value=75 Score=24.59 Aligned_cols=55 Identities=15% Similarity=0.043 Sum_probs=36.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSF 71 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~ 71 (128)
+|+++||+.+++++ . .|.|+++......+-.-- ..+++..+..+|... ..++...
T Consensus 235 ~sl~~lA~~~~~S~---~----~l~r~fk~~~g~s~~~~~--------~~~Rl~~A~~lL~~~-~~~i~~I 289 (322)
T PRK09393 235 HTVASLAARAAMSP---R----TFLRRFEAATGMTPAEWL--------LRERLARARDLLESS-ALSIDQI 289 (322)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHHHCcCHHHHH--------HHHHHHHHHHHHHcC-CCCHHHH
Confidence 47899999999954 7 899999876654443222 346677776677653 2334444
No 436
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=23.42 E-value=1.2e+02 Score=23.16 Aligned_cols=48 Identities=19% Similarity=0.169 Sum_probs=34.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.. + .|.|-|+-|= ..-+|.... +.+.+|+.|+.|.+.
T Consensus 18 s~s~AA~~L~iSQ---p----avS~~I~~LE~~lg~~Lf~R~~-------r~~~lT~~G~~l~~~ 68 (308)
T PRK10094 18 SFSKAAERLCKTT---A----TISYRIKLLEENTGVALFFRTT-------RSVTLTAAGEHLLSQ 68 (308)
T ss_pred CHHHHHHHhcCCH---H----HHHHHHHHHHHHhCCEEEeeCC-------CceeECHhHHHHHHH
Confidence 5677899999843 6 6777777664 234776553 679999999998653
No 437
>PRK10632 transcriptional regulator; Provisional
Probab=23.33 E-value=90 Score=23.73 Aligned_cols=48 Identities=13% Similarity=0.159 Sum_probs=34.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.. + .+.|-++.|= ..-+|.... +.+.+|+.|+.|...
T Consensus 18 S~t~AA~~L~isQ---p----avS~~I~~LE~~lg~~Lf~R~~-------r~i~lT~~G~~l~~~ 68 (309)
T PRK10632 18 SFTAAARQLQMSV---S----SISQTVSKLEDELQVKLLNRST-------RSIGLTEAGRIYYQG 68 (309)
T ss_pred CHHHHHHHhCCCH---H----HHHHHHHHHHHHhCCeeecccC-------CCceechhHHHHHHH
Confidence 5677789999844 5 6666666554 344776553 679999999998753
No 438
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=23.29 E-value=86 Score=23.62 Aligned_cols=29 Identities=14% Similarity=0.211 Sum_probs=18.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
+|..|||+.+|++... +-..|+|.++.|-
T Consensus 178 ~S~~EIA~~Lgis~~T---Vk~rl~RAr~~Lr 206 (244)
T TIGR03001 178 LSMDRIGAMYQVHRST---VSRWVAQARERLL 206 (244)
T ss_pred CCHHHHHHHHCcCHHH---HHHHHHHHHHHHH
Confidence 4889999999996531 1224555555544
No 439
>PF13309 HTH_22: HTH domain
Probab=23.27 E-value=43 Score=19.95 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=14.7
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
+++.+|+++|+.. . .+||-||
T Consensus 44 av~~vA~~L~iS~---~----TVY~YLr 64 (64)
T PF13309_consen 44 AVEYVAEKLGISR---A----TVYRYLR 64 (64)
T ss_pred HHHHHHHHHCCCH---H----HHHHHcC
Confidence 3567888888843 6 6777664
No 440
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=23.01 E-value=96 Score=23.57 Aligned_cols=48 Identities=15% Similarity=0.186 Sum_probs=35.0
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.. + .+.|-|+.|= ...+|.... +.+.+|+.|+.|.+.
