Query 040869
Match_columns 131
No_of_seqs 210 out of 1015
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 12:38:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040869.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040869hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3178 Hydroxyindole-O-methyl 99.6 9.9E-16 2.1E-20 119.5 8.2 116 11-131 2-120 (342)
2 TIGR02716 C20_methyl_CrtF C-20 99.5 6.3E-15 1.4E-19 114.0 5.7 71 28-108 3-73 (306)
3 PF08100 Dimerisation: Dimeris 99.5 3.2E-14 6.9E-19 82.9 3.9 49 30-78 1-51 (51)
4 PF09339 HTH_IclR: IclR helix- 98.4 1.3E-07 2.8E-12 55.0 2.2 46 38-86 6-51 (52)
5 smart00346 HTH_ICLR helix_turn 98.2 2.9E-06 6.3E-11 54.1 5.1 58 38-101 8-65 (91)
6 TIGR02431 pcaR_pcaU beta-ketoa 98.1 3.6E-06 7.8E-11 63.4 4.7 59 38-104 12-70 (248)
7 COG1414 IclR Transcriptional r 98.1 4.6E-06 1E-10 63.1 5.1 59 38-102 7-65 (246)
8 PRK11569 transcriptional repre 98.1 4.2E-06 9.2E-11 64.1 4.8 61 38-104 31-91 (274)
9 PRK10163 DNA-binding transcrip 98.1 5.8E-06 1.3E-10 63.3 5.2 61 38-104 28-88 (271)
10 PRK09834 DNA-binding transcrip 98.0 1.1E-05 2.4E-10 61.4 4.9 61 38-104 14-74 (263)
11 PRK15090 DNA-binding transcrip 98.0 1.3E-05 2.8E-10 60.7 4.9 60 38-104 17-76 (257)
12 PF12840 HTH_20: Helix-turn-he 97.7 6.3E-05 1.4E-09 44.9 3.8 55 29-87 4-58 (61)
13 smart00550 Zalpha Z-DNA-bindin 97.7 0.00017 3.7E-09 44.1 5.7 60 35-99 6-66 (68)
14 PF13463 HTH_27: Winged helix 97.5 0.00015 3.2E-09 43.6 4.0 60 39-101 7-68 (68)
15 cd07153 Fur_like Ferric uptake 97.5 0.00026 5.6E-09 47.1 5.3 62 37-98 3-66 (116)
16 PF01978 TrmB: Sugar-specific 97.4 0.00014 3.1E-09 44.1 2.3 47 37-87 10-56 (68)
17 cd00092 HTH_CRP helix_turn_hel 97.3 0.00041 8.9E-09 41.4 4.2 45 48-99 23-67 (67)
18 PRK10141 DNA-binding transcrip 97.3 0.00059 1.3E-08 46.2 5.1 65 27-99 8-75 (117)
19 PF02082 Rrf2: Transcriptional 97.3 0.00053 1.2E-08 43.3 4.4 47 49-100 24-70 (83)
20 PF13412 HTH_24: Winged helix- 97.3 0.00058 1.3E-08 38.6 4.1 45 36-84 4-48 (48)
21 COG3355 Predicted transcriptio 97.2 0.00079 1.7E-08 46.1 4.9 50 37-89 29-78 (126)
22 smart00419 HTH_CRP helix_turn_ 97.2 0.00065 1.4E-08 37.9 3.9 41 49-97 7-47 (48)
23 PF01022 HTH_5: Bacterial regu 97.2 0.00044 9.5E-09 39.1 3.1 44 36-84 3-46 (47)
24 PRK10857 DNA-binding transcrip 97.2 0.001 2.2E-08 47.5 5.5 47 48-99 23-69 (164)
25 TIGR02944 suf_reg_Xantho FeS a 97.1 0.0026 5.7E-08 43.3 6.4 47 48-99 23-69 (130)
26 PF14947 HTH_45: Winged helix- 97.0 0.00071 1.5E-08 42.3 3.2 57 40-106 11-67 (77)
27 TIGR02010 IscR iron-sulfur clu 97.0 0.0017 3.7E-08 44.7 5.3 48 48-100 23-70 (135)
28 smart00347 HTH_MARR helix_turn 97.0 0.0015 3.3E-08 41.5 4.5 68 36-107 11-80 (101)
29 PF08461 HTH_12: Ribonuclease 97.0 0.0015 3.3E-08 39.7 4.1 59 40-102 3-63 (66)
30 TIGR00738 rrf2_super rrf2 fami 97.0 0.0018 4E-08 44.0 4.9 49 48-101 23-71 (132)
31 PF04703 FaeA: FaeA-like prote 96.9 0.0012 2.6E-08 39.8 3.4 46 39-87 4-49 (62)
32 PF12802 MarR_2: MarR family; 96.9 0.0015 3.3E-08 38.4 3.7 48 37-87 7-55 (62)
33 PRK03902 manganese transport t 96.9 0.0019 4E-08 44.8 4.6 52 47-105 19-70 (142)
34 TIGR02337 HpaR homoprotocatech 96.8 0.0037 7.9E-08 41.8 5.1 69 35-107 28-98 (118)
35 TIGR00122 birA_repr_reg BirA b 96.7 0.0043 9.3E-08 37.7 4.8 59 37-104 2-60 (69)
36 TIGR02702 SufR_cyano iron-sulf 96.7 0.0038 8.3E-08 45.7 5.4 65 37-105 3-71 (203)
37 PRK11050 manganese transport r 96.7 0.0039 8.4E-08 43.9 5.0 59 39-105 41-99 (152)
38 PF09012 FeoC: FeoC like trans 96.7 0.0026 5.6E-08 38.8 3.5 45 39-87 4-48 (69)
39 PF08279 HTH_11: HTH domain; 96.7 0.0042 9E-08 35.9 4.2 42 38-82 3-44 (55)
40 COG4190 Predicted transcriptio 96.7 0.0043 9.3E-08 42.8 4.8 58 26-87 55-112 (144)
41 PHA00738 putative HTH transcri 96.7 0.0048 1E-07 41.1 4.9 62 36-102 13-74 (108)
42 PRK06474 hypothetical protein; 96.7 0.0039 8.5E-08 45.1 4.9 73 29-104 5-82 (178)
43 PF07381 DUF1495: Winged helix 96.6 0.0053 1.2E-07 39.7 4.9 69 34-105 8-87 (90)
44 smart00420 HTH_DEOR helix_turn 96.6 0.0056 1.2E-07 34.4 4.6 44 40-87 5-48 (53)
45 PF08220 HTH_DeoR: DeoR-like h 96.6 0.0053 1.1E-07 36.1 4.4 45 39-87 4-48 (57)
46 COG1959 Predicted transcriptio 96.5 0.0057 1.2E-07 43.1 5.0 47 49-100 24-70 (150)
47 PF13601 HTH_34: Winged helix 96.5 0.0024 5.2E-08 40.3 2.6 64 36-103 1-67 (80)
48 smart00529 HTH_DTXR Helix-turn 96.5 0.0042 9E-08 39.8 3.6 46 53-105 2-47 (96)
49 PF01726 LexA_DNA_bind: LexA D 96.4 0.0059 1.3E-07 37.1 4.0 41 45-87 20-60 (65)
50 smart00344 HTH_ASNC helix_turn 96.4 0.0061 1.3E-07 39.9 4.3 47 36-86 4-50 (108)
51 PRK11014 transcriptional repre 96.4 0.0083 1.8E-07 41.5 5.1 47 48-99 23-69 (141)
52 TIGR01884 cas_HTH CRISPR locus 96.4 0.0074 1.6E-07 44.2 5.1 59 36-100 144-202 (203)
53 PF01475 FUR: Ferric uptake re 96.4 0.0042 9.2E-08 41.6 3.3 66 34-99 7-74 (120)
54 cd00090 HTH_ARSR Arsenical Res 96.4 0.0097 2.1E-07 35.4 4.6 57 37-99 9-65 (78)
55 PF04967 HTH_10: HTH DNA bindi 96.3 0.0069 1.5E-07 35.4 3.7 43 28-77 5-47 (53)
56 smart00418 HTH_ARSR helix_turn 96.3 0.013 2.7E-07 33.9 5.0 43 40-87 2-44 (66)
57 TIGR01610 phage_O_Nterm phage 96.3 0.013 2.7E-07 38.1 5.2 45 48-98 45-89 (95)
58 COG0735 Fur Fe2+/Zn2+ uptake r 96.3 0.0091 2E-07 41.7 4.7 66 35-100 21-88 (145)
59 PRK09462 fur ferric uptake reg 96.3 0.012 2.7E-07 41.0 5.3 65 34-98 16-83 (148)
60 COG4742 Predicted transcriptio 96.2 0.0072 1.6E-07 46.3 4.3 67 31-107 9-75 (260)
61 PRK03573 transcriptional regul 96.2 0.011 2.3E-07 40.8 4.9 65 40-107 36-102 (144)
62 COG2345 Predicted transcriptio 96.2 0.011 2.4E-07 44.1 5.2 61 39-103 15-79 (218)
63 COG1321 TroR Mn-dependent tran 96.2 0.01 2.2E-07 42.0 4.5 53 47-106 21-73 (154)
64 PRK11639 zinc uptake transcrip 96.1 0.013 2.8E-07 42.0 5.0 54 34-87 25-80 (169)
65 PF01047 MarR: MarR family; I 96.1 0.0054 1.2E-07 35.8 2.5 47 37-87 5-51 (59)
66 PRK11512 DNA-binding transcrip 96.1 0.013 2.9E-07 40.4 4.9 66 38-107 43-110 (144)
67 TIGR01889 Staph_reg_Sar staphy 96.0 0.012 2.7E-07 38.8 4.3 67 36-105 26-97 (109)
68 smart00345 HTH_GNTR helix_turn 96.0 0.01 2.2E-07 34.2 3.4 37 48-87 17-54 (60)
69 PRK11920 rirA iron-responsive 96.0 0.017 3.8E-07 40.7 5.0 47 48-99 22-68 (153)
70 cd07377 WHTH_GntR Winged helix 95.9 0.026 5.7E-07 33.0 4.8 34 51-87 26-59 (66)
71 PF06163 DUF977: Bacterial pro 95.9 0.026 5.7E-07 38.6 5.2 51 33-87 10-60 (127)
72 PF03444 HrcA_DNA-bdg: Winged 95.8 0.028 6E-07 35.4 4.8 50 47-102 20-70 (78)
73 PF01325 Fe_dep_repress: Iron 95.8 0.023 5E-07 33.8 4.2 38 47-87 19-56 (60)
74 PF01638 HxlR: HxlR-like helix 95.6 0.014 3E-07 37.3 3.1 61 40-105 10-73 (90)
75 PRK06266 transcription initiat 95.5 0.065 1.4E-06 38.8 6.5 45 38-86 25-69 (178)
76 PF00325 Crp: Bacterial regula 95.4 0.016 3.5E-07 30.3 2.3 31 50-83 2-32 (32)
77 PRK11179 DNA-binding transcrip 95.4 0.032 6.8E-07 39.1 4.5 47 36-86 10-56 (153)
78 COG2512 Predicted membrane-ass 95.3 0.023 5E-07 43.5 3.9 48 37-87 197-244 (258)
79 PRK11169 leucine-responsive tr 95.2 0.032 6.8E-07 39.6 4.1 47 35-85 14-60 (164)
80 COG1522 Lrp Transcriptional re 95.0 0.048 1E-06 37.7 4.5 49 35-87 8-56 (154)
81 PF14394 DUF4423: Domain of un 95.0 0.11 2.3E-06 37.4 6.4 63 25-102 22-86 (171)
82 PF04182 B-block_TFIIIC: B-blo 95.0 0.04 8.7E-07 34.1 3.6 50 35-87 2-52 (75)
83 PRK10870 transcriptional repre 94.9 0.051 1.1E-06 39.0 4.5 67 38-107 58-127 (176)
84 TIGR00498 lexA SOS regulatory 94.9 0.063 1.4E-06 39.0 5.0 49 36-87 7-60 (199)
85 COG3432 Predicted transcriptio 94.9 0.017 3.6E-07 37.7 1.7 60 40-106 20-83 (95)
86 COG4189 Predicted transcriptio 94.8 0.09 1.9E-06 39.9 5.5 73 28-104 16-90 (308)
87 PF02796 HTH_7: Helix-turn-hel 94.7 0.035 7.5E-07 31.0 2.6 23 50-75 21-43 (45)
88 PRK04214 rbn ribonuclease BN/u 94.4 0.089 1.9E-06 42.7 5.1 45 47-98 307-351 (412)
89 COG1378 Predicted transcriptio 94.3 0.083 1.8E-06 40.2 4.6 52 49-105 29-80 (247)
90 PRK11886 bifunctional biotin-- 94.3 0.096 2.1E-06 40.9 5.1 56 37-100 6-62 (319)
91 PRK13509 transcriptional repre 94.3 0.088 1.9E-06 39.9 4.6 47 37-87 7-53 (251)
92 TIGR02787 codY_Gpos GTP-sensin 94.2 0.39 8.5E-06 36.5 7.8 46 39-87 187-232 (251)
93 PRK04172 pheS phenylalanyl-tRN 94.2 0.073 1.6E-06 44.1 4.3 68 36-109 7-75 (489)
94 PRK14165 winged helix-turn-hel 94.1 0.081 1.8E-06 39.5 4.1 54 49-106 20-73 (217)
95 PF13404 HTH_AsnC-type: AsnC-t 93.9 0.11 2.4E-06 28.7 3.4 37 36-76 4-40 (42)
96 PRK05638 threonine synthase; V 93.9 0.1 2.2E-06 42.7 4.6 63 37-104 373-437 (442)
97 TIGR00373 conserved hypothetic 93.9 0.11 2.3E-06 36.9 4.2 45 38-86 17-61 (158)
98 PF13545 HTH_Crp_2: Crp-like h 93.9 0.081 1.8E-06 32.2 3.1 36 49-87 27-62 (76)
99 COG4565 CitB Response regulato 93.8 0.12 2.6E-06 38.6 4.3 45 39-86 162-206 (224)
100 PRK10906 DNA-binding transcrip 93.8 0.11 2.3E-06 39.5 4.3 47 37-87 7-53 (252)
101 PF09929 DUF2161: Uncharacteri 93.6 0.17 3.6E-06 34.3 4.5 52 40-102 64-115 (118)
102 TIGR02698 CopY_TcrY copper tra 93.5 0.22 4.7E-06 34.1 5.0 48 36-87 5-56 (130)
103 PF05732 RepL: Firmicute plasm 93.4 0.11 2.4E-06 37.2 3.6 46 50-102 75-120 (165)
104 PF00392 GntR: Bacterial regul 93.4 0.11 2.3E-06 30.9 3.0 37 48-87 21-58 (64)
105 PF08784 RPA_C: Replication pr 93.4 0.11 2.3E-06 33.9 3.2 48 36-86 48-98 (102)
106 PRK09802 DNA-binding transcrip 93.2 0.15 3.2E-06 39.1 4.3 48 36-87 18-65 (269)
107 PRK10411 DNA-binding transcrip 93.1 0.21 4.6E-06 37.6 4.9 47 37-87 6-52 (240)
108 PRK13777 transcriptional regul 93.0 1 2.2E-05 32.8 8.2 64 39-106 49-114 (185)
109 COG1349 GlpR Transcriptional r 93.0 0.17 3.7E-06 38.4 4.2 46 38-87 8-53 (253)
110 COG1497 Predicted transcriptio 93.0 0.12 2.6E-06 39.3 3.3 74 38-119 13-87 (260)
111 PLN02853 Probable phenylalanyl 92.9 0.15 3.3E-06 42.4 4.2 70 35-109 3-73 (492)
112 COG3413 Predicted DNA binding 92.9 0.1 2.2E-06 38.5 3.0 43 27-76 159-201 (215)
113 COG1846 MarR Transcriptional r 92.7 0.19 4E-06 32.7 3.7 70 34-107 21-92 (126)
114 PHA02943 hypothetical protein; 92.6 0.31 6.8E-06 34.5 4.8 45 38-87 14-58 (165)
115 PRK10434 srlR DNA-bindng trans 92.6 0.19 4.2E-06 38.1 4.1 47 37-87 7-53 (256)
116 PF13730 HTH_36: Helix-turn-he 92.6 0.15 3.3E-06 29.1 2.8 30 51-83 26-55 (55)
117 COG5631 Predicted transcriptio 92.5 1.4 3E-05 31.7 8.0 78 22-102 63-147 (199)
118 PTZ00326 phenylalanyl-tRNA syn 92.4 0.22 4.8E-06 41.5 4.5 70 35-109 6-76 (494)
119 PRK00215 LexA repressor; Valid 92.3 0.39 8.5E-06 34.9 5.3 40 46-87 19-58 (205)
120 TIGR02147 Fsuc_second hypothet 92.2 0.66 1.4E-05 35.8 6.6 46 49-101 136-183 (271)
121 PF02002 TFIIE_alpha: TFIIE al 92.1 0.15 3.3E-06 33.3 2.6 44 39-86 17-60 (105)
122 COG1733 Predicted transcriptio 92.0 0.6 1.3E-05 31.6 5.5 78 14-105 11-91 (120)
123 PRK10046 dpiA two-component re 91.9 0.33 7.2E-06 35.5 4.6 45 39-86 166-210 (225)
124 PF12324 HTH_15: Helix-turn-he 91.8 0.21 4.6E-06 31.3 2.9 35 40-78 29-63 (77)
125 PRK01381 Trp operon repressor; 91.8 0.29 6.3E-06 32.2 3.6 42 34-80 41-82 (99)
126 PRK15431 ferrous iron transpor 91.4 0.47 1E-05 29.8 4.2 44 40-87 7-50 (78)
127 PF13384 HTH_23: Homeodomain-l 91.3 0.17 3.7E-06 28.3 1.9 41 36-82 6-46 (50)
128 PRK09954 putative kinase; Prov 90.9 0.49 1.1E-05 37.3 4.8 44 37-84 5-48 (362)
129 PF01371 Trp_repressor: Trp re 90.8 0.5 1.1E-05 30.3 3.9 41 33-79 34-75 (87)
130 PF10007 DUF2250: Uncharacteri 90.8 0.62 1.4E-05 30.2 4.4 48 36-87 8-55 (92)
131 PRK12423 LexA repressor; Provi 90.6 0.64 1.4E-05 34.0 5.0 38 48-87 23-60 (202)
132 PF13936 HTH_38: Helix-turn-he 90.6 0.34 7.3E-06 26.8 2.7 24 49-75 19-42 (44)
133 TIGR01321 TrpR trp operon repr 90.4 0.48 1E-05 30.9 3.6 41 34-79 41-81 (94)
134 PF08221 HTH_9: RNA polymerase 90.3 0.45 9.8E-06 28.4 3.2 43 40-86 18-60 (62)
135 PF03965 Penicillinase_R: Peni 90.2 0.38 8.3E-06 31.9 3.2 51 36-87 4-55 (115)
136 PF13518 HTH_28: Helix-turn-he 90.2 0.67 1.4E-05 25.8 3.8 38 39-82 4-41 (52)
137 PF07789 DUF1627: Protein of u 90.2 0.6 1.3E-05 32.9 4.2 47 48-98 4-50 (155)
138 PRK04424 fatty acid biosynthes 90.0 0.26 5.6E-06 35.7 2.4 45 38-86 10-54 (185)
139 PF03374 ANT: Phage antirepres 89.8 0.85 1.8E-05 29.9 4.6 44 37-86 11-54 (111)
140 TIGR00635 ruvB Holliday juncti 89.7 0.45 9.7E-06 36.4 3.6 37 48-87 253-290 (305)
141 PRK09334 30S ribosomal protein 89.6 0.45 9.8E-06 30.5 3.0 36 49-87 40-75 (86)
142 PRK00082 hrcA heat-inducible t 89.5 0.79 1.7E-05 36.4 4.9 49 47-101 22-72 (339)
143 PF12793 SgrR_N: Sugar transpo 89.4 0.48 1E-05 31.9 3.2 37 48-87 17-53 (115)
144 COG1510 Predicted transcriptio 89.4 0.42 9E-06 34.5 3.0 36 48-86 39-74 (177)
145 PRK13239 alkylmercury lyase; P 89.4 0.53 1.1E-05 34.9 3.6 41 36-80 23-63 (206)
146 TIGR03697 NtcA_cyano global ni 89.3 0.54 1.2E-05 33.2 3.6 36 49-87 142-177 (193)