T Consensus 23 s~s~AA~~L~iSQ---p----avS~~I~~LE~~lg~~LF~R~~-------r~~~lT~~G~~l~~~ 73 (312)
T PRK10341 23 SIGSAAKELGLTQ---P----AVSKIINDIEDYFGVELIVRKN-------TGVTLTPAGQVLLSR 73 (312)
T ss_pred CHHHHHHHhCCCh---H----HHHHHHHHHHHHhCCeEEEEcC-------CCceEChhHHHHHHH
Confidence 5677889999944 5 6777776664 334776553 679999999998753
No 441
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.98 E-value=62 Score=22.49 Aligned_cols=14 Identities=14% Similarity=0.157 Sum_probs=11.2
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|+.+||+++|+++
T Consensus 31 ~ti~~Ia~~agvs~ 44 (194)
T PRK09480 31 ITTAKLAARVGVSE 44 (194)
T ss_pred cCHHHHHHHhCCCH
Confidence 47889999999843
No 442
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=22.93 E-value=1.1e+02 Score=19.71 Aligned_cols=52 Identities=8% Similarity=0.133 Sum_probs=33.3
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhc
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLK 62 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~ 62 (128)
|+..-|+.+++.+ + .+.|-++.|= ..-+|....... ..+.+.+|+.|+.|..
T Consensus 18 Sis~AA~~L~iS~---s----tvs~~I~~LE~~lg~~Lf~R~~~g~--~~~g~~lT~~G~~l~~ 72 (99)
T TIGR00637 18 SISQAAKDAGISY---K----SAWDYIRAMNNLSGEPLVERATGGK--GGGGAVLTEYGQRLIQ 72 (99)
T ss_pred CHHHHHHHHCCCH---H----HHHHHHHHHHHHhCCCeEEecCCCC--CCCCeeECHHHHHHHH
Confidence 5667788999954 5 6666666654 334676543100 1257999999998863
No 443
>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=22.89 E-value=1.1e+02 Score=17.63 Aligned_cols=13 Identities=38% Similarity=0.537 Sum_probs=10.8
Q ss_pred CCHHHHHHhCCCC
Q 045905 1 MTLNELINALPFH 13 (128)
Q Consensus 1 ~S~~eLA~~~~~~ 13 (128)
+|+.|||.++++.
T Consensus 20 ~~~~ela~~l~~S 32 (59)
T PF08280_consen 20 ITLKELAKKLNIS 32 (59)
T ss_dssp BBHHHHHHHCTS-
T ss_pred CcHHHHHHHHCCC
Confidence 4789999999993
No 444
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=22.83 E-value=1.3e+02 Score=21.95 Aligned_cols=48 Identities=19% Similarity=0.153 Sum_probs=33.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.. + .+.|-++.|= ..-+|.... +.+.+|+.|+.|...
T Consensus 13 s~~~AA~~L~isq---s----avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~ 63 (279)
T TIGR03339 13 SFTRAAERLGLSQ---P----TVTDQVRKLEERYGVELFHRNG-------RRLELTDAGHRLLPI 63 (279)
T ss_pred CHHHHHHHhcCCc---h----HHHHHHHHHHHHhCCccEEEcC-------CeEEEChhHHHHHHH
Confidence 5667788899844 5 5666666553 334777653 679999999988753
No 445
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=22.79 E-value=1.7e+02 Score=23.60 Aligned_cols=60 Identities=10% Similarity=0.232 Sum_probs=43.4
Q ss_pred HHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcChhhHHHHHhHHHhhhcCC
Q 045905 25 YRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95 (128)
Q Consensus 25 ~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~~~~~~~~~~l~~~~~~g~ 95 (128)
.-++--|...|++.... +.+.+|+.|+.|++- +...+..+.+|.+..-|+..-+-|..|.
T Consensus 304 a~iI~~L~~r~Yi~~~~-------k~l~pT~~G~~li~~----l~~~~~~l~~p~lTa~~E~~L~~I~~G~ 363 (381)
T cd00186 304 ASIIETLLDRGYVEKEK-------KKLIPTELGFAVIEL----LEKHFPELVDPEFTAKLEEKLDEIAEGK 363 (381)
T ss_pred HHHHHHHHhCCcEEeeC-------CEEeECHHHHHHHHH----HHHhchhccCHhHHHHHHHHHHHHHcCC
Confidence 34556666778886543 579999999999864 3233234678999999998888888775
No 446
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=22.72 E-value=1.1e+02 Score=23.03 Aligned_cols=48 Identities=13% Similarity=0.104 Sum_probs=34.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHH---hcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILV---HSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~---~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
|+..-|+++++.+ + .+.|-++.|= ..-+|.... +.+.+|+.|+.|.+.