147 PRK11642 exoribonuclease R; Pr 88.8 0.88 1.9E-05 40.2 5.2 56 39-98 23-79 (813)
148 PRK11753 DNA-binding transcrip 88.7 0.72 1.6E-05 33.1 4.0 35 50-87 168-202 (211)
149 PRK11161 fumarate/nitrate redu 88.7 0.61 1.3E-05 34.2 3.6 35 50-87 184-218 (235)
150 PRK09775 putative DNA-binding 88.7 0.9 2E-05 37.4 4.9 53 40-100 5-57 (442)
151 PRK11534 DNA-binding transcrip 88.6 0.86 1.9E-05 33.4 4.3 37 48-87 28-64 (224)
152 PF02319 E2F_TDP: E2F/DP famil 88.4 0.18 4E-06 30.9 0.5 39 48-87 22-63 (71)
153 PRK09391 fixK transcriptional 88.3 0.7 1.5E-05 34.1 3.8 34 50-86 179-212 (230)
154 TIGR00331 hrcA heat shock gene 88.1 1 2.2E-05 35.7 4.7 41 43-87 15-57 (337)
155 PF05584 Sulfolobus_pRN: Sulfo 88.0 1.5 3.1E-05 27.2 4.3 44 38-86 8-51 (72)
156 PF03297 Ribosomal_S25: S25 ri 88.0 0.63 1.4E-05 30.9 2.9 36 49-87 58-93 (105)
157 TIGR03433 padR_acidobact trans 87.8 1.3 2.9E-05 28.6 4.4 69 37-107 6-83 (100)
158 TIGR03338 phnR_burk phosphonat 87.7 0.93 2E-05 32.9 4.0 37 48-87 32-68 (212)
159 PF03428 RP-C: Replication pro 87.7 0.9 2E-05 32.9 3.8 57 28-87 45-105 (177)
160 TIGR02531 yecD_yerC TrpR-relat 87.6 0.91 2E-05 29.1 3.4 35 38-78 41-75 (88)
161 PF00126 HTH_1: Bacterial regu 87.6 0.98 2.1E-05 26.4 3.3 55 37-102 3-60 (60)
162 PF00165 HTH_AraC: Bacterial r 87.5 0.75 1.6E-05 24.8 2.6 28 49-79 7-34 (42)
163 PF01418 HTH_6: Helix-turn-hel 87.5 0.64 1.4E-05 28.7 2.6 31 49-82 33-63 (77)
164 COG3682 Predicted transcriptio 87.4 1.3 2.7E-05 30.3 4.2 62 35-100 6-68 (123)
165 COG1725 Predicted transcriptio 87.2 1 2.2E-05 30.8 3.7 45 49-99 34-78 (125)
166 COG4901 Ribosomal protein S25 87.1 0.77 1.7E-05 30.3 2.9 46 39-87 45-93 (107)
167 PRK13918 CRP/FNR family transc 87.0 0.83 1.8E-05 32.6 3.4 35 49-86 148-182 (202)
168 COG1802 GntR Transcriptional r 86.8 1.3 2.8E-05 32.7 4.4 37 48-87 37-73 (230)
169 COG1675 TFA1 Transcription ini 86.7 1.3 2.8E-05 32.1 4.1 45 38-86 21-65 (176)
170 PF03551 PadR: Transcriptional 86.3 0.79 1.7E-05 28.0 2.5 60 41-102 2-70 (75)
171 PF08280 HTH_Mga: M protein tr 86.2 0.85 1.8E-05 26.7 2.6 40 35-78 5-44 (59)
172 COG2524 Predicted transcriptio 86.0 1.9 4.2E-05 33.3 5.0 55 46-105 21-76 (294)
173 TIGR03879 near_KaiC_dom probab 85.5 0.75 1.6E-05 28.5 2.1 34 49-85 31-64 (73)
174 KOG2165 Anaphase-promoting com 85.0 1.4 3E-05 38.2 4.1 50 48-100 614-663 (765)
175 PRK10430 DNA-binding transcrip 85.0 1.3 2.9E-05 32.5 3.7 35 49-86 177-211 (239)
176 PF05331 DUF742: Protein of un 84.9 1.7 3.7E-05 29.2 3.8 42 40-87 48-89 (114)
177 COG2188 PhnF Transcriptional r 84.8 1.3 2.8E-05 33.1 3.6 43 51-99 32-74 (236)
178 PRK11414 colanic acid/biofilm 84.6 2 4.2E-05 31.5 4.4 37 48-87 32-68 (221)
179 PF13542 HTH_Tnp_ISL3: Helix-t 84.5 2.1 4.5E-05 23.9 3.6 35 37-77 17-51 (52)
180 PRK00135 scpB segregation and 84.5 2.7 5.9E-05 30.7 5.0 57 38-101 93-152 (188)
181 PHA02701 ORF020 dsRNA-binding 84.3 2.2 4.7E-05 31.1 4.4 47 36-85 5-51 (183)
182 PRK14096 pgi glucose-6-phospha 84.3 1.9 4.2E-05 36.3 4.7 42 38-80 466-507 (528)
183 smart00421 HTH_LUXR helix_turn 84.1 2.2 4.7E-05 23.6 3.6 26 49-77 17-42 (58)
184 PF10668 Phage_terminase: Phag 84.0 1.6 3.5E-05 26.0 3.0 29 41-72 13-41 (60)
185 PRK10736 hypothetical protein; 83.8 2.1 4.6E-05 34.6 4.6 51 39-98 312-362 (374)
186 PF00356 LacI: Bacterial regul 83.7 0.88 1.9E-05 25.6 1.7 21 52-75 1-21 (46)
187 TIGR01764 excise DNA binding d 83.5 1.3 2.8E-05 24.0 2.4 22 51-75 2-23 (49)
188 PF14338 Mrr_N: Mrr N-terminal 83.4 6.1 0.00013 25.0 5.9 56 50-109 34-92 (92)
189 TIGR02719 repress_PhaQ poly-be 83.4 9.1 0.0002 26.6 7.1 75 29-105 18-99 (138)
190 smart00342 HTH_ARAC helix_turn 83.3 1.6 3.5E-05 26.0 3.0 29 50-81 1-29 (84)
191 TIGR02404 trehalos_R_Bsub treh 83.1 1.8 3.9E-05 32.0 3.7 42 51-98 25-66 (233)
192 PRK10402 DNA-binding transcrip 82.9 1.8 4E-05 31.7 3.7 35 50-87 169-203 (226)
193 COG2378 Predicted transcriptio 82.7 2.4 5.1E-05 33.3 4.3 58 38-100 11-68 (311)
194 PF12728 HTH_17: Helix-turn-he 82.6 1.4 3E-05 24.6 2.3 23 51-76 2-24 (51)
195 PRK00080 ruvB Holliday junctio 82.3 1.5 3.3E-05 34.2 3.2 47 48-102 274-321 (328)
196 COG1654 BirA Biotin operon rep 82.3 3.7 8.1E-05 25.8 4.3 51 48-104 17-67 (79)
197 TIGR02844 spore_III_D sporulat 82.1 2.1 4.6E-05 27.0 3.2 32 38-74 9-40 (80)
198 PF05491 RuvB_C: Holliday junc 82.0 2.3 4.9E-05 26.6 3.2 58 37-102 10-70 (76)
199 COG2390 DeoR Transcriptional r 82.0 1.8 4E-05 34.2 3.5 35 49-86 25-59 (321)
200 PF06971 Put_DNA-bind_N: Putat 81.8 1 2.2E-05 25.8 1.5 32 38-72 15-47 (50)
201 PHA02591 hypothetical protein; 81.8 2.7 5.9E-05 26.4 3.5 32 40-76 51-82 (83)
202 PF13443 HTH_26: Cro/C1-type H 81.8 1.2 2.7E-05 25.8 2.0 31 40-75 2-32 (63)
203 TIGR02325 C_P_lyase_phnF phosp 81.7 2.2 4.7E-05 31.5 3.7 43 51-99 33-75 (238)
204 PRK13558 bacterio-opsin activa 81.6 1.4 3E-05 37.4 2.9 44 27-77 611-654 (665)
205 PF09681 Phage_rep_org_N: N-te 81.5 3 6.4E-05 28.3 4.0 49 49-104 52-100 (121)
206 smart00531 TFIIE Transcription 81.4 2.5 5.4E-05 29.4 3.7 40 39-82 5-44 (147)
207 PF11972 HTH_13: HTH DNA bindi 81.4 3.9 8.5E-05 23.9 3.9 46 40-96 4-49 (54)
208 PRK14999 histidine utilization 81.3 2.5 5.4E-05 31.5 3.9 45 49-99 34-79 (241)
209 PF04545 Sigma70_r4: Sigma-70, 81.2 1.8 3.9E-05 24.1 2.5 26 49-77 19-44 (50)
210 PRK11511 DNA-binding transcrip 81.2 3 6.5E-05 28.1 3.9 33 49-84 24-56 (127)
211 TIGR02018 his_ut_repres histid 80.9 2.5 5.5E-05 31.1 3.8 45 49-99 23-68 (230)
212 PRK10219 DNA-binding transcrip 80.9 3.4 7.3E-05 26.7 4.0 34 48-84 19-52 (107)
213 PF04539 Sigma70_r3: Sigma-70 80.9 1.5 3.2E-05 26.7 2.2 36 48-86 18-53 (78)
214 cd04762 HTH_MerR-trunc Helix-T 80.7 1.9 4E-05 23.1 2.4 23 51-76 1-23 (49)
215 PRK09990 DNA-binding transcrip 80.6 3.1 6.8E-05 31.0 4.3 45 48-98 28-73 (251)
216 PF04492 Phage_rep_O: Bacterio 80.6 2.9 6.2E-05 27.4 3.5 35 49-86 53-87 (100)
217 PF13551 HTH_29: Winged helix- 80.4 2.6 5.6E-05 27.0 3.3 27 52-81 14-40 (112)
218 PRK09464 pdhR transcriptional 80.4 3.1 6.6E-05 31.1 4.1 46 48-99 31-77 (254)
219 PRK10225 DNA-binding transcrip 80.2 3.2 7E-05 31.1 4.2 45 48-98 30-75 (257)
220 PRK04984 fatty acid metabolism 80.1 3.2 6.9E-05 30.6 4.1 45 48-98 28-73 (239)
221 PRK09764 DNA-binding transcrip 80.0 2.7 5.9E-05 31.2 3.8 45 48-98 26-71 (240)
222 PF06969 HemN_C: HemN C-termin 79.9 2.7 5.8E-05 24.7 3.0 46 49-102 19-65 (66)
223 COG0640 ArsR Predicted transcr 79.9 6.5 0.00014 23.9 5.0 55 29-87 19-73 (110)
224 cd06170 LuxR_C_like C-terminal 79.8 3.9 8.5E-05 22.6 3.6 33 39-77 7-39 (57)
225 COG3398 Uncharacterized protei 79.5 14 0.00031 27.9 7.3 53 31-87 97-149 (240)
226 PF08222 HTH_CodY: CodY helix- 79.4 2.7 5.9E-05 24.9 2.8 36 49-87 3-38 (61)
227 PRK10421 DNA-binding transcrip 79.2 3.4 7.4E-05 30.9 4.1 45 48-98 23-68 (253)
228 PRK10681 DNA-binding transcrip 78.7 3.4 7.5E-05 31.2 4.0 41 37-81 9-49 (252)
229 COG2186 FadR Transcriptional r 78.7 3.3 7E-05 31.1 3.8 42 51-98 35-76 (241)
230 TIGR02812 fadR_gamma fatty aci 78.5 3.9 8.4E-05 30.2 4.2 45 48-98 27-72 (235)
231 TIGR02063 RNase_R ribonuclease 78.5 4.6 9.9E-05 35.2 5.1 56 39-98 6-63 (709)
232 PRK11302 DNA-binding transcrip 78.5 2.2 4.8E-05 32.3 2.9 45 36-83 17-64 (284)
233 PF04218 CENP-B_N: CENP-B N-te 78.5 4.7 0.0001 23.1 3.6 35 35-75 10-44 (53)
234 PRK10079 phosphonate metabolis 78.1 4.1 8.9E-05 30.3 4.2 44 50-99 35-78 (241)
235 PRK11402 DNA-binding transcrip 78.0 3.8 8.2E-05 30.4 4.0 44 50-99 33-76 (241)
236 PRK11557 putative DNA-binding 77.9 2.6 5.6E-05 31.9 3.1 43 37-82 14-59 (278)
237 PF00196 GerE: Bacterial regul 77.8 3.4 7.3E-05 23.8 2.9 36 36-77 7-42 (58)
238 PF09821 AAA_assoc_C: C-termin 77.8 2.8 6E-05 28.4 2.9 46 55-108 2-47 (120)
239 PF13814 Replic_Relax: Replica 77.5 3.5 7.5E-05 29.3 3.5 58 49-106 8-71 (191)
240 smart00422 HTH_MERR helix_turn 77.2 3.1 6.8E-05 24.5 2.8 44 51-101 1-45 (70)
241 PRK15418 transcriptional regul 77.0 3.3 7.1E-05 32.6 3.5 35 49-86 28-62 (318)
242 PRK03837 transcriptional regul 76.8 5.3 0.00012 29.4 4.5 45 48-98 34-79 (241)
243 PF00440 TetR_N: Bacterial reg 76.6 2.3 4.9E-05 23.5 1.9 22 49-73 15-36 (47)
244 PF13022 HTH_Tnp_1_2: Helix-tu 75.9 3 6.5E-05 29.2 2.7 31 42-75 26-56 (142)
245 PF07638 Sigma70_ECF: ECF sigm 75.5 3.2 7E-05 29.7 2.9 27 49-78 150-176 (185)
246 COG1737 RpiR Transcriptional r 75.4 2.1 4.5E-05 32.9 2.0 46 36-84 19-67 (281)
247 PRK10094 DNA-binding transcrip 74.9 4.5 9.8E-05 31.0 3.8 60 36-106 5-67 (308)
248 PF13744 HTH_37: Helix-turn-he 74.2 8.7 0.00019 23.7 4.3 30 40-74 23-52 (80)
249 smart00351 PAX Paired Box doma 73.7 6.7 0.00014 26.5 4.0 47 34-86 20-66 (125)
250 PRK11523 DNA-binding transcrip 73.6 6.5 0.00014 29.4 4.3 46 48-99 29-75 (253)
251 PRK13824 replication initiatio 73.3 5 0.00011 32.8 3.8 35 51-88 83-118 (404)
252 PF01381 HTH_3: Helix-turn-hel 73.2 2.9 6.3E-05 23.4 1.8 25 49-76 8-32 (55)
253 TIGR00637 ModE_repress ModE mo 72.9 6.6 0.00014 25.5 3.6 64 37-106 6-72 (99)
254 PRK11337 DNA-binding transcrip 72.8 4 8.6E-05 31.2 3.0 44 37-83 30-76 (292)
255 PRK11062 nhaR transcriptional 72.8 6.8 0.00015 29.6 4.3 60 36-106 7-69 (296)
256 PRK03601 transcriptional regul 72.7 6.2 0.00013 29.6 4.0 60 37-107 5-67 (275)
257 TIGR00475 selB selenocysteine- 72.7 5.7 0.00012 33.8 4.1 56 49-111 487-542 (581)
258 TIGR01714 phage_rep_org_N phag 72.7 8.1 0.00018 26.2 4.1 49 49-104 50-98 (119)
259 COG1695 Predicted transcriptio 72.6 8 0.00017 26.2 4.2 69 35-105 9-86 (138)
260 COG4367 Uncharacterized protei 72.5 4.3 9.2E-05 26.2 2.5 25 49-76 22-46 (97)
261 TIGR02277 PaaX_trns_reg phenyl 72.5 5.2 0.00011 30.9 3.5 58 43-104 10-70 (280)
262 PF05158 RNA_pol_Rpc34: RNA po 72.3 4.4 9.5E-05 32.1 3.2 45 40-87 89-134 (327)
263 PRK09906 DNA-binding transcrip 71.9 6.5 0.00014 29.5 4.0 60 37-107 5-67 (296)
264 PRK09791 putative DNA-binding 71.8 6 0.00013 29.9 3.8 61 36-107 8-71 (302)
265 PF14502 HTH_41: Helix-turn-he 71.8 11 0.00024 21.4 3.9 36 49-87 5-40 (48)
266 cd00131 PAX Paired Box domain 71.4 1.9 4E-05 29.4 0.8 55 26-86 12-66 (128)
267 PF13309 HTH_22: HTH domain 71.2 3.8 8.1E-05 24.5 2.0 38 29-75 27-64 (64)
268 smart00753 PAM PCI/PINT associ 71.2 15 0.00033 22.5 5.0 51 32-86 7-57 (88)
269 smart00088 PINT motif in prote 71.2 15 0.00033 22.5 5.0 51 32-86 7-57 (88)
270 PRK10341 DNA-binding transcrip 71.2 6.2 0.00013 30.1 3.7 61 35-106 9-72 (312)
271 PRK09392 ftrB transcriptional 71.1 4.8 0.0001 29.5 3.0 30 50-82 173-202 (236)
272 PF08281 Sigma70_r4_2: Sigma-7 70.9 4.7 0.0001 22.6 2.3 24 49-75 25-48 (54)
273 PRK11233 nitrogen assimilation 70.7 7.6 0.00016 29.5 4.1 59 37-106 5-66 (305)
274 PF09904 HTH_43: Winged helix- 70.3 7.3 0.00016 25.1 3.3 59 37-100 10-71 (90)
275 PRK10837 putative DNA-binding 70.2 7.8 0.00017 28.9 4.0 59 37-106 7-68 (290)
276 PF14557 AphA_like: Putative A 70.1 11 0.00023 27.3 4.4 68 32-102 8-83 (175)
277 COG3695 Predicted methylated D 70.0 3.6 7.8E-05 27.2 1.8 40 40-80 11-52 (103)
278 smart00354 HTH_LACI helix_turn 69.8 3.9 8.4E-05 24.6 1.9 11 52-62 2-12 (70)
279 PRK15482 transcriptional regul 69.8 5.3 0.00012 30.4 3.1 45 37-84 18-65 (285)
280 PRK04217 hypothetical protein; 69.4 6 0.00013 26.4 2.9 25 49-76 57-81 (110)
281 PF02295 z-alpha: Adenosine de 69.4 2.5 5.4E-05 25.6 0.9 50 36-87 5-54 (66)
282 COG4465 CodY Pleiotropic trans 69.3 20 0.00044 27.1 5.9 44 40-86 194-237 (261)
283 COG4977 Transcriptional regula 69.1 6.4 0.00014 31.3 3.4 31 48-81 234-264 (328)
284 PRK13626 transcriptional regul 69.0 5.2 0.00011 33.6 3.1 37 48-87 21-57 (552)
285 TIGR03339 phn_lysR aminoethylp 68.9 9.2 0.0002 28.2 4.2 59 38-107 2-63 (279)
286 PF07848 PaaX: PaaX-like prote 68.7 5.5 0.00012 24.3 2.4 47 47-100 17-69 (70)
287 PRK05472 redox-sensing transcr 68.3 12 0.00027 27.3 4.7 46 33-81 14-60 (213)
288 TIGR02036 dsdC D-serine deamin 68.1 7.8 0.00017 29.5 3.7 61 36-107 11-74 (302)
289 PF09202 Rio2_N: Rio2, N-termi 68.0 10 0.00023 23.8 3.6 49 49-102 23-71 (82)
290 cd07977 TFIIE_beta_winged_heli 67.9 17 0.00038 22.4 4.6 34 40-76 14-50 (75)
291 COG3398 Uncharacterized protei 67.9 12 0.00027 28.2 4.5 66 32-102 171-236 (240)
292 cd06171 Sigma70_r4 Sigma70, re 67.8 6.9 0.00015 20.9 2.6 26 49-77 25-50 (55)
293 PHA03103 double-strand RNA-bin 67.5 8.9 0.00019 28.0 3.6 44 39-86 17-60 (183)
294 PRK14997 LysR family transcrip 67.4 7.6 0.00016 29.3 3.5 60 36-106 5-67 (301)
295 PRK11074 putative DNA-binding 67.2 8 0.00017 29.3 3.6 59 37-106 6-67 (300)
296 TIGR02424 TF_pcaQ pca operon t 67.1 7.8 0.00017 29.2 3.5 59 37-106 7-68 (300)
297 cd04761 HTH_MerR-SF Helix-Turn 66.9 6.4 0.00014 21.3 2.3 27 51-84 1-27 (49)
298 PRK09986 DNA-binding transcrip 66.7 10 0.00022 28.3 4.0 60 36-106 10-72 (294)
299 PF11994 DUF3489: Protein of u 66.6 24 0.00053 21.8 4.9 56 40-97 15-71 (72)
300 PRK15092 DNA-binding transcrip 66.4 8.8 0.00019 29.5 3.7 60 36-106 14-76 (310)
301 PRK15121 right oriC-binding tr 66.1 10 0.00023 28.9 4.1 31 49-82 20-50 (289)
302 PRK15201 fimbriae regulatory p 66.1 10 0.00022 27.8 3.7 35 34-74 135-169 (198)
303 TIGR03826 YvyF flagellar opero 66.1 11 0.00024 26.2 3.7 34 40-76 35-69 (137)
304 PRK00118 putative DNA-binding 66.0 6.7 0.00015 25.9 2.6 35 49-86 32-74 (104)
305 PRK08558 adenine phosphoribosy 65.9 7.8 0.00017 29.2 3.2 39 34-75 7-45 (238)
306 PRK15411 rcsA colanic acid cap 65.7 9.9 0.00022 27.7 3.7 35 34-74 139-173 (207)
307 PRK13413 mpi multiple promoter 65.7 9.2 0.0002 27.6 3.5 24 49-75 171-194 (200)
308 TIGR03418 chol_sulf_TF putativ 65.2 6.9 0.00015 29.3 2.9 59 37-106 5-66 (291)
309 PRK09416 lstR lineage-specific 64.9 18 0.00039 25.1 4.6 65 37-104 45-114 (135)
310 PRK10632 transcriptional regul 64.7 11 0.00023 28.8 3.9 59 37-106 6-67 (309)
311 PRK11242 DNA-binding transcrip 64.7 11 0.00025 28.1 4.0 59 37-106 5-66 (296)
312 PRK12682 transcriptional regul 64.6 12 0.00025 28.5 4.1 62 37-107 5-69 (309)
313 PHA00542 putative Cro-like pro 64.6 10 0.00022 23.6 3.1 24 49-75 30-53 (82)
314 TIGR03337 phnR transcriptional 64.1 11 0.00023 27.6 3.6 41 52-98 27-67 (231)
315 PF04433 SWIRM: SWIRM domain; 64.1 20 0.00044 22.3 4.5 53 29-84 31-85 (86)
316 COG2344 AT-rich DNA-binding pr 64.1 11 0.00023 28.0 3.5 40 39-81 20-60 (211)
317 CHL00180 rbcR LysR transcripti 63.8 12 0.00026 28.4 3.9 59 36-105 8-69 (305)
318 PF02186 TFIIE_beta: TFIIE bet 63.8 9.8 0.00021 22.9 2.8 33 40-75 10-43 (65)
319 PRK11013 DNA-binding transcrip 63.6 10 0.00022 28.8 3.6 61 36-107 7-70 (309)
320 PF02042 RWP-RK: RWP-RK domain 63.6 9.2 0.0002 22.1 2.5 25 50-77 15-39 (52)
321 PF08535 KorB: KorB domain; I 63.5 5.3 0.00011 25.4 1.7 28 50-80 3-30 (93)
322 PRK10086 DNA-binding transcrip 63.3 11 0.00024 28.8 3.7 61 36-107 17-80 (311)
323 PRK15481 transcriptional regul 62.8 16 0.00034 29.4 4.7 44 48-97 26-70 (431)
324 KOG2578 Transcription factor E 62.7 4.4 9.5E-05 32.0 1.3 36 49-87 43-78 (388)
325 COG3645 Uncharacterized phage- 62.4 11 0.00023 26.2 3.1 43 38-86 35-77 (135)
326 PF10771 DUF2582: Protein of u 62.3 11 0.00025 22.7 2.9 38 40-81 13-50 (65)
327 PF05066 HARE-HTH: HB1, ASXL, 61.8 8.6 0.00019 23.1 2.4 54 41-98 8-70 (72)
328 PF01399 PCI: PCI domain; Int 61.7 19 0.00042 22.4 4.2 52 31-85 41-92 (105)
329 PRK09492 treR trehalose repres 61.7 2.7 5.9E-05 31.8 0.1 23 50-75 4-26 (315)
330 PRK12679 cbl transcriptional r 61.6 14 0.00031 28.2 4.1 61 37-106 5-68 (316)
331 PRK09863 putative frv operon r 61.3 14 0.00031 31.2 4.3 36 37-77 6-41 (584)
332 COG4496 Uncharacterized protei 61.2 14 0.0003 23.9 3.2 39 34-78 43-81 (100)
333 PF04157 EAP30: EAP30/Vps36 fa 61.2 8 0.00017 28.7 2.5 43 39-84 178-221 (223)
334 PRK10572 DNA-binding transcrip 61.1 15 0.00033 27.7 4.1 42 40-84 188-230 (290)
335 PRK10082 cell density-dependen 60.8 15 0.00033 27.8 4.1 60 36-106 14-76 (303)
336 PRK11139 DNA-binding transcrip 60.7 14 0.00031 27.8 3.9 61 36-107 9-72 (297)
337 COG5340 Predicted transcriptio 60.5 8.6 0.00019 29.2 2.5 46 49-101 29-74 (269)
338 TIGR03070 couple_hipB transcri 60.5 9 0.00019 21.2 2.2 24 49-75 14-37 (58)
339 COG2865 Predicted transcriptio 60.3 12 0.00027 31.1 3.7 45 39-87 406-450 (467)
340 PRK08208 coproporphyrinogen II 60.1 13 0.00029 30.2 3.8 51 49-107 360-410 (430)
341 PRK13503 transcriptional activ 60.1 15 0.00034 27.3 4.0 42 40-84 176-218 (278)
342 COG1386 scpB Chromosome segreg 60.0 25 0.00054 25.6 4.8 57 37-100 94-153 (184)
343 PF07106 TBPIP: Tat binding pr 60.0 22 0.00048 25.1 4.5 46 39-87 5-52 (169)
344 PRK15340 transcriptional regul 60.0 30 0.00066 25.8 5.4 43 39-84 113-156 (216)
345 PF01710 HTH_Tnp_IS630: Transp 59.9 14 0.00031 24.6 3.3 33 48-86 69-101 (119)
346 PRK05660 HemN family oxidoredu 59.7 13 0.00028 29.7 3.7 50 49-106 320-369 (378)
347 PRK11151 DNA-binding transcrip 59.5 14 0.00031 27.9 3.7 60 37-107 5-67 (305)
348 TIGR02366 DHAK_reg probable di 59.3 17 0.00036 25.2 3.8 29 40-71 12-41 (176)
349 TIGR02405 trehalos_R_Ecol treh 59.3 3.1 6.8E-05 31.6 0.1 22 51-75 2-23 (311)
350 PF05930 Phage_AlpA: Prophage 59.3 7.3 0.00016 21.9 1.6 22 51-75 4-25 (51)
351 PRK00441 argR arginine repress 59.3 17 0.00037 25.4 3.8 52 39-98 8-64 (149)
352 PRK15421 DNA-binding transcrip 58.9 14 0.00031 28.4 3.6 60 36-106 5-67 (317)
353 COG2169 Ada Adenosine deaminas 58.5 16 0.00035 26.8 3.6 41 41-84 88-128 (187)
354 PRK15466 carboxysome structura 58.4 16 0.00036 26.2 3.5 48 43-98 117-164 (166)
355 PF04552 Sigma54_DBD: Sigma-54 58.3 3.3 7.1E-05 29.5 0.0 24 49-75 48-71 (160)
356 PF06056 Terminase_5: Putative 58.1 10 0.00023 22.2 2.2 24 49-75 12-35 (58)
357 PRK09975 DNA-binding transcrip 58.0 14 0.0003 26.4 3.3 26 44-72 24-50 (213)
358 TIGR03613 RutR pyrimidine util 57.7 12 0.00027 26.4 3.0 27 43-72 20-47 (202)
359 cd04763 HTH_MlrA-like Helix-Tu 57.6 15 0.00032 21.6 2.9 45 51-101 1-45 (68)
360 COG5647 Cullin, a subunit of E 57.5 26 0.00055 30.9 5.1 52 32-87 605-656 (773)
361 PLN03238 probable histone acet 57.5 23 0.00051 27.7 4.5 48 25-87 207-254 (290)
362 TIGR02297 HpaA 4-hydroxyphenyl 57.3 18 0.00039 27.2 3.9 55 42-105 193-248 (287)
363 PRK09508 leuO leucine transcri 57.3 20 0.00044 27.3 4.2 60 36-106 25-87 (314)
364 PF13560 HTH_31: Helix-turn-he 57.1 8.5 0.00018 22.4 1.7 24 49-75 13-36 (64)
365 PRK09801 transcriptional activ 57.0 19 0.00041 27.5 4.1 62 34-106 7-71 (310)
366 PRK15044 transcriptional regul 56.7 28 0.0006 27.3 4.9 37 37-76 194-231 (295)
367 PRK10371 DNA-binding transcrip 56.6 18 0.00039 27.9 3.9 42 40-84 196-238 (302)
368 PF09940 DUF2172: Domain of un 56.5 7.8 0.00017 31.4 1.8 44 38-84 343-386 (386)
369 cd00569 HTH_Hin_like Helix-tur 56.3 10 0.00022 18.0 1.8 21 50-73 21-41 (42)
370 PF10078 DUF2316: Uncharacteri 55.8 13 0.00027 24.0 2.4 25 49-76 22-46 (89)
371 PRK11482 putative DNA-binding 55.7 21 0.00046 27.4 4.2 61 35-106 31-94 (317)
372 TIGR03384 betaine_BetI transcr 55.5 15 0.00033 25.4 3.1 26 43-71 20-46 (189)
373 TIGR00721 tfx DNA-binding prot 55.4 20 0.00043 24.9 3.5 32 37-74 11-42 (137)
374 TIGR03882 cyclo_dehyd_2 bacter 55.3 23 0.00051 25.7 4.1 39 48-87 40-78 (193)
375 PRK15186 AraC family transcrip 55.1 18 0.0004 28.0 3.7 34 40-76 186-220 (291)
376 PRK12684 transcriptional regul 55.0 22 0.00048 27.1 4.2 61 37-106 5-68 (313)
377 PF02387 IncFII_repA: IncFII R 54.9 18 0.00039 28.2 3.5 39 49-87 94-139 (281)
378 PF09286 Pro-kuma_activ: Pro-k 54.9 13 0.00027 25.4 2.5 36 48-86 45-80 (143)
379 PRK09393 ftrA transcriptional 54.9 22 0.00047 27.5 4.1 42 40-84 223-265 (322)
380 COG1339 Transcriptional regula 54.6 25 0.00055 26.1 4.1 53 49-105 18-70 (214)
381 PRK13719 conjugal transfer tra 54.5 20 0.00044 26.8 3.7 43 34-82 145-188 (217)
382 PF08721 Tn7_Tnp_TnsA_C: TnsA 54.4 37 0.0008 20.2 4.4 41 40-84 32-76 (79)
383 PRK13500 transcriptional activ 54.3 23 0.00049 27.4 4.1 57 40-105 211-268 (312)
384 PF07574 SMC_Nse1: Nse1 non-SM 54.2 11 0.00023 27.6 2.1 41 54-101 156-196 (200)
385 PF04760 IF2_N: Translation in 54.1 4.5 9.7E-05 23.0 0.1 29 49-83 2-31 (54)
386 PRK10401 DNA-binding transcrip 53.9 3.3 7.1E-05 31.9 -0.6 22 51-75 2-23 (346)
387 PF14493 HTH_40: Helix-turn-he 53.9 20 0.00043 22.6 3.2 33 49-84 12-45 (91)
388 PRK12683 transcriptional regul 53.7 23 0.0005 27.0 4.1 60 37-106 5-68 (309)
389 PRK04158 transcriptional repre 53.5 26 0.00057 26.9 4.2 45 39-86 190-234 (256)
390 PRK12680 transcriptional regul 53.1 22 0.00047 27.5 3.9 62 36-107 4-69 (327)
391 PF10141 ssDNA-exonuc_C: Singl 52.9 22 0.00047 25.9 3.6 41 52-100 118-158 (195)
392 PHA01976 helix-turn-helix prot 52.9 15 0.00032 21.4 2.3 24 49-75 14-37 (67)
393 PRK09685 DNA-binding transcrip 52.6 15 0.00034 27.8 2.9 35 39-76 201-237 (302)
394 PF09079 Cdc6_C: CDC6, C termi 52.6 21 0.00046 22.0 3.1 36 52-87 24-59 (85)
395 PF03979 Sigma70_r1_1: Sigma-7 52.6 18 0.00039 22.5 2.7 38 48-85 19-56 (82)
396 PF05344 DUF746: Domain of Unk 52.4 29 0.00062 21.0 3.4 29 48-79 11-39 (65)
397 PRK07037 extracytoplasmic-func 52.3 15 0.00033 25.0 2.6 23 49-74 124-146 (163)
398 PF09106 SelB-wing_2: Elongati 52.1 24 0.00051 20.4 3.1 36 49-87 16-54 (59)
399 PRK10512 selenocysteinyl-tRNA- 52.0 41 0.00088 29.0 5.6 44 49-99 505-548 (614)
400 PRK09480 slmA division inhibit 51.9 19 0.00042 25.1 3.2 21 48-71 28-48 (194)
401 PRK09483 response regulator; P 51.7 24 0.00052 24.6 3.7 36 35-76 151-186 (217)
402 COG1309 AcrR Transcriptional r 51.2 23 0.0005 23.4 3.4 23 49-74 31-53 (201)
403 PF02954 HTH_8: Bacterial regu 51.1 32 0.0007 18.4 3.3 31 40-75 10-40 (42)
404 PRK14101 bifunctional glucokin 51.1 16 0.00035 31.3 3.0 43 37-82 358-403 (638)
405 TIGR01529 argR_whole arginine 51.1 32 0.0007 23.9 4.1 56 40-99 6-63 (146)
406 PF00376 MerR: MerR family reg 50.8 9.7 0.00021 20.3 1.1 26 52-84 1-26 (38)
407 PRK09978 DNA-binding transcrip 50.7 24 0.00052 27.3 3.6 35 39-76 146-181 (274)
408 TIGR02985 Sig70_bacteroi1 RNA 50.6 19 0.00042 24.1 2.9 25 49-76 128-152 (161)
409 COG1693 Repressor of nif and g 50.6 24 0.00053 27.7 3.6 50 38-87 9-60 (325)
410 cd04766 HTH_HspR Helix-Turn-He 50.4 24 0.00052 22.2 3.1 44 51-101 2-45 (91)
411 PRK15185 transcriptional regul 50.4 25 0.00053 27.8 3.7 35 39-76 210-245 (309)
412 PRK00767 transcriptional regul 50.3 21 0.00045 25.0 3.1 25 44-71 22-47 (197)
413 PRK10840 transcriptional regul 50.3 26 0.00056 25.0 3.7 32 34-71 152-183 (216)
414 PRK13501 transcriptional activ 50.1 21 0.00046 27.0 3.3 43 40-85 181-224 (290)
415 TIGR02607 antidote_HigA addict 50.0 17 0.00037 21.7 2.3 24 49-75 17-40 (78)
416 PLN00104 MYST -like histone ac 49.8 43 0.00094 27.9 5.2 49 24-87 357-405 (450)
417 COG1405 SUA7 Transcription ini 49.7 46 0.00099 25.9 5.1 34 48-84 155-188 (285)
418 PF12298 Bot1p: Eukaryotic mit 49.6 29 0.00063 25.0 3.7 39 35-78 20-58 (172)
419 PRK13502 transcriptional activ 49.6 30 0.00066 25.9 4.1 58 39-105 180-238 (282)
420 COG4754 Uncharacterized conser 49.5 46 0.001 23.5 4.6 66 35-108 12-78 (157)
421 TIGR02937 sigma70-ECF RNA poly 49.4 21 0.00046 23.2 2.9 25 49-76 125-149 (158)
422 PF05225 HTH_psq: helix-turn-h 49.4 25 0.00055 19.3 2.7 25 50-77 16-40 (45)
423 PF06413 Neugrin: Neugrin; In 49.4 20 0.00043 27.0 2.9 24 49-75 28-51 (225)
424 PRK10216 DNA-binding transcrip 49.2 31 0.00067 26.3 4.1 58 37-105 12-72 (319)
425 cd06445 ATase The DNA repair p 49.2 14 0.0003 22.8 1.8 28 48-76 15-42 (79)
426 cd04780 HTH_MerR-like_sg5 Heli 49.0 20 0.00043 23.0 2.6 44 51-101 1-45 (95)
427 TIGR02395 rpoN_sigma RNA polym 48.9 13 0.00028 30.6 2.0 24 49-75 317-340 (429)
428 PRK08898 coproporphyrinogen II 48.8 22 0.00048 28.6 3.3 50 49-106 337-386 (394)
429 PF13411 MerR_1: MerR HTH fami 48.8 16 0.00035 21.3 2.0 43 52-101 2-44 (69)
430 PRK15435 bifunctional DNA-bind 48.8 31 0.00067 27.6 4.1 27 48-77 97-123 (353)
431 PRK10668 DNA-binding transcrip 48.8 23 0.0005 25.3 3.2 25 44-71 24-49 (215)
432 TIGR00180 parB_part ParB-like 48.8 19 0.00042 25.8 2.8 27 49-78 119-145 (187)
433 PRK09940 transcriptional regul 48.4 25 0.00054 26.9 3.4 34 40-76 139-173 (253)
434 COG0758 Smf Predicted Rossmann 48.1 40 0.00087 27.1 4.6 37 48-87 307-343 (350)
435 PRK13890 conjugal transfer pro 48.1 21 0.00045 23.9 2.7 20 41-62 11-30 (120)
436 cd04775 HTH_Cfa-like Helix-Tur 47.8 24 0.00053 22.7 2.9 44 51-101 2-45 (102)
437 PF05043 Mga: Mga helix-turn-h 47.8 16 0.00035 22.5 2.0 38 37-78 18-55 (87)
438 PF09382 RQC: RQC domain; Int 47.7 19 0.00041 23.0 2.4 42 66-107 55-96 (106)
439 PF00382 TFIIB: Transcription 47.6 49 0.0011 19.6 4.1 28 27-62 39-66 (71)
440 PRK09333 30S ribosomal protein 47.6 59 0.0013 23.0 4.9 54 48-106 65-129 (150)
441 PF07120 DUF1376: Protein of u 47.5 33 0.00071 21.6 3.4 45 47-100 35-81 (88)
442 PF04297 UPF0122: Putative hel 47.4 18 0.0004 23.8 2.2 36 37-77 22-57 (101)
443 PF07037 DUF1323: Putative tra 47.4 19 0.0004 24.5 2.3 22 51-75 1-22 (122)
444 COG3703 ChaC Uncharacterized p 47.1 25 0.00054 25.8 3.1 37 49-85 130-170 (190)
445 PF09107 SelB-wing_3: Elongati 47.0 53 0.0011 18.6 4.0 42 42-87 3-44 (50)
446 cd01104 HTH_MlrA-CarA Helix-Tu 47.0 21 0.00045 20.7 2.3 22 51-75 1-22 (68)
447 PRK14996 TetR family transcrip 47.0 21 0.00045 25.1 2.7 25 44-71 21-46 (192)
448 PRK09726 antitoxin HipB; Provi 46.9 19 0.0004 22.6 2.2 24 49-75 24-47 (88)
449 PRK09751 putative ATP-dependen 46.8 22 0.00048 33.9 3.4 65 48-119 987-1060(1490)
450 PRK10265 chaperone-modulator p 46.8 20 0.00044 23.3 2.4 31 50-87 7-37 (101)
451 PRK09413 IS2 repressor TnpA; R 46.8 38 0.00082 22.5 3.8 31 49-82 28-58 (121)