T Consensus 17 S~s~AA~~L~itQ---p----avS~~i~~LE~~lg~~LF~R~~-------r~~~lT~~G~~l~~~ 67 (305)
T PRK11151 17 HFRRAADSCHVSQ---P----TLSGQIRKLEDELGVMLLERTS-------RKVLFTQAGLLLVDQ 67 (305)
T ss_pred CHHHHHHHhCCCc---h----HHHHHHHHHHHHhCchheeeCC-------CceeECccHHHHHHH
Confidence 5667789999854 5 6666666654 345786653 679999999988754
No 447
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=22.67 E-value=64 Score=22.77 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=16.8
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMW 29 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR 29 (128)
|.+|||+.+|+++ . .|||-..
T Consensus 36 T~~eiAee~Gis~---~----tLYrWr~ 56 (142)
T PF13022_consen 36 TQAEIAEEVGISR---S----TLYRWRQ 56 (142)
T ss_dssp -HHHHHHHHTS-H---H----HHHHHHH
T ss_pred hHHHHHHHhCCCH---H----HHHHHHh
Confidence 7899999999944 7 8999886
No 448
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=22.66 E-value=88 Score=23.94 Aligned_cols=28 Identities=21% Similarity=0.162 Sum_probs=17.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
+|+.|||+.+|+++ .-+-+.+.|-++.|
T Consensus 243 ~s~~EIA~~Lgis~---~tVk~~l~rAlkkL 270 (285)
T TIGR02394 243 ATLEEVAAEVGLTR---ERVRQIQVEALKKL 270 (285)
T ss_pred ccHHHHHHHHCCCH---HHHHHHHHHHHHHH
Confidence 48899999999965 42223444444443
No 449
>PRK15044 transcriptional regulator SirC; Provisional
Probab=22.56 E-value=73 Score=25.19 Aligned_cols=55 Identities=15% Similarity=0.021 Sum_probs=33.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFL 72 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~ 72 (128)
+|++|||+.+++++ . .|.|.++.- ..+ |.+- -..+++..+.++|..+. .++....
T Consensus 209 ~SLeeLA~~lgmS~---~----tL~R~Fk~e-g~T-~~~y-------~~~~RL~~A~~LL~~t~-~sIseIA 263 (295)
T PRK15044 209 WSQAEVAGKLFMSV---S----SLKRKLAAE-EVS-FSKI-------YLDARMNQAIKLLRMGA-GNISQVA 263 (295)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHHHHc-CCC-HHHH-------HHHHHHHHHHHHHHcCC-CCHHHHH
Confidence 47899999999955 7 899998862 111 1111 12467777777776542 2344443
No 450
>PF08820 DUF1803: Domain of unknown function (DUF1803); InterPro: IPR014924 This small protein is found in one or two copies in bacteria. The function of this is unknown.
Probab=22.43 E-value=85 Score=20.52 Aligned_cols=25 Identities=20% Similarity=0.428 Sum_probs=21.1
Q ss_pred hHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905 23 YVYRFMWILVHSGFFAQQNFGQNDQERSYVAT 54 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T 54 (128)
.++|++..|+..|.... + +++|.++
T Consensus 43 ~~D~fie~li~~GYI~r-e------~krY~L~ 67 (93)
T PF08820_consen 43 RLDIFIEALIKLGYIER-E------EKRYYLN 67 (93)
T ss_pred chhHHHHHHHHcCCeEe-c------CCEEEEe
Confidence 78899999999999987 3 4788876
No 451
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=22.30 E-value=70 Score=24.88 Aligned_cols=55 Identities=11% Similarity=0.144 Sum_probs=34.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFL 72 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~ 72 (128)
+|+++||..+++++ . .|.|+.+.. |. +-.+- -..+++..+..+|... ..++....
T Consensus 159 lsl~~lA~~~g~S~---~----~L~R~Fk~~---G~-S~~~y-----l~~~Rl~~A~~LL~~t-~~sI~eIA 213 (274)
T PRK09978 159 WTLARIASELLMSP---S----LLKKKLREE---ET-SYSQL-----LTECRMQRALQLIVIH-GFSIKRVA 213 (274)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHhc---CC-CHHHH-----HHHHHHHHHHHHHHcC-CCCHHHHH
Confidence 48899999999955 7 888988742 31 10000 1246788888888753 23455443
No 452
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=22.10 E-value=73 Score=22.66 Aligned_cols=14 Identities=29% Similarity=0.377 Sum_probs=11.8
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|++|||+++|++.