452 cd04783 HTH_MerR1 Helix-Turn-H 46.8 21 0.00046 23.9 2.6 28 51-85 1-28 (126)
453 cd00592 HTH_MerR-like Helix-Tu 46.5 31 0.00067 21.8 3.2 44 51-101 1-44 (100)
454 COG2207 AraC AraC-type DNA-bin 46.5 30 0.00065 22.0 3.2 32 49-83 35-66 (127)
455 PLN03239 histone acetyltransfe 46.3 80 0.0017 25.4 6.0 52 24-87 264-315 (351)
456 PRK11475 DNA-binding transcrip 46.3 32 0.0007 25.1 3.6 34 34-73 136-169 (207)
457 PRK13756 tetracycline represso 46.0 26 0.00057 25.6 3.1 21 49-72 23-43 (205)
458 cd04764 HTH_MlrA-like_sg1 Heli 45.9 22 0.00049 20.7 2.3 22 51-75 1-22 (67)
459 cd08768 Cdc6_C Winged-helix do 45.9 35 0.00076 20.8 3.3 36 52-87 31-66 (87)
460 PRK00135 scpB segregation and 45.9 35 0.00076 24.9 3.7 29 47-78 16-45 (188)
461 PRK11083 DNA-binding response 45.9 45 0.00098 23.3 4.3 47 34-80 156-209 (228)
462 PF05402 PqqD: Coenzyme PQQ sy 45.6 41 0.0009 19.5 3.5 39 40-84 22-68 (68)
463 COG0664 Crp cAMP-binding prote 45.5 35 0.00075 23.7 3.7 36 49-87 170-205 (214)
464 PRK12681 cysB transcriptional 45.5 36 0.00079 26.2 4.0 61 36-106 4-68 (324)
465 COG3415 Transposase and inacti 45.5 34 0.00075 23.7 3.5 39 40-83 13-51 (138)
466 PF08820 DUF1803: Domain of un 45.4 50 0.0011 21.4 4.0 49 42-99 20-68 (93)
467 PF09269 DUF1967: Domain of un 45.4 18 0.0004 21.8 1.9 32 53-86 18-49 (69)
468 smart00530 HTH_XRE Helix-turn- 45.3 40 0.00087 17.3 3.2 23 49-74 9-31 (56)
469 PRK10130 transcriptional regul 45.2 34 0.00074 27.2 3.9 49 48-105 254-302 (350)
470 COG0583 LysR Transcriptional r 45.1 40 0.00086 24.7 4.1 60 37-107 5-67 (297)
471 PRK05932 RNA polymerase factor 44.9 16 0.00035 30.3 2.0 24 49-75 342-365 (455)
472 PF01498 HTH_Tnp_Tc3_2: Transp 44.8 21 0.00045 21.2 2.1 35 48-86 11-48 (72)
473 PRK15008 HTH-type transcriptio 44.8 27 0.00059 25.1 3.0 26 43-71 30-56 (212)
474 COG2238 RPS19A Ribosomal prote 44.8 52 0.0011 23.1 4.2 55 48-107 65-130 (147)
475 TIGR02392 rpoH_proteo alternat 44.7 22 0.00049 26.9 2.7 25 49-76 235-259 (270)
476 PRK10100 DNA-binding transcrip 44.6 35 0.00076 25.1 3.6 36 34-75 157-192 (216)
477 COG3177 Fic family protein [Fu 44.6 35 0.00075 27.1 3.8 37 48-87 302-338 (348)
478 TIGR02999 Sig-70_X6 RNA polyme 44.4 24 0.00052 24.6 2.7 23 49-74 149-171 (183)
479 cd01392 HTH_LacI Helix-turn-he 44.4 13 0.00028 20.4 1.1 16 67-82 26-41 (52)
480 PRK10651 transcriptional regul 44.3 38 0.00081 23.3 3.7 37 35-77 158-194 (216)
481 PRK09526 lacI lac repressor; R 44.1 19 0.0004 27.5 2.2 24 49-75 4-27 (342)
482 cd04789 HTH_Cfa Helix-Turn-Hel 43.9 28 0.00061 22.5 2.7 44 51-101 2-45 (102)
483 PRK10403 transcriptional regul 43.7 39 0.00085 23.2 3.7 36 36-77 157-192 (215)
484 PRK03975 tfx putative transcri 43.6 36 0.00078 23.7 3.3 23 49-74 20-42 (141)
485 PRK09642 RNA polymerase sigma 43.6 25 0.00054 23.9 2.6 20 49-71 121-140 (160)
486 PRK11303 DNA-binding transcrip 43.5 18 0.00039 27.4 2.0 22 51-75 1-22 (328)
487 COG4567 Response regulator con 43.1 43 0.00092 24.1 3.6 36 24-62 88-123 (182)
488 PF00888 Cullin: Cullin family 42.4 10 0.00022 31.6 0.5 35 48-85 532-566 (588)
489 TIGR00281 segregation and cond 42.0 81 0.0018 23.0 5.1 55 39-100 91-148 (186)
490 PRK13749 transcriptional regul 41.9 27 0.00058 23.6 2.4 46 50-102 3-49 (121)
491 COG2197 CitB Response regulato 41.8 39 0.00085 24.7 3.5 38 34-77 150-191 (211)
492 cd01279 HTH_HspR-like Helix-Tu 41.7 37 0.00079 21.8 3.0 45 51-102 2-46 (98)
493 PRK10703 DNA-binding transcrip 41.7 20 0.00042 27.4 2.0 22 51-75 2-23 (341)
494 PRK11202 DNA-binding transcrip 41.6 44 0.00095 23.9 3.7 26 44-72 25-51 (203)
495 PRK06759 RNA polymerase factor 41.6 29 0.00062 23.4 2.6 23 49-74 121-143 (154)
496 PF00538 Linker_histone: linke 41.5 53 0.0012 19.9 3.6 50 49-98 20-76 (77)
497 TIGR01481 ccpA catabolite cont 41.1 21 0.00045 27.1 2.1 22 51-75 2-23 (329)
498 PRK10014 DNA-binding transcrip 40.9 22 0.00047 27.2 2.1 24 49-75 5-28 (342)
499 PF09743 DUF2042: Uncharacteri 40.9 46 0.00099 25.7 3.9 40 39-81 59-98 (272)
500 PRK08599 coproporphyrinogen II 40.8 38 0.00083 26.9 3.6 50 49-106 317-367 (377)
No 1
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.63 E-value=9.9e-16 Score=119.46 Aligned_cols=116 Identities=28% Similarity=0.334 Sum_probs=97.7
Q ss_pred HHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcC--CCCCCcchHHHHHHHhhcCCceeeccc
Q 040869 11 ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALD--IQPTKTTGLFRLMRLLVHSSCFNKTKV 88 (131)
Q Consensus 11 e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~--~~~~~~~~l~RlLr~L~~~gl~~~~~~ 88 (131)
++......++++++++..++++++|++|||||+|+++++ .+|||..+. .+|++|..+.|+||.|++++++++...
T Consensus 2 ~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~~---p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~~~ 78 (342)
T KOG3178|consen 2 EENEASLRAMRLANGFALPMVLKAACELGVFDILANAGS---PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCRLV 78 (342)
T ss_pred chhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCCC---HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceeeee
Confidence 345566889999999999999999999999999997544 788888777 467789999999999999999998752
Q ss_pred CCCCcceecchhcccccc-CcccChHHhHHhhcCchhhccCCCC
Q 040869 89 NGQEEAYGLTAASTLLIK-DKPYCMSPTVSAFVDPLFVAPFQSL 131 (131)
Q Consensus 89 ~~~~~~y~~t~~s~~L~~-~~~~sl~~~~~~~~~~~~~~~w~~L 131 (131)
. +. .|++||+++++.. ++..|++++++..+++..++.|.+|
T Consensus 79 ~-~~-~Y~~~~~~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l 120 (342)
T KOG3178|consen 79 G-GE-VYSATPVCKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFL 120 (342)
T ss_pred c-ce-eeeccchhhhheecCCCCchhHHHHHhcccchhhhHHHH
Confidence 1 12 8999999997764 3457999999999999999999764
No 2
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=99.55 E-value=6.3e-15 Score=113.96 Aligned_cols=71 Identities=18% Similarity=0.200 Sum_probs=63.9
Q ss_pred HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869 28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
...+|++|++|||||.|++ +|.|++|||+++|+ +++.++|+||+|+++|+|++. +++|++|+.++.+..+
T Consensus 3 ~~~~l~aa~~Lglfd~L~~--gp~t~~eLA~~~~~---~~~~~~~lL~~L~~lgll~~~-----~~~y~~t~~~~~~l~~ 72 (306)
T TIGR02716 3 EFSCMKAAIELDLFSHMAE--GPKDLATLAADTGS---VPPRLEMLLETLRQMRVINLE-----DGKWSLTEFADYMFSP 72 (306)
T ss_pred hHHHHHHHHHcCcHHHHhc--CCCCHHHHHHHcCC---ChHHHHHHHHHHHhCCCeEec-----CCcEecchhHHhhccC
Confidence 4679999999999999984 79999999999999 999999999999999999986 5899999999855544
Q ss_pred c
Q 040869 108 K 108 (131)
Q Consensus 108 ~ 108 (131)
+
T Consensus 73 ~ 73 (306)
T TIGR02716 73 T 73 (306)
T ss_pred C
Confidence 3
No 3
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=99.49 E-value=3.2e-14 Score=82.90 Aligned_cols=49 Identities=53% Similarity=0.852 Sum_probs=42.9
Q ss_pred HHHHHHHHhChHHHHHhCC-CCCCHHHHHhhcC-CCCCCcchHHHHHHHhh
Q 040869 30 MSLKCAIELGIADIIHSHG-RAITLSELVSALD-IQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 30 ~aL~~a~~L~ifd~l~~~~-~~~s~~eLA~~~~-~~~~~~~~l~RlLr~L~ 78 (131)
++|++|++|||||+|+++| +++|++||+.+++ .+|.++..|+|+||+|+
T Consensus 1 MaLk~aveLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~ 51 (51)
T PF08100_consen 1 MALKCAVELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV 51 (51)
T ss_dssp HHHHHHHHTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred CcHHHHHHcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence 5899999999999999876 8999999999999 66667889999999986
No 4
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=98.43 E-value=1.3e-07 Score=54.96 Aligned_cols=46 Identities=28% Similarity=0.491 Sum_probs=41.3
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
+.|++.|.+.++++|+.|||+++|+ +...++|+|+.|+..|++.++
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl---~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGL---PKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCcCeecC
Confidence 5688889877788999999999999 999999999999999999875
No 5
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=98.23 E-value=2.9e-06 Score=54.12 Aligned_cols=58 Identities=19% Similarity=0.283 Sum_probs=49.9
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
+.|++.|.+.++++|+.|||+.+|+ +...++|+++.|...|++..... ++.|.+++..
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i---~~~tv~r~l~~L~~~g~l~~~~~---~~~y~l~~~~ 65 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGL---SKSTAHRLLNTLQELGYVEQDGQ---NGRYRLGPKV 65 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCCeeecCC---CCceeecHHH
Confidence 5688888865478999999999999 99999999999999999998631 5789988754
No 6
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=98.13 E-value=3.6e-06 Score=63.40 Aligned_cols=59 Identities=17% Similarity=0.233 Sum_probs=51.6
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
+.|.+.|.+.++++|+.|||+++|+ ++..++|+|..|+..|++.++ +++|.+++....|
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lgl---pksT~~RlL~tL~~~G~l~~~-----~~~Y~lG~~~~~l 70 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGL---TRAAARRFLLTLVELGYVTSD-----GRLFWLTPRVLRL 70 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeC-----CCEEEecHHHHHH
Confidence 5688888866689999999999999 999999999999999999875 5789999865444
No 7
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=98.12 E-value=4.6e-06 Score=63.10 Aligned_cols=59 Identities=22% Similarity=0.359 Sum_probs=51.2
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
+.|++.|.+.+.++++.|||+++|+ ++..++|+|..|+..|++.+++. .++|.+++..-
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~gl---pksT~~RlL~tL~~~G~v~~d~~---~g~Y~Lg~~~~ 65 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGL---PKSTVHRLLQTLVELGYVEQDPE---DGRYRLGPRLL 65 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCc---CHHHHHHHHHHHHHCCCEEEcCC---CCcEeehHHHH
Confidence 5688889875566789999999999 99999999999999999999862 57899998654
No 8
>PRK11569 transcriptional repressor IclR; Provisional
Probab=98.11 E-value=4.2e-06 Score=64.06 Aligned_cols=61 Identities=13% Similarity=0.247 Sum_probs=52.1
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
+.|.+.|.+.++++|+.|||+.+|+ ++..++|+|+.|+..|++.++.. .++|.+++....|
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lgl---pksTv~RlL~tL~~~G~l~~~~~---~~~Y~lG~~l~~L 91 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGL---PNSTTHRLLTTMQQQGFVRQVGE---LGHWAIGAHAFIV 91 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEcCC---CCeEecCHHHHHH
Confidence 5688888876688999999999999 99999999999999999987642 6889998765433
No 9
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=98.09 E-value=5.8e-06 Score=63.25 Aligned_cols=61 Identities=15% Similarity=0.258 Sum_probs=52.0
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
+.|++.|.+.++++|+.|||+++|+ ++..++|+|..|+..|++.++.. .++|.+++-...|
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lgl---pkStv~RlL~tL~~~G~l~~~~~---~~~Y~lG~~l~~L 88 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDL---PLSTTFRLLKVLQAADFVYQDSQ---LGWWHIGLGVFNV 88 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEcCC---CCeEEecHHHHHH
Confidence 5688888866678999999999999 99999999999999999988642 6889998865433
No 10
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=97.98 E-value=1.1e-05 Score=61.41 Aligned_cols=61 Identities=16% Similarity=0.234 Sum_probs=52.1
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
+.|++.|...++++|+.|||+++|+ ++..++|+|+.|+..|++.+... +++|.+++....|
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl---~kstv~RlL~tL~~~g~v~~~~~---~~~Y~Lg~~~~~l 74 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGL---HRTTVRRLLETLQEEGYVRRSAS---DDSFRLTLKVRQL 74 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEecC---CCcEEEcHHHHHH
Confidence 5678888765667999999999999 99999999999999999998642 6789999866544
No 11
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=97.96 E-value=1.3e-05 Score=60.71 Aligned_cols=60 Identities=20% Similarity=0.330 Sum_probs=50.6
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
+.|.+.|.+ .+++|+.|||+++|+ ++..++|+|+.|+..|++.+... .++|.+++....|
T Consensus 17 l~IL~~l~~-~~~l~l~eia~~lgl---~kstv~Rll~tL~~~G~l~~~~~---~~~Y~lG~~~~~l 76 (257)
T PRK15090 17 FGILQALGE-EREIGITELSQRVMM---SKSTVYRFLQTMKTLGYVAQEGE---SEKYSLTLKLFEL 76 (257)
T ss_pred HHHHHHhhc-CCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEcCC---CCcEEecHHHHHH
Confidence 567777875 468999999999999 99999999999999999988642 6889999875443
No 12
>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=97.69 E-value=6.3e-05 Score=44.87 Aligned_cols=55 Identities=20% Similarity=0.242 Sum_probs=46.8
Q ss_pred HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..+|.--.++.|+..|.. ++|+|+.|||+.+|+ ++..+++-|+.|...|+++...