T Consensus 32 ~ti~~Ia~~agvsk 45 (213)
T PRK09975 32 TTLNDIADAANVTR 45 (213)
T ss_pred CCHHHHHHHcCCCH
Confidence 58999999999843
No 453
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=22.03 E-value=1.6e+02 Score=24.31 Aligned_cols=30 Identities=17% Similarity=0.259 Sum_probs=24.2
Q ss_pred HHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 27 FMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 27 lLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
.|+.|...|++..+. +++.+|+.|+++.+.
T Consensus 404 ~l~~l~~~gll~~~~-------~~~~lT~~G~~~~d~ 433 (453)
T PRK09249 404 RLAPLEADGLVELDE-------NGITVTPKGRLLVRN 433 (453)
T ss_pred HHHHHHHCCCEEEEC-------CEEEECccchHHHHH
Confidence 367888899998764 679999999998754
No 454
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=21.86 E-value=1.3e+02 Score=16.80 Aligned_cols=29 Identities=14% Similarity=0.053 Sum_probs=17.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILV 32 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~ 32 (128)
.|..|||..+++++ .-+-..+.++++-|-
T Consensus 20 ~s~~eia~~l~is~---~tV~~h~~~i~~Kl~ 48 (65)
T COG2771 20 KSNKEIARILGISE---ETVKTHLRNIYRKLG 48 (65)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHC
Confidence 36789999999855 422224555555543
No 455
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=21.84 E-value=84 Score=19.42 Aligned_cols=23 Identities=17% Similarity=0.284 Sum_probs=17.5
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWI 30 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~ 30 (128)
+.+.|+++.+|+ ..+ .+||+|.-
T Consensus 14 lrl~ev~~~~Gl---Srs----tiYr~i~~ 36 (70)
T COG3311 14 LRLPEVAQLTGL---SRS----TIYRLIKD 36 (70)
T ss_pred hhHHHHHHHHCc---cHH----HHHHHHcc
Confidence 357889999998 446 78888864
No 456
>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=21.78 E-value=96 Score=17.54 Aligned_cols=28 Identities=25% Similarity=0.216 Sum_probs=16.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL 31 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L 31 (128)
.|..|||..+++.+ .-+-..+.+|++-|
T Consensus 19 ~~~~eIA~~l~is~---~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 19 MSNKEIAEELGISE---KTVKSHRRRIMKKL 46 (58)
T ss_dssp S-HHHHHHHHTSHH---HHHHHHHHHHHHHH
T ss_pred CCcchhHHhcCcch---hhHHHHHHHHHHHh
Confidence 36789999999944 41222355555543
No 457
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=21.62 E-value=97 Score=23.99 Aligned_cols=30 Identities=7% Similarity=0.053 Sum_probs=21.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVH 33 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~ 33 (128)
+|+.|||+.+|+++ ..+-..|+|..+.|-.
T Consensus 135 ~s~~EIA~~Lgis~---~tVr~~l~RAr~~Lr~ 164 (290)
T PRK09635 135 LPYQQIATTIGSQA---STCRQLAHRARRKINE 164 (290)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHHHHHHHHHh
Confidence 47899999999965 4333457777777765
No 458
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=21.48 E-value=1e+02 Score=23.56 Aligned_cols=30 Identities=17% Similarity=0.024 Sum_probs=20.7
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHh
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVH 33 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~ 33 (128)
+|+.|||+.+|+++ ..+-..|.|..+.|-.
T Consensus 125 ~s~~EIA~~lg~s~---~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 125 YPYEEIASIVGKSE---ANCRQLVSRARRHLDA 154 (281)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHHHHHHHHHh
Confidence 47899999999955 3233356676666654
No 459
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=21.43 E-value=76 Score=24.38 Aligned_cols=54 Identities=11% Similarity=0.071 Sum_probs=32.6
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFL 72 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~ 72 (128)
+|+++||+.+++++ . .|.|+++.. ...+-.- -...+...+.++|..+. ++....
T Consensus 151 ~tl~~LA~~~gmS~---s----~l~R~FK~~-G~T~~ey--------l~~~Rl~~A~~LL~~~~--sI~eIA 204 (253)
T PRK09940 151 WKLKDICDCLYISE---S----LLKKKLKQE-QTTFSQI--------LLDARMQHAKNLIRVEG--SVNKIA 204 (253)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHHc-CCCHHHH--------HHHHHHHHHHHHHccCC--CHHHHH
Confidence 58999999999955 7 888888862 2111110 12356666667666432 454443
No 460
>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=21.42 E-value=90 Score=19.38 Aligned_cols=18 Identities=6% Similarity=0.078 Sum_probs=15.5
Q ss_pred hHHHHHHHHHhcCcceee
Q 045905 23 YVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~ 40 (128)
+|+||.|.+...|+=-..
T Consensus 13 LL~~i~~~l~~~~l~i~~ 30 (75)
T cd04896 13 LLYDILRTSKDCNIQISY 30 (75)
T ss_pred HHHHHHHHHHHCCeEEEE
Confidence 999999999999976543
No 461
>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=21.41 E-value=95 Score=19.08 Aligned_cols=19 Identities=5% Similarity=0.093 Sum_probs=16.5
Q ss_pred hHHHHHHHHHhcCcceeec
Q 045905 23 YVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~~ 41 (128)
+|++|.|.|...|+--...
T Consensus 14 LL~~i~~~l~~~gl~I~~A 32 (72)
T cd04895 14 ILLEAVQVLTDLDLCITKA 32 (72)
T ss_pred HHHHHHHHHHHCCcEEEEE
Confidence 9999999999999876554
No 462
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=21.40 E-value=68 Score=21.55 Aligned_cols=13 Identities=31% Similarity=0.202 Sum_probs=10.3
Q ss_pred CCHHHHHHhCCCC
Q 045905 1 MTLNELINALPFH 13 (128)
Q Consensus 1 ~S~~eLA~~~~~~ 13 (128)
+|..|||.++|++
T Consensus 19 lsq~eLA~~~Gis 31 (120)
T PRK13890 19 MTKKELSERSGVS 31 (120)
T ss_pred CCHHHHHHHHCcC
Confidence 4778899998873
No 463
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=21.37 E-value=99 Score=21.25 Aligned_cols=31 Identities=23% Similarity=0.378 Sum_probs=23.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
||.+|||..+|. ..+ -+.|-.| ..|-=++..
T Consensus 1 MT~eELA~~tG~---srQ----TINrWvR---kegW~T~p~ 31 (122)
T PF07037_consen 1 MTPEELAELTGY---SRQ----TINRWVR---KEGWKTEPK 31 (122)
T ss_pred CCHHHHHHHhCc---cHH----HHHHHHH---hcCceeccC
Confidence 789999999998 335 7888887 456655554
No 464
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=21.15 E-value=1.7e+02 Score=24.09 Aligned_cols=30 Identities=17% Similarity=0.367 Sum_probs=23.9
Q ss_pred HHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905 27 FMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 27 lLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|+.|...|++..+. +++.+|+.|++|.+.
T Consensus 404 ~l~~l~~~gll~~~~-------~~~~lT~~G~~~~~~ 433 (455)
T TIGR00538 404 LLKPLEEDGLLDVDE-------KGIEVTPKGRLLIRN 433 (455)
T ss_pred HHHHHHhCCCEEEEC-------CEEEECcCChHHHHH
Confidence 467778899988653 679999999998754
No 465
>PRK15185 transcriptional regulator HilD; Provisional
Probab=21.13 E-value=78 Score=25.18 Aligned_cols=57 Identities=16% Similarity=0.051 Sum_probs=34.0
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQA 74 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~ 74 (128)
+|+++||+.+++++ . .|.|.++. ....+-.-- ...+...+.++|..+. .++......