T Consensus 4 ~~aL~~p~R~~Il~~L~~-~~~~t~~ela~~l~~---~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 4 FKALSDPTRLRILRLLAS-NGPMTVSELAEELGI---SQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHTSHHHHHHHHHHHH-CSTBEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHhCCHHHHHHHHHHhc-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEec
Confidence 345666678889999943 589999999999999 9999999999999999999765
No 13
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.68 E-value=0.00017 Score=44.14 Aligned_cols=60 Identities=18% Similarity=0.214 Sum_probs=48.2
Q ss_pred HHHhChHHHHHhCCC-CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 35 AIELGIADIIHSHGR-AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 35 a~~L~ifd~l~~~~~-~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
..+-.|.+.|.+.++ ++|+.|||+++|+ +...++|+|..|...|++..... .++.|..+.
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl---~~~~v~r~L~~L~~~G~V~~~~~--~~~~W~i~~ 66 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGL---PKKEVNRVLYSLEKKGKVCKQGG--TPPLWKLTD 66 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecCC--CCCceEeec
Confidence 345578888987655 3999999999999 99999999999999999987541 146776654
No 14
>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=97.54 E-value=0.00015 Score=43.64 Aligned_cols=60 Identities=20% Similarity=0.304 Sum_probs=42.0
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAAS 101 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s 101 (131)
-|...|....++++..+|++.+++ +...+.|+++.|...|++++.... ++ ...|.+||.+
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~~~---~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERLGI---SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHHccCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 344455533689999999999999 999999999999999999876532 22 2458888753
No 15
>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=97.51 E-value=0.00026 Score=47.12 Aligned_cols=62 Identities=16% Similarity=0.308 Sum_probs=46.7
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
+..|++.|.+.++++|++||.+++.- ...+..++||.|+.|+..|++.+....++...|..+
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN 66 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence 45688999876789999999999842 111889999999999999999986532223456554
No 16
>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=97.36 E-value=0.00014 Score=44.14 Aligned_cols=47 Identities=15% Similarity=0.243 Sum_probs=40.1
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+..|...|-. .++.|+.|||+.+|+ +...+++.|+.|...|++....
T Consensus 10 E~~vy~~Ll~-~~~~t~~eIa~~l~i---~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 10 EAKVYLALLK-NGPATAEEIAEELGI---SRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHH-HCHEEHHHHHHHHTS---SHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEc
Confidence 4455656643 478999999999999 9999999999999999999875
No 17
>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=97.34 E-value=0.00041 Score=41.42 Aligned_cols=45 Identities=13% Similarity=0.220 Sum_probs=40.0
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
..++|..|||+.+|+ +...+.|+|+.|...|++.... .+.|..+|
T Consensus 23 ~~~~s~~ela~~~g~---s~~tv~r~l~~L~~~g~i~~~~----~~~~~l~~ 67 (67)
T cd00092 23 QLPLTRQEIADYLGL---TRETVSRTLKELEEEGLISRRG----RGKYRVNP 67 (67)
T ss_pred cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecC----CCeEEeCC
Confidence 368999999999999 9999999999999999999874 47888765
No 18
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=97.30 E-value=0.00059 Score=46.23 Aligned_cols=65 Identities=23% Similarity=0.290 Sum_probs=55.0
Q ss_pred HHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcc---eecch
Q 040869 27 LSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEA---YGLTA 99 (131)
Q Consensus 27 ~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~---y~~t~ 99 (131)
-..++|.--.++.|+..|.. +++.++.||++.+++ .+..+.+-|+.|...|+++... .|+ |.+++
T Consensus 8 ~~fkaLadptRl~IL~~L~~-~~~~~v~ela~~l~l---sqstvS~HL~~L~~AGLV~~~r----~Gr~~~Y~l~~ 75 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRE-SGELCVCDLCTALDQ---SQPKISRHLALLRESGLLLDRK----QGKWVHYRLSP 75 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCceEEEE----EcCEEEEEECc
Confidence 34567777889999999974 468999999999999 9999999999999999998765 343 77776
No 19
>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=97.28 E-value=0.00053 Score=43.33 Aligned_cols=47 Identities=15% Similarity=0.309 Sum_probs=37.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
+++|..|||+++++ ++..+.++++.|...|+++.... .+|.|.++.-
T Consensus 24 ~~~s~~eiA~~~~i---~~~~l~kil~~L~~~Gli~s~~G--~~GGy~L~~~ 70 (83)
T PF02082_consen 24 KPVSSKEIAERLGI---SPSYLRKILQKLKKAGLIESSRG--RGGGYRLARP 70 (83)
T ss_dssp C-BEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEETS--TTSEEEESS-
T ss_pred CCCCHHHHHHHHCc---CHHHHHHHHHHHhhCCeeEecCC--CCCceeecCC
Confidence 56999999999999 99999999999999999987641 1477876654
No 20
>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=97.28 E-value=0.00058 Score=38.56 Aligned_cols=45 Identities=20% Similarity=0.266 Sum_probs=37.9
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
.+..|+..|.+ .+.+|..|||+.+|+ +...+.+.++-|...|+++
T Consensus 4 ~~~~Il~~l~~-~~~~t~~ela~~~~i---s~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRE-NPRITQKELAEKLGI---SRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHH-CTTS-HHHHHHHHTS----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHhCC---CHHHHHHHHHHHHHCcCcC
Confidence 45678889986 456999999999999 9999999999999999874
No 21
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=97.22 E-value=0.00079 Score=46.13 Aligned_cols=50 Identities=18% Similarity=0.370 Sum_probs=41.0
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN 89 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~ 89 (131)
+..++-+|-+..+|+|++|||+.++. +.+.++|-|+-|...|++.+....
T Consensus 29 Dv~v~~~LL~~~~~~tvdelae~lnr---~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 29 DVEVYKALLEENGPLTVDELAEILNR---SRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred HHHHHHHHHhhcCCcCHHHHHHHHCc---cHHHHHHHHHHHHHcCCeeeeeec
Confidence 33455555423589999999999999 999999999999999999987543
No 22
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=97.22 E-value=0.00065 Score=37.86 Aligned_cols=41 Identities=12% Similarity=0.173 Sum_probs=36.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL 97 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~ 97 (131)
-++|..|||+.+|+ +...+.|.|+.|...|++... .+.|..
T Consensus 7 ~~~s~~~la~~l~~---s~~tv~~~l~~L~~~g~l~~~-----~~~~~i 47 (48)
T smart00419 7 LPLTRQEIAELLGL---TRETVSRTLKRLEKEGLISRE-----GGRIVI 47 (48)
T ss_pred eccCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEe-----CCEEEE
Confidence 46899999999999 999999999999999999865 466654
No 23
>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=97.21 E-value=0.00044 Score=39.11 Aligned_cols=44 Identities=18% Similarity=0.305 Sum_probs=38.9
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
.++.|...|.+ +|.++.||++.+|+ +...+.+-|+.|...|+++
T Consensus 3 ~R~~Il~~L~~--~~~~~~el~~~l~~---s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE--GPLTVSELAEELGL---SQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHHTT--SSEEHHHHHHHHTS----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHh--CCCchhhHHHhccc---cchHHHHHHHHHHHCcCee
Confidence 35678888884 89999999999999 9999999999999999986
No 24
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=97.18 E-value=0.001 Score=47.51 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=39.8
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
++++|+++||+++++ ++..+.++|+.|...|++..... .+|.|.+..
T Consensus 23 ~~~vs~~eIA~~~~i---p~~~l~kIl~~L~~aGLv~s~rG--~~GGy~Lar 69 (164)
T PRK10857 23 AGPVPLADISERQGI---SLSYLEQLFSRLRKNGLVSSVRG--PGGGYLLGK 69 (164)
T ss_pred CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeCCC--CCCCeeccC
Confidence 468999999999999 99999999999999999997531 146687754
No 25
>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=97.05 E-value=0.0026 Score=43.27 Aligned_cols=47 Identities=11% Similarity=0.243 Sum_probs=38.8
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
++++|..|||+++++ ++..+.++|+.|...|++..... ..|.|.+..
T Consensus 23 ~~~~s~~eia~~l~i---s~~~v~~~l~~L~~~Gli~~~~g--~~ggy~l~~ 69 (130)
T TIGR02944 23 SQPYSAAEIAEQTGL---NAPTVSKILKQLSLAGIVTSKRG--VEGGYTLAR 69 (130)
T ss_pred CCCccHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEecCC--CCCChhhcC
Confidence 468999999999999 99999999999999999986431 145676654
No 26
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=97.05 E-value=0.00071 Score=42.32 Aligned_cols=57 Identities=16% Similarity=0.274 Sum_probs=43.2
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
|...+. .++.+..+|+..+++ +...+.+.+..|...|++... ++.|.+|+.+..+..
T Consensus 11 IL~~l~--~~~~~~t~i~~~~~L---~~~~~~~yL~~L~~~gLI~~~-----~~~Y~lTekG~~~l~ 67 (77)
T PF14947_consen 11 ILKILS--KGGAKKTEIMYKANL---NYSTLKKYLKELEEKGLIKKK-----DGKYRLTEKGKEFLE 67 (77)
T ss_dssp HHHHH---TT-B-HHHHHTTST-----HHHHHHHHHHHHHTTSEEEE-----TTEEEE-HHHHHHHH
T ss_pred HHHHHH--cCCCCHHHHHHHhCc---CHHHHHHHHHHHHHCcCeeCC-----CCEEEECccHHHHHH
Confidence 444444 478999999999999 999999999999999999764 799999999985543
No 27
>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=97.03 E-value=0.0017 Score=44.66 Aligned_cols=48 Identities=17% Similarity=0.192 Sum_probs=39.7
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
++++|..|||+.+++ ++..+.++|+.|...|++..... ..|.|.++.-
T Consensus 23 ~~~~s~~~ia~~~~i---p~~~l~kil~~L~~~glv~s~~G--~~Ggy~l~~~ 70 (135)
T TIGR02010 23 TGPVTLADISERQGI---SLSYLEQLFAKLRKAGLVKSVRG--PGGGYQLGRP 70 (135)
T ss_pred CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCceEEEeC--CCCCEeccCC
Confidence 468999999999999 99999999999999999986431 1456777653
No 28
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.99 E-value=0.0015 Score=41.54 Aligned_cols=68 Identities=16% Similarity=0.242 Sum_probs=52.4
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-C-CCcceecchhccccccC
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-G-QEEAYGLTAASTLLIKD 107 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~-~~~~y~~t~~s~~L~~~ 107 (131)
.++.|+..|.. .++++..+||+.+++ ++..+.+.++-|...|++...... + ....|.+|+.+..+...
T Consensus 11 ~~~~il~~l~~-~~~~~~~~la~~~~~---s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 11 TQFLVLRILYE-EGPLSVSELAKRLGV---SPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred HHHHHHHHHHH-cCCcCHHHHHHHHCC---CchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 35667888875 357999999999999 999999999999999999876421 0 02358888888765543
No 29
>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=96.97 E-value=0.0015 Score=39.75 Aligned_cols=59 Identities=14% Similarity=0.197 Sum_probs=46.0
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCC--cchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTK--TTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~--~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
|.++|.++++|++..+|++.+.....+ +..++|.||+|-..|+..... .+.+.+|+.+.
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g----~~G~~iT~~G~ 63 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVG----RQGRIITEKGL 63 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccC----CcccccCHHHH
Confidence 678888888999999999998753334 488999999999999766544 45566777654
No 30
>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=96.96 E-value=0.0018 Score=43.95 Aligned_cols=49 Identities=14% Similarity=0.247 Sum_probs=39.9
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
++++|.++||+.+++ ++..++++|+.|...|++..... .+|.|.++.-.
T Consensus 23 ~~~~s~~eia~~~~i---~~~~v~~il~~L~~~gli~~~~g--~~ggy~l~~~~ 71 (132)
T TIGR00738 23 EGPVSVKEIAERQGI---SRSYLEKILRTLRRAGLVESVRG--PGGGYRLARPP 71 (132)
T ss_pred CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEeccC--CCCCccCCCCH
Confidence 358999999999999 99999999999999999986531 14567776443
No 31
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=96.94 E-value=0.0012 Score=39.82 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=38.9
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.|.+.|....+|++..|||+.+|+ +....+++|..|...|.+...+
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gl---s~~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGL---SIYQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS----HHHHHHHHHHHHHCTSEEEES
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec
Confidence 567777754689999999999999 9999999999999999998764
No 32
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=96.92 E-value=0.0015 Score=38.41 Aligned_cols=48 Identities=19% Similarity=0.311 Sum_probs=39.6
Q ss_pred HhChHHHHHhCCCC-CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 37 ELGIADIIHSHGRA-ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 37 ~L~ifd~l~~~~~~-~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
++.|+-.|...+++ +|..|||+.+++ ++..+.|+++.|...|++.+..
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~~---~~~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLGI---SKSTVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEeC
Confidence 45566677654433 899999999999 9999999999999999999875
No 33
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=96.90 E-value=0.0019 Score=44.76 Aligned_cols=52 Identities=13% Similarity=0.154 Sum_probs=45.4
Q ss_pred CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
.+++.++.+||+.+++ ++..+.+.++.|...|++.... .+.|.+|+.++.+.
T Consensus 19 ~~~~~~~~ela~~l~v---s~~svs~~l~~L~~~Gli~~~~----~~~i~LT~~G~~~a 70 (142)
T PRK03902 19 EKGYARVSDIAEALSV---HPSSVTKMVQKLDKDEYLIYEK----YRGLVLTPKGKKIG 70 (142)
T ss_pred cCCCcCHHHHHHHhCC---ChhHHHHHHHHHHHCCCEEEec----CceEEECHHHHHHH
Confidence 3578999999999999 9999999999999999998654 57799999986543
No 34
>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=96.77 E-value=0.0037 Score=41.77 Aligned_cols=69 Identities=14% Similarity=0.169 Sum_probs=53.8
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-C-CCcceecchhccccccC
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-G-QEEAYGLTAASTLLIKD 107 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~-~~~~y~~t~~s~~L~~~ 107 (131)
..+..|+..|.. .+++|..|||+.+++ +...+.|+++-|...|++...... | ..-.|.+|+.++.+...
T Consensus 28 ~~q~~iL~~l~~-~~~~t~~ela~~~~~---~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~ 98 (118)
T TIGR02337 28 EQQWRILRILAE-QGSMEFTQLANQACI---LRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS 98 (118)
T ss_pred HHHHHHHHHHHH-cCCcCHHHHHHHhCC---CchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence 344457777765 468999999999999 999999999999999999986432 1 12359999999866543
No 35
>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=96.74 E-value=0.0043 Score=37.66 Aligned_cols=59 Identities=19% Similarity=0.194 Sum_probs=45.9
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
++.|+..|. +++.|..+||+++|+ ....+.+-++.|...|+..... +..|...+....|
T Consensus 2 ~~~il~~L~--~~~~~~~eLa~~l~v---S~~tv~~~l~~L~~~g~~i~~~----~~g~~l~~~~~ll 60 (69)
T TIGR00122 2 PLRLLALLA--DNPFSGEKLGEALGM---SRTAVNKHIQTLREWGVDVLTV----GKGYRLPPPIPLL 60 (69)
T ss_pred hHHHHHHHH--cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEec----CCceEecCccccC
Confidence 466788887 467899999999999 9999999999999999865543 3556665544443
No 36
>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=96.74 E-value=0.0038 Score=45.73 Aligned_cols=65 Identities=17% Similarity=0.123 Sum_probs=50.0
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc----ceecchhccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE----AYGLTAASTLLI 105 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~----~y~~t~~s~~L~ 105 (131)
+-.|+..|.. .+++|..|||+.+|+ ++..+.|.|+.|...|++.......+.| .|.+|+.++.+.
T Consensus 3 r~~IL~~L~~-~~~~t~~eLA~~lgi---s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~ 71 (203)
T TIGR02702 3 KEDILSYLLK-QGQATAAALAEALAI---SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF 71 (203)
T ss_pred HHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence 3457777765 367999999999999 9999999999999999998752100122 379998887544
No 37
>PRK11050 manganese transport regulator MntR; Provisional
Probab=96.69 E-value=0.0039 Score=43.86 Aligned_cols=59 Identities=15% Similarity=0.164 Sum_probs=49.5
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
-|...+.. +++.+..|||+.+++ ++..+.|.++.|...|++.... .+.+.+|+.++.+.
T Consensus 41 ~I~~~l~~-~~~~t~~eLA~~l~i---s~stVsr~l~~Le~~GlI~r~~----~~~v~LT~~G~~l~ 99 (152)
T PRK11050 41 LIADLIAE-VGEARQVDIAARLGV---SQPTVAKMLKRLARDGLVEMRP----YRGVFLTPEGEKLA 99 (152)
T ss_pred HHHHHHHh-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec----CCceEECchHHHHH
Confidence 35556653 578999999999999 9999999999999999998765 56789999888664
No 38
>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=96.68 E-value=0.0026 Score=38.83 Aligned_cols=45 Identities=18% Similarity=0.341 Sum_probs=37.3
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.|-+.|.. .+.+|..|||.++++ +++.+.-+|..|...|.+.+..
T Consensus 4 ~i~~~l~~-~~~~S~~eLa~~~~~---s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 4 EIRDYLRE-RGRVSLAELAREFGI---SPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHH-S-SEEHHHHHHHTT-----HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEEec
Confidence 35677775 578999999999999 9999999999999999999875
No 39
>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=96.66 E-value=0.0042 Score=35.87 Aligned_cols=42 Identities=19% Similarity=0.190 Sum_probs=35.0
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
..|...|.+.++++|+.+||+.+++ +...++|-+..|...|+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~v---S~rTi~~~i~~L~~~~~ 44 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGV---SRRTIRRDIKELREWGI 44 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS----HHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCC
Confidence 3467778555678999999999999 99999999999999993
No 40
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=96.66 E-value=0.0043 Score=42.79 Aligned_cols=58 Identities=10% Similarity=0.115 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 26 HLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 26 ~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|-..+.+-+--.+.+.+.|+. .+|.|..|+|+.+|- ++..++|-||.|...|++.-..