T Consensus 223 ~SledLA~~lgmS~---~----tL~R~FK~-~G~S~~~yl--------~~~Ri~~A~~LL~~t~-~sIseIA~~ 279 (309)
T PRK15185 223 WKLTDVADHIFMST---S----TLKRKLAE-EGTSFSDIY--------LSARMNQAAKLLRIGN-HNVNAVALK 279 (309)
T ss_pred CCHHHHHHHHCcCH---H----HHHHHHHH-cCCCHHHHH--------HHHHHHHHHHHHHcCC-CCHHHHHHH
Confidence 48899999999955 7 88888774 222121111 2366666667776543 245544333
No 466
>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=21.12 E-value=64 Score=24.46 Aligned_cols=53 Identities=9% Similarity=-0.006 Sum_probs=29.8
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccC---CCCcccceechHhhhhhhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG---QNDQERSYVATNASKLLLKD 63 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~---~~~~~~~y~~T~~s~~L~~~ 63 (128)
+|+.|||+.+|+.+ . -+.|+|+- .+-+++.... +--++-.|.++...+.|...
T Consensus 2 ~ti~dIA~~agvS~---~----TVSrvLn~---~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~ 57 (329)
T TIGR01481 2 VTIYDVAREAGVSM---A----TVSRVVNG---NPNVKPATRKKVLEVIKRLDYRPNAVARGLASK 57 (329)
T ss_pred CcHHHHHHHhCCCH---H----HHHHHhCC---CCCCCHHHHHHHHHHHHHHCCCCCHHHHHHhhC
Confidence 48899999999944 5 66676653 2222222110 00002247777777777643
No 467
>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=21.10 E-value=78 Score=19.96 Aligned_cols=21 Identities=14% Similarity=0.086 Sum_probs=15.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHH
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFM 28 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlL 28 (128)
+|+.+||+.+|+.. . .+.|.|
T Consensus 20 ~ti~dvA~~~gvS~---~----TVsr~L 40 (80)
T TIGR02844 20 ATVRETAKVFGVSK---S----TVHKDV 40 (80)
T ss_pred CCHHHHHHHhCCCH---H----HHHHHh
Confidence 47889999999843 5 566644
No 468
>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=21.07 E-value=1.3e+02 Score=17.74 Aligned_cols=16 Identities=6% Similarity=0.052 Sum_probs=11.2
Q ss_pred hHHHHHHHHHhcCcce
Q 045905 23 YVYRFMWILVHSGFFA 38 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~ 38 (128)
..-.++|+|++.+.+.
T Consensus 61 ~~L~~l~~LiA~k~i~ 76 (79)
T PF08721_consen 61 TALPLLRHLIATKRIK 76 (79)
T ss_dssp HHHHHHHHHHHTTSEE
T ss_pred ChHHHHHHHHhCChhc
Confidence 5557778888777654
No 469
>COG1983 PspC Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]
Probab=20.87 E-value=1.1e+02 Score=18.94 Aligned_cols=24 Identities=17% Similarity=0.336 Sum_probs=17.6
Q ss_pred HHHHHhCCCCCCCchhhhhhHHHHHHHHHhcC
Q 045905 4 NELINALPFHPIKAQYVAQYVYRFMWILVHSG 35 (128)
Q Consensus 4 ~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~g 35 (128)
.-||+..+++| .|-|+++.|....
T Consensus 19 gGla~yf~id~--------tlVRll~vl~~~~ 42 (70)
T COG1983 19 GGLAEYFGIDP--------TLVRLLFVLLTLF 42 (70)
T ss_pred hhHHHHhCCCh--------HHHHHHHHHHHHH
Confidence 45889999965 5778888877543
No 470
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=20.81 E-value=94 Score=22.70 Aligned_cols=28 Identities=18% Similarity=0.174 Sum_probs=22.1
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcC
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSG 35 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~g 35 (128)
+|..|||+.+|++| . .++|=|+.|-..|
T Consensus 33 vs~~~L~~~~~v~~---~----tirrDl~~l~~~G 60 (213)
T PRK05472 33 VSSKELAEALGVDS---A----QIRKDLSYFGEFG 60 (213)
T ss_pred EeHHHHHHHhCcCH---H----HHHHHHHHHHhcC
Confidence 47899999999954 6 8888888875554
No 471
>COG1485 Predicted ATPase [General function prediction only]
Probab=20.57 E-value=88 Score=25.54 Aligned_cols=18 Identities=17% Similarity=0.159 Sum_probs=15.8
Q ss_pred hHHHHHHHHHhcCcceee
Q 045905 23 YVYRFMWILVHSGFFAQQ 40 (128)
Q Consensus 23 ~L~RlLR~L~~~gvf~e~ 40 (128)
.|.|||..|...||+--.
T Consensus 149 iL~rL~~~Lf~~GV~lva 166 (367)
T COG1485 149 ILGRLLEALFARGVVLVA 166 (367)
T ss_pred HHHHHHHHHHHCCcEEEE
Confidence 899999999999987543
No 472
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=20.38 E-value=74 Score=18.80 Aligned_cols=14 Identities=7% Similarity=0.261 Sum_probs=8.8
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|+.|+|..+.+++
T Consensus 11 lsl~~va~~t~I~~ 24 (62)
T PF13413_consen 11 LSLEDVAEETKISV 24 (62)
T ss_dssp --HHHHHHHCS--H
T ss_pred CCHHHHHHHhCCCH
Confidence 58899999999843
No 473
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=20.36 E-value=1.5e+02 Score=20.42 Aligned_cols=34 Identities=21% Similarity=0.295 Sum_probs=27.9
Q ss_pred CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905 1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN 41 (128)
Q Consensus 1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~ 41 (128)
+|-.+||..+|+.. . .+.|+|.-|...|++....
T Consensus 172 ~~~~~ia~~~g~~~---~----~vsr~l~~l~~~g~i~~~~ 205 (214)
T COG0664 172 LTHKDLAEYLGLSR---E----TVSRILKELRKDGLISVRG 205 (214)
T ss_pred CCHHHHHHHhCCch---h----hHHHHHHHHHhCCcEeeCC
Confidence 46678999998844 6 8999999999999987553
No 474
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=20.35 E-value=82 Score=22.56 Aligned_cols=14 Identities=21% Similarity=0.441 Sum_probs=11.8
Q ss_pred CCHHHHHHhCCCCC
Q 045905 1 MTLNELINALPFHP 14 (128)
Q Consensus 1 ~S~~eLA~~~~~~~ 14 (128)
+|+.+||++.|+++
T Consensus 33 ~si~~IA~~Agvs~ 46 (203)
T PRK11202 33 LSLREVAREAGIAP 46 (203)
T ss_pred CCHHHHHHHhCCCc
Confidence 58899999999844
No 475
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=20.30 E-value=1.9e+02 Score=23.41 Aligned_cols=49 Identities=10% Similarity=0.148 Sum_probs=33.5
Q ss_pred CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccc-eechH-hhhhhhcC
Q 045905 2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERS-YVATN-ASKLLLKD 63 (128)
Q Consensus 2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~-y~~T~-~s~~L~~~ 63 (128)
+.+++.++.|.+. .. .+...+..|...|++..+. ++ +.+|+ .|.+|.+.
T Consensus 337 ~~~~~~~~~g~~~--~~----~~~~~l~~l~~~gll~~~~-------~~~~~lT~~~G~~~~~~ 387 (400)
T PRK07379 337 SLSALTERFGKEI--VE----QILQCLQPYFQQGWVELEG-------DRRLRLTDPEGFLFSNT 387 (400)
T ss_pred CHHHHHHHHCCCH--HH----HHHHHHHHHHHCCCEEEeC-------CeEEEECchHHhHHHHH
Confidence 3456666666521 02 4566778888999988654 56 99995 89988765
No 476
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=20.21 E-value=2.2e+02 Score=25.86 Aligned_cols=60 Identities=13% Similarity=0.220 Sum_probs=43.6
Q ss_pred HHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcChhhHHHHHhHHHhhhcCC
Q 045905 26 RFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95 (128)
Q Consensus 26 RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~~~~~~~~~~l~~~~~~g~ 95 (128)
-|+.-|...|++.... .+++.+|++|+.|++- +...+.-+++|.+...|+.--+-|..|.
T Consensus 601 sIIetL~~R~YV~~~~------kkrl~PT~lG~~Li~~----L~~~fp~lv~p~~TA~~E~~Ld~Ia~G~ 660 (805)
T PTZ00407 601 MIVKTLLARGYIAVNP------KGRCETTPVGRMLVET----AKSTFPSIVDIGFTAAFEKKLDRIAKPG 660 (805)
T ss_pred HHHHHHHhcCCEEecc------CceeeecHHHHHHHHH----HHHhhhhhcChHHHHHHHHHHHHHHcCC
Confidence 3456666677675441 2579999999999854 4444455788999999998888888774
Done!