T Consensus 55 ye~la~vLsp~nleLl~~Ia~-~~P~Si~ElAe~vgR---dv~nvhr~Ls~l~~~GlI~fe~ 112 (144)
T COG4190 55 YEDLARVLSPRNLELLELIAQ-EEPASINELAELVGR---DVKNVHRTLSTLADLGLIFFEE 112 (144)
T ss_pred HHHHHHHhChhHHHHHHHHHh-cCcccHHHHHHHhCc---chHHHHHHHHHHHhcCeEEEec
Confidence 444455666667888999985 589999999999999 9999999999999999988765
No 41
>PHA00738 putative HTH transcription regulator
Probab=96.66 E-value=0.0048 Score=41.10 Aligned_cols=62 Identities=15% Similarity=0.169 Sum_probs=49.4
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
.++.|++.|.. ++++++.||++.+++ ..+.+-+-|+.|...|++...... ..-.|++++-..
T Consensus 13 tRr~IL~lL~~-~e~~~V~eLae~l~l---SQptVS~HLKvLreAGLV~srK~G-r~vyY~Ln~~~~ 74 (108)
T PHA00738 13 LRRKILELIAE-NYILSASLISHTLLL---SYTTVLRHLKILNEQGYIELYKEG-RTLYAKIRENSK 74 (108)
T ss_pred HHHHHHHHHHH-cCCccHHHHHHhhCC---CHHHHHHHHHHHHHCCceEEEEEC-CEEEEEECCCcc
Confidence 57789999985 457999999999999 999999999999999999987610 012377776544
No 42
>PRK06474 hypothetical protein; Provisional
Probab=96.66 E-value=0.0039 Score=45.05 Aligned_cols=73 Identities=21% Similarity=0.359 Sum_probs=55.8
Q ss_pred HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccC---CC-Ccceecchhccc
Q 040869 29 SMSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQ-EEAYGLTAASTL 103 (131)
Q Consensus 29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~---~~-~~~y~~t~~s~~ 103 (131)
..+|.-..++.|++.|...++++|+.||++.+ ++ +...++|.|+.|...|++...... ++ ...|..++..-.
T Consensus 5 ~~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~i---s~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~ 81 (178)
T PRK06474 5 AEILMHPVRMKICQVLMRNKEGLTPLELVKILKDV---PQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAK 81 (178)
T ss_pred HHhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCC---CHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceee
Confidence 34666778899999998655569999999999 67 888999999999999999975421 01 134777776544
Q ss_pred c
Q 040869 104 L 104 (131)
Q Consensus 104 L 104 (131)
+
T Consensus 82 ~ 82 (178)
T PRK06474 82 I 82 (178)
T ss_pred e
Confidence 4
No 43
>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=96.64 E-value=0.0053 Score=39.70 Aligned_cols=69 Identities=14% Similarity=0.174 Sum_probs=52.6
Q ss_pred HHHHhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHH----------HhhcCCceeecccCCCCcceecchhcc
Q 040869 34 CAIELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMR----------LLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 34 ~a~~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr----------~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
.=++.+|+..|.+. +.+.++.|||+.+++ ++..+.-.|+ .|+.+|++.+.....+...|.+|+-++
T Consensus 8 S~~R~~vl~~L~~~yp~~~~~~eIar~v~~---~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~lT~~G~ 84 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYPEPAYPSEIARSVGS---DYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRLTEKGK 84 (90)
T ss_pred HHHHHHHHHHHHHcCCCcCCHHHHHHHHCC---CHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEeChhhh
Confidence 55778899999876 689999999999999 8888877774 589999993322112345799999876
Q ss_pred ccc
Q 040869 103 LLI 105 (131)
Q Consensus 103 ~L~ 105 (131)
.++
T Consensus 85 ~~~ 87 (90)
T PF07381_consen 85 RIA 87 (90)
T ss_pred hHH
Confidence 543
No 44
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=96.64 E-value=0.0056 Score=34.39 Aligned_cols=44 Identities=14% Similarity=0.271 Sum_probs=38.0
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|.+.|.+ .+++|..+|++.+++ ++..+++.|..|...|++....
T Consensus 5 il~~l~~-~~~~s~~~l~~~l~~---s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 5 ILELLAQ-QGKVSVEELAELLGV---SEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHH-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEee
Confidence 5566654 357999999999999 9999999999999999998764
No 45
>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=96.61 E-value=0.0053 Score=36.14 Aligned_cols=45 Identities=13% Similarity=0.276 Sum_probs=40.3
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.|.+.|.+ .+.+|+.|||+.+|+ ++..++|=|..|...|++.+..
T Consensus 4 ~Il~~l~~-~~~~s~~ela~~~~V---S~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 4 QILELLKE-KGKVSVKELAEEFGV---SEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHH-cCCEEHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEc
Confidence 36777775 478999999999999 9999999999999999999875
No 46
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=96.55 E-value=0.0057 Score=43.05 Aligned_cols=47 Identities=13% Similarity=0.213 Sum_probs=39.9
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
++.|+++||+..++ ++..|.|+|..|...|+++-... -.|.|.+..-
T Consensus 24 ~~~s~~~IA~~~~i---s~~~L~kil~~L~kaGlV~S~rG--~~GGy~Lar~ 70 (150)
T COG1959 24 GPVSSAEIAERQGI---SPSYLEKILSKLRKAGLVKSVRG--KGGGYRLARP 70 (150)
T ss_pred CcccHHHHHHHhCc---CHHHHHHHHHHHHHcCCEEeecC--CCCCccCCCC
Confidence 38999999999999 99999999999999999997651 1577877644
No 47
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=96.51 E-value=0.0024 Score=40.29 Aligned_cols=64 Identities=22% Similarity=0.296 Sum_probs=49.0
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC--Ccceecchhccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ--EEAYGLTAASTL 103 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~--~~~y~~t~~s~~ 103 (131)
++++|...|.. .+.++..+|.+.+|+ +...+.+-|+.|...|+++....- ++ .-.|++|+.++.
T Consensus 1 vRl~Il~~L~~-~~~~~f~~L~~~l~l---t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~ 67 (80)
T PF13601_consen 1 VRLAILALLYA-NEEATFSELKEELGL---TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGRE 67 (80)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHH
T ss_pred CHHHHHHHHhh-cCCCCHHHHHHHhCc---CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHH
Confidence 57888999985 467999999999999 999999999999999999976432 11 124888988873
No 48
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.45 E-value=0.0042 Score=39.79 Aligned_cols=46 Identities=15% Similarity=0.196 Sum_probs=41.2
Q ss_pred HHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 53 LSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 53 ~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
+.+||+.+++ ++..+.|+++.|...|++.... +..|.+|+.+..+.
T Consensus 2 ~~ela~~l~i---s~stvs~~l~~L~~~glI~r~~----~~~~~lT~~g~~~~ 47 (96)
T smart00529 2 TSEIAERLNV---SPPTVTQMLKKLEKDGLVEYEP----YRGITLTEKGRRLA 47 (96)
T ss_pred HHHHHHHhCC---ChHHHHHHHHHHHHCCCEEEcC----CCceEechhHHHHH
Confidence 5799999999 9999999999999999999986 56899999887654
No 49
>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=96.44 E-value=0.0059 Score=37.06 Aligned_cols=41 Identities=20% Similarity=0.337 Sum_probs=32.8
Q ss_pred HhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 45 HSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 45 ~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+.|-|-|+.|||+.+|++ ++..+.+.|+.|...|+++...
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~--S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLK--STSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHSS---HHHHHHHHTSS--SHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHcCCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCcCccCCC
Confidence 3456788999999999992 3889999999999999999874
No 50
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=96.42 E-value=0.0061 Score=39.90 Aligned_cols=47 Identities=15% Similarity=0.259 Sum_probs=41.7
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.+..|...|.. ++++|..+||+.+|+ ++..+.|.++.|...|++...
T Consensus 4 ~D~~il~~L~~-~~~~~~~~la~~l~~---s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQK-DARISLAELAKKVGL---SPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHH-hCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeece
Confidence 46778888886 468999999999999 999999999999999999843
No 51
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=96.41 E-value=0.0083 Score=41.51 Aligned_cols=47 Identities=13% Similarity=0.293 Sum_probs=39.0
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
+.++|..+||+..|+ ++..++++|+.|...|++..... .+|.|.+..
T Consensus 23 g~~~s~~~ia~~~~i---s~~~vrk~l~~L~~~Glv~s~~G--~~GG~~l~~ 69 (141)
T PRK11014 23 GRMTSISEVTEVYGV---SRNHMVKIINQLSRAGYVTAVRG--KNGGIRLGK 69 (141)
T ss_pred CCccCHHHHHHHHCc---CHHHHHHHHHHHHhCCEEEEecC--CCCCeeecC
Confidence 467999999999999 99999999999999999987651 135676653
No 52
>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=96.40 E-value=0.0074 Score=44.23 Aligned_cols=59 Identities=15% Similarity=0.246 Sum_probs=47.5
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
.++.|...|.+ .++++..|||+.+++ ++..+.|.++.|...|++.+... ....|.+|+.
T Consensus 144 ~~~~IL~~l~~-~g~~s~~eia~~l~i---s~stv~r~L~~Le~~GlI~r~~~--r~~~~~lT~~ 202 (203)
T TIGR01884 144 EELKVLEVLKA-EGEKSVKNIAKKLGK---SLSTISRHLRELEKKGLVEQKGR--KGKRYSLTKL 202 (203)
T ss_pred HHHHHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEcC--CccEEEeCCC
Confidence 34567777764 357999999999999 99999999999999999998741 1456888765
No 53
>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=96.37 E-value=0.0042 Score=41.62 Aligned_cols=66 Identities=18% Similarity=0.308 Sum_probs=48.3
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
+..+.-|++.|.+.+++.|++||.+.+.- ...+..++||.|+.|...|++.+....++...|....
T Consensus 7 T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~ 74 (120)
T PF01475_consen 7 TPQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence 44567789999876789999999998853 1117778999999999999999875322234565554
No 54
>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=96.35 E-value=0.0097 Score=35.37 Aligned_cols=57 Identities=21% Similarity=0.324 Sum_probs=43.5
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
+..|...+.. ++.+..||++.+++ +...+.|.++.|...|++...... ....|..|+
T Consensus 9 ~~~il~~l~~--~~~~~~ei~~~~~i---~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~~~~ 65 (78)
T cd00090 9 RLRILRLLLE--GPLTVSELAERLGL---SQSTVSRHLKKLEEAGLVESRREG-RRVYYSLTD 65 (78)
T ss_pred HHHHHHHHHH--CCcCHHHHHHHHCc---CHhHHHHHHHHHHHCCCeEEEEec-cEEEEEeCC
Confidence 4456666664 23999999999999 999999999999999999976410 124566665
No 55
>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=96.35 E-value=0.0069 Score=35.35 Aligned_cols=43 Identities=37% Similarity=0.435 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
.-.+|.+|.++|-|| . +...|+.|||+.+|+ ++..+...||-.
T Consensus 5 Q~e~L~~A~~~GYfd-~---PR~~tl~elA~~lgi---s~st~~~~LRra 47 (53)
T PF04967_consen 5 QREILKAAYELGYFD-V---PRRITLEELAEELGI---SKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHHHHHcCCCC-C---CCcCCHHHHHHHhCC---CHHHHHHHHHHH
Confidence 346899999999998 3 367999999999999 888877777643
No 56
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.34 E-value=0.013 Score=33.89 Aligned_cols=43 Identities=12% Similarity=0.251 Sum_probs=37.3
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|+..|. .++.|..+|++.+++ +...+.+.++.|...|++....
T Consensus 2 il~~l~--~~~~~~~~i~~~l~i---s~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGL---SQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCC---CHHHHHHHHHHHHHCCCeeeee
Confidence 455665 478999999999999 9999999999999999998654
No 57
>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=96.31 E-value=0.013 Score=38.07 Aligned_cols=45 Identities=9% Similarity=0.099 Sum_probs=39.2
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
..++|..|||+.+|+ ++..+.|.|..|...|++.... +.+.|+.+
T Consensus 45 ~~~is~~eLa~~~g~---sr~tVsr~L~~Le~~GlI~r~~---~~~~~~~n 89 (95)
T TIGR01610 45 QDRVTATVIAELTGL---SRTHVSDAIKSLARRRIIFRQG---MMGIVGVN 89 (95)
T ss_pred CCccCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeeeec---CCceeecC
Confidence 468999999999999 9999999999999999999763 14777766
No 58
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=96.27 E-value=0.0091 Score=41.75 Aligned_cols=66 Identities=15% Similarity=0.315 Sum_probs=49.6
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
--++.|+++|.+++++.|+.+|-.++.- .+..+.++||.|..|+..|++.+....++.-+|..+.-
T Consensus 21 ~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~ 88 (145)
T COG0735 21 PQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE 88 (145)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence 3567799999877788999999988763 23378899999999999999998753222234655544
No 59
>PRK09462 fur ferric uptake regulator; Provisional
Probab=96.25 E-value=0.012 Score=40.97 Aligned_cols=65 Identities=12% Similarity=0.264 Sum_probs=47.4
Q ss_pred HHHHhChHHHHHhC-CCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 34 CAIELGIADIIHSH-GRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 34 ~a~~L~ifd~l~~~-~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
+.-+.-|++.|... ++++|++||-+++.- .+.+..++||.|+.|+..|++.+....++...|..+
T Consensus 16 T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~~~ 83 (148)
T PRK09462 16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELT 83 (148)
T ss_pred CHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEEeC
Confidence 44567789999864 479999999998843 112788999999999999999886422223456543
No 60
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=96.25 E-value=0.0072 Score=46.26 Aligned_cols=67 Identities=9% Similarity=0.253 Sum_probs=57.8
Q ss_pred HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869 31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
.+....+.+|+=.|. ++|.|.+||-..+++ ++..+..=++-|...|++.+. ++.|++|+.++.++..
T Consensus 9 if~SekRk~lLllL~--egPkti~EI~~~l~v---s~~ai~pqiKkL~~~~LV~~~-----~~~Y~LS~~G~iiv~k 75 (260)
T COG4742 9 LFLSEKRKDLLLLLK--EGPKTIEEIKNELNV---SSSAILPQIKKLKDKGLVVQE-----GDRYSLSSLGKIIVEK 75 (260)
T ss_pred HHccHHHHHHHHHHH--hCCCCHHHHHHHhCC---CcHHHHHHHHHHhhCCCEEec-----CCEEEecchHHHHHHH
Confidence 344556778888888 489999999999999 888898899999999999988 6999999999988764
No 61
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=96.24 E-value=0.011 Score=40.75 Aligned_cols=65 Identities=18% Similarity=0.233 Sum_probs=50.3
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD 107 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~ 107 (131)
++..|...+++.|..|||+.+++ ++..+.|++..|...|++...... |. .-...+|+.++.+...
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~---~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~ 102 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGI---EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISE 102 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCC---ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHH
Confidence 45556544456899999999999 999999999999999999987532 21 1347899998866543
No 62
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=96.23 E-value=0.011 Score=44.11 Aligned_cols=61 Identities=18% Similarity=0.265 Sum_probs=48.0
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCC----cceecchhccc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQE----EAYGLTAASTL 103 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~----~~y~~t~~s~~ 103 (131)
.|...|.+ .+|+|+.|||+++|+ ++..++|-|..|.+.|++.......|- ..|.+|..++.
T Consensus 15 ~il~lL~~-~g~~sa~elA~~Lgi---s~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 15 RILELLKK-SGPVSADELAEELGI---SPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HHHHHHhc-cCCccHHHHHHHhCC---CHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 35556664 589999999999999 999999999999999998865322212 35999988764
No 63
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=96.17 E-value=0.01 Score=42.03 Aligned_cols=53 Identities=9% Similarity=0.063 Sum_probs=47.6
Q ss_pred CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869 47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
..+++...+||+.+++ .|+.+..+++-|...|++...+ .+.+.+|+.++.++.
T Consensus 21 ~~~~~~~~diA~~L~V---sp~sVt~ml~rL~~~GlV~~~~----y~gi~LT~~G~~~a~ 73 (154)
T COG1321 21 EKGFARTKDIAERLKV---SPPSVTEMLKRLERLGLVEYEP----YGGVTLTEKGREKAK 73 (154)
T ss_pred ccCcccHHHHHHHhCC---CcHHHHHHHHHHHHCCCeEEec----CCCeEEChhhHHHHH
Confidence 3689999999999999 9999999999999999999987 789999998875544
No 64
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=96.14 E-value=0.013 Score=41.98 Aligned_cols=54 Identities=17% Similarity=0.294 Sum_probs=44.5
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecc
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+.-+..|++.|...++++|++||.+++.- ...+..++||.|+.|+..|++.+..
T Consensus 25 T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 25 TPQRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence 45667789999876789999999998864 1227789999999999999999875
No 65
>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=96.12 E-value=0.0054 Score=35.77 Aligned_cols=47 Identities=23% Similarity=0.375 Sum_probs=38.8
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
++.+...|.+. +++|..+||+.+++ ++..+.|+++-|...|++....
T Consensus 5 q~~iL~~l~~~-~~~~~~~la~~~~~---~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 5 QFRILRILYEN-GGITQSELAEKLGI---SRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHH-SSEEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHCC---ChhHHHHHHHHHHHCCCEEecc
Confidence 44555666653 57999999999999 9999999999999999999864
No 66
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=96.11 E-value=0.013 Score=40.44 Aligned_cols=66 Identities=18% Similarity=0.202 Sum_probs=51.1
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD 107 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~ 107 (131)
..|+-.|.. .+++|..|||+.+++ ++..+.|++..|...|++.+.... |+ .-...+|+.++.+...
T Consensus 43 ~~vL~~l~~-~~~~t~~eLa~~l~i---~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 43 FKVLCSIRC-AACITPVELKKVLSV---DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred HHHHHHHHH-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 345666664 468999999999999 999999999999999999986532 21 1346889888866543
No 67
>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=96.05 E-value=0.012 Score=38.85 Aligned_cols=67 Identities=18% Similarity=0.275 Sum_probs=49.9
Q ss_pred HHhChHHHHH--hC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869 36 IELGIADIIH--SH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI 105 (131)
Q Consensus 36 ~~L~ifd~l~--~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~ 105 (131)
.++.|+..|. .. ++++|..+||..+++ ++..+.|+++.|...|++.+.... |. .-.+.+|+.++.+.
T Consensus 26 ~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~---~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~ 97 (109)
T TIGR01889 26 EELLILYYLGKLENNEGKLTLKEIIKEILI---KQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKI 97 (109)
T ss_pred HHHHHHHHHHhhhccCCcCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHH
Confidence 3445566665 22 478999999999999 999999999999999999986532 21 12367788776554
No 68
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=96.01 E-value=0.01 Score=34.17 Aligned_cols=37 Identities=16% Similarity=0.232 Sum_probs=33.1
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+..+ |..|||+.+|+ +...+.+.++.|...|++....
T Consensus 17 ~~~l~s~~~la~~~~v---s~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 17 GDKLPSERELAAQLGV---SRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CCcCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec
Confidence 3456 99999999999 9999999999999999998764
No 69
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=95.98 E-value=0.017 Score=40.67 Aligned_cols=47 Identities=17% Similarity=0.312 Sum_probs=39.7
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
++++|..+||++.++ ++..|.++|..|+..|+++-... ..|.|.++.
T Consensus 22 ~~~~s~~eIA~~~~i---s~~~L~kIl~~L~~aGlv~S~rG--~~GGy~La~ 68 (153)
T PRK11920 22 GKLSRIPEIARAYGV---SELFLFKILQPLVEAGLVETVRG--RNGGVRLGR 68 (153)
T ss_pred CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeecC--CCCCeeecC
Confidence 467899999999999 99999999999999999997652 146677664
No 70
>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=95.87 E-value=0.026 Score=33.04 Aligned_cols=34 Identities=18% Similarity=0.179 Sum_probs=31.0
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.|..+||..+++ +...+.+.+..|...|++....
T Consensus 26 ~~~~~la~~~~i---s~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 26 PSERELAEELGV---SRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecC
Confidence 459999999999 9999999999999999998654
No 71
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=95.85 E-value=0.026 Score=38.58 Aligned_cols=51 Identities=18% Similarity=0.275 Sum_probs=44.5
Q ss_pred HHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 33 KCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 33 ~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+..++..|.+.+.+ .|.+|..|++..+|+ +...+.+.+|.|++.|-+...+
T Consensus 10 r~eLk~rIvElVRe-~GRiTi~ql~~~TGa---sR~Tvk~~lreLVa~G~l~~~G 60 (127)
T PF06163_consen 10 REELKARIVELVRE-HGRITIKQLVAKTGA---SRNTVKRYLRELVARGDLYRHG 60 (127)
T ss_pred HHHHHHHHHHHHHH-cCCccHHHHHHHHCC---CHHHHHHHHHHHHHcCCeEeCC
Confidence 45567788888876 478999999999999 9999999999999999888765
No 72
>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=95.82 E-value=0.028 Score=35.40 Aligned_cols=50 Identities=10% Similarity=0.001 Sum_probs=42.4
Q ss_pred CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee-cccCCCCcceecchhcc
Q 040869 47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK-TKVNGQEEAYGLTAAST 102 (131)
Q Consensus 47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~-~~~~~~~~~y~~t~~s~ 102 (131)
.+.|+...+||+.++. ++..++-.|..|..+|++.. ... .+.|-+|..+-
T Consensus 20 ~~~PVgSk~ia~~l~~---s~aTIRN~M~~Le~lGlve~~p~~---s~GriPT~~aY 70 (78)
T PF03444_consen 20 TGEPVGSKTIAEELGR---SPATIRNEMADLEELGLVESQPHP---SGGRIPTDKAY 70 (78)
T ss_pred cCCCcCHHHHHHHHCC---ChHHHHHHHHHHHHCCCccCCCCC---CCCCCcCHHHH
Confidence 3789999999999999 99999999999999999974 321 47788887764
No 73
>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=95.76 E-value=0.023 Score=33.84 Aligned_cols=38 Identities=8% Similarity=0.242 Sum_probs=34.4
Q ss_pred CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+++++..+||+.+|+ .+..+..+++-|...|++...+
T Consensus 19 ~~~~v~~~~iA~~L~v---s~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGV---SPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp CTSSBBHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEET
T ss_pred CCCCccHHHHHHHHCC---ChHHHHHHHHHHHHCCCEEecC
Confidence 4689999999999999 9999999999999999999764
No 74
>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=95.62 E-value=0.014 Score=37.33 Aligned_cols=61 Identities=20% Similarity=0.221 Sum_probs=46.5
Q ss_pred hHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccCCC--Ccceecchhccccc
Q 040869 40 IADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQ--EEAYGLTAASTLLI 105 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~--~~~y~~t~~s~~L~ 105 (131)
|...|. .++....||.+.+ |+ ++..|.+-|+.|...|++.+...... .-.|.+|+.++.|.
T Consensus 10 IL~~l~--~g~~rf~el~~~l~~i---s~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 10 ILRALF--QGPMRFSELQRRLPGI---SPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHT--TSSEEHHHHHHHSTTS----HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHH--hCCCcHHHHHHhcchh---HHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 455565 3799999999999 89 89999999999999999988642111 13599999998775
No 75
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=95.50 E-value=0.065 Score=38.79 Aligned_cols=45 Identities=11% Similarity=0.131 Sum_probs=39.8
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
..|++.|.. .+++|.+|||..+|+ ....++|+|..|...|++...
T Consensus 25 ~~Vl~~L~~-~g~~tdeeLA~~Lgi---~~~~VRk~L~~L~e~gLv~~~ 69 (178)
T PRK06266 25 FEVLKALIK-KGEVTDEEIAEQTGI---KLNTVRKILYKLYDARLADYK 69 (178)
T ss_pred hHHHHHHHH-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEe
Confidence 448888875 468999999999999 999999999999999999943
No 76
>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=95.44 E-value=0.016 Score=30.30 Aligned_cols=31 Identities=13% Similarity=0.276 Sum_probs=25.8
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF 83 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~ 83 (131)
|+|-+|||..+|+ .++.+.|+|..|...|++
T Consensus 2 ~mtr~diA~~lG~---t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGL---TRETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS----HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCC---cHHHHHHHHHHHHHcCCC
Confidence 5788999999999 999999999999988874
No 77
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=95.38 E-value=0.032 Score=39.11 Aligned_cols=47 Identities=11% Similarity=0.221 Sum_probs=42.3
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.+..|.+.|.+ ++..|..+||+++|+ ++..+.|=++-|...|++...
T Consensus 10 ~D~~Il~~Lq~-d~R~s~~eiA~~lgl---S~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 10 LDRGILEALME-NARTPYAELAKQFGV---SPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeeeE
Confidence 57789999986 578999999999999 999999999999999999843
No 78
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=95.35 E-value=0.023 Score=43.49 Aligned_cols=48 Identities=35% Similarity=0.453 Sum_probs=43.6
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+..|.++|.+.||-++-+||.+++|. +...+.|++|-|..+|++++..
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lgl---sktTvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGL---SKTTVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred HHHHHHHHHHhCCEEeHHHHHHhhCC---ChHHHHHHHHHHHhCCceEEEE
Confidence 44588888877888999999999999 9999999999999999999876
No 79
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=95.24 E-value=0.032 Score=39.59 Aligned_cols=47 Identities=17% Similarity=0.204 Sum_probs=42.5
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
.++..|...|.+ ++.+|..|||+++|+ ++..+.|=++-|...|++..
T Consensus 14 ~~D~~IL~~Lq~-d~R~s~~eiA~~lgl---S~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQK-DGRISNVELSKRVGL---SPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhcc-CCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEE
Confidence 368889999986 578999999999999 99999999999999999985
No 80
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=95.04 E-value=0.048 Score=37.66 Aligned_cols=49 Identities=14% Similarity=0.268 Sum_probs=43.2
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..+..|...|.+ +++.|..+||+++|+ ++..+.+-++-|...|++....
T Consensus 8 ~~D~~IL~~L~~-d~r~~~~eia~~lgl---S~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 8 DIDRRILRLLQE-DARISNAELAERVGL---SPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred HHHHHHHHHHHH-hCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCceeeEE
Confidence 356788899986 567999999999999 9999999999999999998764
No 81
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=95.04 E-value=0.11 Score=37.39 Aligned_cols=63 Identities=16% Similarity=0.072 Sum_probs=50.2
Q ss_pred hHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc--CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 25 SHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL--DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 25 ~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~--~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
..|...+++..+.+. ++.-.+.+||+++ ++ +...+..-|..|...|++++.+ +|.|..|..+-
T Consensus 22 ~~W~~~~ir~l~~l~--------~~~~d~~~iak~l~p~i---s~~ev~~sL~~L~~~gli~k~~----~g~y~~t~~~l 86 (171)
T PF14394_consen 22 SSWYHPAIRELLPLM--------PFAPDPEWIAKRLRPKI---SAEEVRDSLEFLEKLGLIKKDG----DGKYVQTDKSL 86 (171)
T ss_pred hhhHHHHHHHHhhcC--------CCCCCHHHHHHHhcCCC---CHHHHHHHHHHHHHCCCeEECC----CCcEEEeccee
Confidence 456666776665543 2334899999999 89 9999999999999999999987 78999887543
No 82
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=95.00 E-value=0.04 Score=34.14 Aligned_cols=50 Identities=22% Similarity=0.278 Sum_probs=43.8
Q ss_pred HHHhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 35 AIELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 35 a~~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..+..+.+.|+++. .+++..||++.+|. |+..+...++.|...|++....
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~---D~r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGI---DPRSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCC---CchHHHHHHHHHHHCCCEEEEE
Confidence 35667888898654 68999999999999 9999999999999999999875
No 83
>PRK10870 transcriptional repressor MprA; Provisional
Probab=94.94 E-value=0.051 Score=39.03 Aligned_cols=67 Identities=18% Similarity=0.179 Sum_probs=50.8
Q ss_pred hChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869 38 LGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD 107 (131)
Q Consensus 38 L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~ 107 (131)
..|.-.|... ++++|..|||+.+++ ++..+.|++.-|...|++.+.... |+ .-...+|+.++.+...
T Consensus 58 ~~iL~~L~~~~~~~it~~eLa~~l~l---~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~ 127 (176)
T PRK10870 58 FMALITLESQENHSIQPSELSCALGS---SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE 127 (176)
T ss_pred HHHHHHHhcCCCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 3355555432 367999999999999 999999999999999999986532 21 2347899998866543
No 84
>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=94.90 E-value=0.063 Score=38.97 Aligned_cols=49 Identities=14% Similarity=0.287 Sum_probs=39.5
Q ss_pred HHhChHHHHH----hCCCCCCHHHHHhhcCCCCCC-cchHHHHHHHhhcCCceeecc
Q 040869 36 IELGIADIIH----SHGRAITLSELVSALDIQPTK-TTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 36 ~~L~ifd~l~----~~~~~~s~~eLA~~~~~~~~~-~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+..|++.|. +.+-+.|..|||+.+|+ + +..+++.|+.|...|++....
T Consensus 7 ~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~---~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 7 RQQEVLDLIRAHIESTGYPPSIREIARAVGL---RSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCC---CChHHHHHHHHHHHHCCCEecCC
Confidence 3445555554 23457899999999999 8 899999999999999999874
No 85
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=94.90 E-value=0.017 Score=37.74 Aligned_cols=60 Identities=17% Similarity=0.309 Sum_probs=48.2
Q ss_pred hHHHHH-hCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc---ceecchhcccccc
Q 040869 40 IADIIH-SHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE---AYGLTAASTLLIK 106 (131)
Q Consensus 40 ifd~l~-~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~---~y~~t~~s~~L~~ 106 (131)
|||+|. ..++++...-|.-.+++ +-....+++..|+..|++.... ++ .|.+|+.+.-|.+
T Consensus 20 i~dIL~~~~~~~~~~Tri~y~aNl---ny~~~~~yi~~L~~~Gli~~~~----~~~~~~y~lT~KG~~fle 83 (95)
T COG3432 20 IFDILKAISEGGIGITRIIYGANL---NYKRAQKYIEMLVEKGLIIKQD----NGRRKVYELTEKGKRFLE 83 (95)
T ss_pred HHHHHHHhcCCCCCceeeeeecCc---CHHHHHHHHHHHHhCCCEEecc----CCccceEEEChhHHHHHH
Confidence 466665 34678889999999999 9999999999999999666554 33 6999999986643
No 86
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=94.77 E-value=0.09 Score=39.95 Aligned_cols=73 Identities=11% Similarity=0.253 Sum_probs=56.1
Q ss_pred HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC--CCCcceecchhcccc
Q 040869 28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQEEAYGLTAASTLL 104 (131)
Q Consensus 28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~~~~y~~t~~s~~L 104 (131)
..++|...+++.|.+.|+. .+|+.+.|||+++|+ +.+.+.-=+..|...|+++..... -|.++.+-......+
T Consensus 16 v~kalaS~vRv~Il~lL~~-k~plNvneiAe~lgL---pqst~s~~ik~Le~aGlirT~t~karkG~QKiC~s~~~ei~ 90 (308)
T COG4189 16 VLKALASKVRVAILQLLHR-KGPLNVNEIAEALGL---PQSTMSANIKVLEKAGLIRTETVKARKGSQKICISTTDEIE 90 (308)
T ss_pred HHHHHHHHHHHHHHHHHHH-hCCCCHHHHHHHhCC---chhhhhhhHHHHHhcCceeeeeeccccCceeEeEeecceEE
Confidence 4568889999999999986 579999999999999 888898899999999999865321 223444444444433
No 87
>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=94.74 E-value=0.035 Score=30.98 Aligned_cols=23 Identities=9% Similarity=0.508 Sum_probs=18.3
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+.|+.+||+.+|+ +...++|+++
T Consensus 21 G~si~~IA~~~gv---sr~TvyR~l~ 43 (45)
T PF02796_consen 21 GMSIAEIAKQFGV---SRSTVYRYLN 43 (45)
T ss_dssp T--HHHHHHHTTS----HHHHHHHHC
T ss_pred CCCHHHHHHHHCc---CHHHHHHHHh
Confidence 3999999999999 9999999985
No 88
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=94.36 E-value=0.089 Score=42.67 Aligned_cols=45 Identities=18% Similarity=0.251 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
.++|.|.+||++++++ +++.+++++..|...|++.+.+ ++.|.+.
T Consensus 307 ~g~~~t~~~La~~l~~---~~~~v~~iL~~L~~agLI~~~~----~g~~~l~ 351 (412)
T PRK04214 307 HGKALDVDEIRRLEPM---GYDELGELLCELARIGLLRRGE----RGQWVLA 351 (412)
T ss_pred cCCCCCHHHHHHHhCC---CHHHHHHHHHHHHhCCCeEecC----CCceEec
Confidence 3679999999999999 9999999999999999999765 4567655
No 89
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=94.32 E-value=0.083 Score=40.16 Aligned_cols=52 Identities=13% Similarity=0.202 Sum_probs=44.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
|+.|+.|||+.+|+ +...+|.+||.|...|++..... .+..|+.-+....+.
T Consensus 29 g~~tA~eis~~sgv---P~~kvY~vl~sLe~kG~v~~~~g--~P~~y~av~p~~~i~ 80 (247)
T COG1378 29 GEATAKEISEASGV---PRPKVYDVLRSLEKKGLVEVIEG--RPKKYRAVPPEELIE 80 (247)
T ss_pred CCccHHHHHHHcCC---CchhHHHHHHHHHHCCCEEeeCC--CCceEEeCCHHHHHH
Confidence 78999999999999 99999999999999999998641 267898887765443
No 90
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=94.31 E-value=0.096 Score=40.88 Aligned_cols=56 Identities=16% Similarity=0.246 Sum_probs=43.8
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc-eeecccCCCCcceecchh
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC-FNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl-~~~~~~~~~~~~y~~t~~ 100 (131)
...|.+.|.+ +.+.+.++||+++|+ +...+.|.++.|...|+ +.... +..|.+.+-
T Consensus 6 ~~~il~~L~~-~~~~s~~~LA~~lgv---sr~tV~~~l~~L~~~G~~i~~~~----~~Gy~L~~~ 62 (319)
T PRK11886 6 MLQLLSLLAD-GDFHSGEQLGEELGI---SRAAIWKHIQTLEEWGLDIFSVK----GKGYRLAEP 62 (319)
T ss_pred HHHHHHHHHc-CCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCceEEec----CCeEEecCc
Confidence 4567778874 578999999999999 99999999999999999 44333 345765443
No 91
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=94.27 E-value=0.088 Score=39.88 Aligned_cols=47 Identities=15% Similarity=0.172 Sum_probs=41.6
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+..|.+.|.+ .+.++..|||+.+|+ .+..++|-|+.|...|++.+..
T Consensus 7 ~~~Il~~l~~-~~~~~~~ela~~l~v---S~~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 7 HQILLELLAQ-LGFVTVEKVIERLGI---SPATARRDINKLDESGKLKKVR 53 (251)
T ss_pred HHHHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEec
Confidence 3457888875 578999999999999 9999999999999999999875
No 92
>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=94.18 E-value=0.39 Score=36.52 Aligned_cols=46 Identities=11% Similarity=0.195 Sum_probs=40.5
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.|++.|...++-++..+||+++|+ .+..+++-+|.|.+.|++.-.+
T Consensus 187 ~IL~~L~~~egrlse~eLAerlGV---SRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 187 HIFEELDGNEGLLVASKIADRVGI---TRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHhccccccccHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecc
Confidence 578888754478999999999999 9999999999999999999763
No 93
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=94.16 E-value=0.073 Score=44.14 Aligned_cols=68 Identities=21% Similarity=0.238 Sum_probs=53.4
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc-Ccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK-DKP 109 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~-~~~ 109 (131)
.+..|...|.. .+++|..+||+++++ ++..+.|++.-|.+.|++..... ....|.+|+-++.+.. ..|
T Consensus 7 ~e~~vL~~L~~-~~~~s~~eLA~~l~l---~~~tVt~~i~~Le~kGlV~~~~~--~~~~i~LTeeG~~~~~~g~p 75 (489)
T PRK04172 7 NEKKVLKALKE-LKEATLEELAEKLGL---PPEAVMRAAEWLEEKGLVKVEER--VEEVYVLTEEGKKYAEEGLP 75 (489)
T ss_pred HHHHHHHHHHh-CCCCCHHHHHHHhCc---CHHHHHHHHHHHHhCCCEEEEee--eEEEEEECHHHHHHHHhcCH
Confidence 44556677764 468999999999999 99999999999999999997641 1356999999985544 444
No 94
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=94.13 E-value=0.081 Score=39.53 Aligned_cols=54 Identities=15% Similarity=0.170 Sum_probs=44.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
..+|..|||+.+++ ++..+.|+++.|...|++.+.... ....+.+|+.++.+..
T Consensus 20 ~~IS~~eLA~~L~i---S~~Tvsr~Lk~LEe~GlI~R~~~~-r~~~v~LTekG~~ll~ 73 (217)
T PRK14165 20 VKISSSEFANHTGT---SSKTAARILKQLEDEGYITRTIVP-RGQLITITEKGLDVLY 73 (217)
T ss_pred CCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEEcC-CceEEEECHHHHHHHH
Confidence 56999999999999 999999999999999999876421 1456899998885543
No 95
>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=93.92 E-value=0.11 Score=28.66 Aligned_cols=37 Identities=16% Similarity=0.287 Sum_probs=26.7
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
++..|...|.+ ++..|+.+||+.+|+ ++..+.+=++.
T Consensus 4 ~D~~Il~~Lq~-d~r~s~~~la~~lgl---S~~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQE-DGRRSYAELAEELGL---SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHH--TTS-HHHHHHHHTS----HHHHHHHHHH
T ss_pred HHHHHHHHHHH-cCCccHHHHHHHHCc---CHHHHHHHHHH
Confidence 56778889986 578999999999999 77766554443
No 96
>PRK05638 threonine synthase; Validated
Probab=93.92 E-value=0.1 Score=42.70 Aligned_cols=63 Identities=22% Similarity=0.299 Sum_probs=46.8
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcC--CCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALD--IQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~--~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
++.|+..|.+ ++++..||++.++ + ....+++.|+.|...|+++..........|.+|+.++.+
T Consensus 373 r~~IL~~L~~--~~~~~~el~~~l~~~~---s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~ 437 (442)
T PRK05638 373 KLEILKILSE--REMYGYEIWKALGKPL---KYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRL 437 (442)
T ss_pred HHHHHHHHhh--CCccHHHHHHHHcccC---CcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHH
Confidence 3446666763 6899999999998 7 788999999999999999753110112348999887744
No 97
>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=93.90 E-value=0.11 Score=36.90 Aligned_cols=45 Identities=13% Similarity=-0.012 Sum_probs=39.0
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
..|+++|.. .+.+|-+|||..+|+ +...++|+|..|...|++...
T Consensus 17 v~Vl~aL~~-~~~~tdEeLa~~Lgi---~~~~VRk~L~~L~e~~Lv~~~ 61 (158)
T TIGR00373 17 GLVLFSLGI-KGEFTDEEISLELGI---KLNEVRKALYALYDAGLADYK 61 (158)
T ss_pred HHHHHHHhc-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCceee
Confidence 457888874 368999999999999 999999999999999999543
No 98
>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=93.86 E-value=0.081 Score=32.15 Aligned_cols=36 Identities=14% Similarity=0.272 Sum_probs=33.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
-++|-++||..+|+ ....+.|+|+.|...|++....
T Consensus 27 ~~lt~~~iA~~~g~---sr~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 27 LPLTQEEIADMLGV---SRETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp EESSHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEET
T ss_pred ecCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEcC
Confidence 47999999999999 9999999999999999999763
No 99
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=93.79 E-value=0.12 Score=38.64 Aligned_cols=45 Identities=20% Similarity=0.314 Sum_probs=38.3
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.|.+.|...+.+.|++|+|+++|+ +....+|-|-+|++.|++..+
T Consensus 162 ~i~~~~~~~~~~~Taeela~~~gi---SRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 162 KVREALKEPDQELTAEELAQALGI---SRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred HHHHHHhCcCCccCHHHHHHHhCc---cHHHHHHHHHHHHhcCeeeEE
Confidence 355566633589999999999999 999999999999999999864
No 100
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=93.76 E-value=0.11 Score=39.50 Aligned_cols=47 Identities=13% Similarity=0.194 Sum_probs=41.8
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+-.|.+.|.+ .+.+++.|||+.+++ ++..++|-|..|...|++.+..
T Consensus 7 ~~~Il~~l~~-~~~~~~~ela~~l~v---S~~TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 7 HDAIIELVKQ-QGYVSTEELVEHFSV---SPQTIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred HHHHHHHHHH-cCCEeHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec
Confidence 4457888875 578999999999999 9999999999999999999875
No 101
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=93.60 E-value=0.17 Score=34.28 Aligned_cols=52 Identities=19% Similarity=0.248 Sum_probs=41.0
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
+...|.. .+|.+..+|++.+++ ....+||+. -..|-|++.+ .|.|.+|+.++
T Consensus 64 ~A~~L~~-~Gp~~~~~l~~~~~~-----~~A~~IL~~-N~YGWFeRv~----rGvY~LT~~G~ 115 (118)
T PF09929_consen 64 CAAALAE-HGPSRPADLRKATGV-----PKATSILRD-NHYGWFERVE----RGVYALTPAGR 115 (118)
T ss_pred HHHHHHH-cCCCCHHHHHHhcCC-----ChHHHHHHh-Ccccceeeec----cceEecCcchh
Confidence 3445664 479999999999998 355666664 6789999987 89999999876
No 102
>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=93.50 E-value=0.22 Score=34.14 Aligned_cols=48 Identities=19% Similarity=0.334 Sum_probs=39.5
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhc----CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 36 IELGIADIIHSHGRAITLSELVSAL----DIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~----~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.++.|..+|.+ .++.|+.||.+.+ +. +...+.++|+-|...|++....
T Consensus 5 ~E~~VM~vlW~-~~~~t~~eI~~~l~~~~~~---~~tTv~T~L~rL~~KG~v~~~k 56 (130)
T TIGR02698 5 AEWEVMRVVWT-LGETTSRDIIRILAEKKDW---SDSTIKTLLGRLVDKGCLTTEK 56 (130)
T ss_pred HHHHHHHHHHc-CCCCCHHHHHHHHhhccCC---cHHHHHHHHHHHHHCCceeeec
Confidence 56778888875 4689999977765 56 7889999999999999998764
No 103
>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=93.40 E-value=0.11 Score=37.16 Aligned_cols=46 Identities=20% Similarity=0.244 Sum_probs=41.4
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
-.|..+||+.+|+ +.+.+.|.+..|...+++.+.. .|.|..+|--.
T Consensus 75 ~~t~~~ia~~l~i---S~~Tv~r~ik~L~e~~iI~k~~----~G~Y~iNP~~~ 120 (165)
T PF05732_consen 75 VATQKEIAEKLGI---SKPTVSRAIKELEEKNIIKKIR----NGAYMINPNFF 120 (165)
T ss_pred EeeHHHHHHHhCC---CHHHHHHHHHHHHhCCcEEEcc----CCeEEECcHHh
Confidence 3789999999999 9999999999999999999876 78999999743
No 104
>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=93.39 E-value=0.11 Score=30.92 Aligned_cols=37 Identities=16% Similarity=0.237 Sum_probs=32.0
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|..+ |..+||++.|+ +...+++.++.|...|++....
T Consensus 21 g~~lps~~~la~~~~v---sr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 21 GDRLPSERELAERYGV---SRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp TSBE--HHHHHHHHTS----HHHHHHHHHHHHHTTSEEEET
T ss_pred CCEeCCHHHHHHHhcc---CCcHHHHHHHHHHHCCcEEEEC
Confidence 4567 99999999999 9999999999999999998765
No 105
>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=93.36 E-value=0.11 Score=33.86 Aligned_cols=48 Identities=10% Similarity=0.261 Sum_probs=39.1
Q ss_pred HHhChHHHHHh---CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 36 IELGIADIIHS---HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 36 ~~L~ifd~l~~---~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
++-.|+++|.. .+.++++++|++++++ +...++..++.|+..|.+-.+
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~---~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGM---SENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHHSTS----HHHHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHHhCc---CHHHHHHHHHHHHhCCeEecc
Confidence 45567888865 2467999999999999 999999999999999987654
No 106
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=93.24 E-value=0.15 Score=39.10 Aligned_cols=48 Identities=8% Similarity=0.097 Sum_probs=42.3
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
-...|.+.|.+ .+.+++.|||+.+++ ++.+++|=|+.|...|++.+..
T Consensus 18 R~~~Il~~L~~-~~~vtv~eLa~~l~V---S~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 18 RREQIIQRLRQ-QGSVQVNDLSALYGV---STVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHH-cCCEeHHHHHHHHCC---CHHHHHHHHHHHHhCCCeEEEe
Confidence 34568888876 457999999999999 9999999999999999999876
No 107
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=93.05 E-value=0.21 Score=37.59 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=40.7
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
...|.+.|.+ .+.++..|||+.+++ ++..++|-|..|...|.+....
T Consensus 6 ~~~Il~~l~~-~~~~~~~eLa~~l~V---S~~TiRRdL~~L~~~~~l~r~~ 52 (240)
T PRK10411 6 QQAIVDLLLN-HTSLTTEALAEQLNV---SKETIRRDLNELQTQGKILRNH 52 (240)
T ss_pred HHHHHHHHHH-cCCCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEec
Confidence 3457788875 468999999999999 9999999999999999888764
No 108
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=92.98 E-value=1 Score=32.77 Aligned_cols=64 Identities=16% Similarity=0.115 Sum_probs=49.0
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK 106 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~ 106 (131)
.|.-.|.. .+++|..+||+.+++ +...+.|++.-|...|++.+.... |. .-...+|+.++.+..
T Consensus 49 ~iL~~L~~-~~~itq~eLa~~l~l---~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~ 114 (185)
T PRK13777 49 HILWIAYH-LKGASISEIAKFGVM---HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLL 114 (185)
T ss_pred HHHHHHHh-CCCcCHHHHHHHHCC---CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence 35556654 368999999999999 999999999999999999986432 11 123678888876654
No 109
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=92.97 E-value=0.17 Score=38.44 Aligned_cols=46 Identities=11% Similarity=0.205 Sum_probs=41.8
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
-.|.+.|.+ .+.++++|||+.+++ .+.+++|=|+.|...|++.+..
T Consensus 8 ~~Il~~l~~-~g~v~v~eLa~~~~V---S~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 8 QKILELLKE-KGKVSVEELAELFGV---SEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHH-cCcEEHHHHHHHhCC---CHHHHHHhHHHHHHCCcEEEEe
Confidence 457888886 578999999999999 9999999999999999999976
No 110
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=92.96 E-value=0.12 Score=39.26 Aligned_cols=74 Identities=15% Similarity=0.184 Sum_probs=55.1
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-ccccCcccChHHhH
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLIKDKPYCMSPTV 116 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~~~~~~sl~~~~ 116 (131)
+.|.-.|.....-....|||+++|+ -+..+.--++-|+..|++.+.. .+.|..|.-+. +|.+ +-..++.|+
T Consensus 13 fqIL~ei~~~qp~v~q~eIA~~lgi---T~QaVsehiK~Lv~eG~i~~~g----R~~Y~iTkkG~e~l~~-~~~dlr~f~ 84 (260)
T COG1497 13 FQILSEIAVRQPRVKQKEIAKKLGI---TLQAVSEHIKELVKEGLIEKEG----RGEYEITKKGAEWLLE-QLSDLRRFS 84 (260)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHcCC---CHHHHHHHHHHHHhccceeecC----CeeEEEehhHHHHHHH-HHHHHHHHH
Confidence 3444444433356999999999999 8999999999999999999975 78999999886 4433 222466655
Q ss_pred Hhh
Q 040869 117 SAF 119 (131)
Q Consensus 117 ~~~ 119 (131)
...
T Consensus 85 ~ev 87 (260)
T COG1497 85 EEV 87 (260)
T ss_pred HHH
Confidence 543
No 111
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=92.94 E-value=0.15 Score=42.38 Aligned_cols=70 Identities=9% Similarity=0.174 Sum_probs=55.1
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-ccccCcc
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLIKDKP 109 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~~~~~ 109 (131)
+++..|...|...+..++..+||+.+|+ +...+.+.+..|.+.|+++-.... ...|.+|.-++ ++..+.|
T Consensus 3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~---~~~~v~~~~~~L~~kg~v~~~~~~--~~~~~LT~eG~~~l~~G~P 73 (492)
T PLN02853 3 MAEEALLGALSNNEEISDSGQFAASHGL---DHNEVVGVIKSLHGFRYVDAQDIK--RETWVLTEEGKKYAAEGSP 73 (492)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHcCC---CHHHHHHHHHHHHhCCCEEEEEEE--EEEEEECHHHHHHHHcCCH
Confidence 4567788888753323899999999999 999999999999999988865321 57799999988 5555555
No 112
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=92.93 E-value=0.1 Score=38.49 Aligned_cols=43 Identities=26% Similarity=0.336 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 27 LSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 27 ~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
..-.+|+.|.++|-|| . ++..++.|||+.+|+ .+..+...||-
T Consensus 159 rQ~~vL~~A~~~GYFd-~---PR~~~l~dLA~~lGI---Skst~~ehLRr 201 (215)
T COG3413 159 RQLEVLRLAYKMGYFD-Y---PRRVSLKDLAKELGI---SKSTLSEHLRR 201 (215)
T ss_pred HHHHHHHHHHHcCCCC-C---CccCCHHHHHHHhCC---CHHHHHHHHHH
Confidence 4678999999999998 3 367999999999999 77776666654
No 113
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=92.74 E-value=0.19 Score=32.66 Aligned_cols=70 Identities=16% Similarity=0.201 Sum_probs=51.6
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD 107 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~ 107 (131)
...+..+...|... ++.+..+||+.+++ ++..+.|+++-|...|++...... |. .-.+.+|+.++.+...
T Consensus 21 t~~q~~~L~~l~~~-~~~~~~~la~~l~i---~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~ 92 (126)
T COG1846 21 TPPQYQVLLALYEA-GGITVKELAERLGL---DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQ 92 (126)
T ss_pred CHHHHHHHHHHHHh-CCCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHH
Confidence 33455566667653 34444999999999 999999999999999999987543 21 2358899988865543
No 114
>PHA02943 hypothetical protein; Provisional
Probab=92.63 E-value=0.31 Score=34.55 Aligned_cols=45 Identities=11% Similarity=0.107 Sum_probs=39.7
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..|.+.|. .|..|..|||+++|+ +-..++=+|..|...|.+.+..
T Consensus 14 ~eILE~Lk--~G~~TtseIAkaLGl---S~~qa~~~LyvLErEG~VkrV~ 58 (165)
T PHA02943 14 IKTLRLLA--DGCKTTSRIANKLGV---SHSMARNALYQLAKEGMVLKVE 58 (165)
T ss_pred HHHHHHHh--cCCccHHHHHHHHCC---CHHHHHHHHHHHHHcCceEEEe
Confidence 35777774 578999999999999 8899999999999999999875
No 115
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=92.62 E-value=0.19 Score=38.14 Aligned_cols=47 Identities=17% Similarity=0.243 Sum_probs=41.9
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+-.|.+.|.+ .+.+++.|||+.+++ ++.+++|=|+.|...|++.+..
T Consensus 7 ~~~Il~~L~~-~~~v~v~eLa~~l~V---S~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 7 QAAILEYLQK-QGKTSVEELAQYFDT---TGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHH-cCCEEHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEEE
Confidence 4568888886 468999999999999 9999999999999999999875
No 116
>PF13730 HTH_36: Helix-turn-helix domain
Probab=92.56 E-value=0.15 Score=29.13 Aligned_cols=30 Identities=13% Similarity=0.165 Sum_probs=27.9
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF 83 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~ 83 (131)
.|.+.||+.+|+ ....+.|.++.|...|++
T Consensus 26 pS~~~la~~~g~---s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLGV---SRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHCc---CHHHHHHHHHHHHHCcCC
Confidence 389999999999 999999999999999975
No 117
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=92.55 E-value=1.4 Score=31.72 Aligned_cols=78 Identities=21% Similarity=0.307 Sum_probs=57.7
Q ss_pred HHHhHHHHHHHHHHHHhC-------hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcc
Q 040869 22 LMFSHLSSMSLKCAIELG-------IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEA 94 (131)
Q Consensus 22 ~~~~~~~~~aL~~a~~L~-------ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~ 94 (131)
.+++.|...|+.++...+ |..+|...+.|+++.+|+..++.. |...+.=-||-|...|+++..... ..-+
T Consensus 63 ~Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrdR~K~laDic~~ln~e--Dth~itYslrKL~k~gLit~t~~g-kevT 139 (199)
T COG5631 63 EAFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRDRPKSLADICQMLNRE--DTHNITYSLRKLLKGGLITRTGSG-KEVT 139 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcCchhhHHHHHHHhccc--cchhHHHHHHHHHhccceecCCCC-ceEE
Confidence 456778989998887766 344454457999999999999982 444667778999999999987521 1245
Q ss_pred eecchhcc
Q 040869 95 YGLTAAST 102 (131)
Q Consensus 95 y~~t~~s~ 102 (131)
|..|+.+.
T Consensus 140 y~vTa~G~ 147 (199)
T COG5631 140 YEVTALGH 147 (199)
T ss_pred EEEecchH
Confidence 88888763
No 118
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=92.38 E-value=0.22 Score=41.48 Aligned_cols=70 Identities=16% Similarity=0.212 Sum_probs=55.4
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-ccccCcc
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLIKDKP 109 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~~~~~ 109 (131)
..+..|...|.+..+..+..+||+.+|+ +...+.+.+..|.+.|+++-.... ...|.+|.-++ ++..+.|
T Consensus 6 ~~e~~iL~~l~~~~~~~~~~~la~~~~~---~~~~v~~~~~~L~~kg~v~~~~~~--~~~~~LT~eG~~~~~~G~P 76 (494)
T PTZ00326 6 LEENTILSKLESENEIVNSLALAESLNI---DHQKVVGAIKSLESANYITTEMKK--SNTWTLTEEGEDYLKNGSP 76 (494)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHcCC---CHHHHHHHHHHHHhCCCEEEEEEE--EEEEEECHHHHHHHHcCCH
Confidence 4556677888753457999999999999 999999999999999998865321 57799999988 5555555
No 119
>PRK00215 LexA repressor; Validated
Probab=92.26 E-value=0.39 Score=34.94 Aligned_cols=40 Identities=13% Similarity=0.267 Sum_probs=34.3
Q ss_pred hCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 46 SHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 46 ~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+.+.+.|..|||+++|+. +...+.|+++.|...|+++...
T Consensus 19 ~~~~~~s~~ela~~~~~~--~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 19 ETGYPPSRREIADALGLR--SPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred HhCCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCCCEEeCC
Confidence 346789999999999972 4678999999999999998765
No 120
>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=92.17 E-value=0.66 Score=35.79 Aligned_cols=46 Identities=20% Similarity=0.112 Sum_probs=39.1
Q ss_pred CCCCHHHHHhhcC--CCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 49 RAITLSELVSALD--IQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 49 ~~~s~~eLA~~~~--~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
+...+.+||++++ + +...+..-|..|...|++++.+ +|.|..|..+
T Consensus 136 ~~~~~~~ia~~l~p~i---s~~ev~~sL~~L~~~glikk~~----~g~y~~t~~~ 183 (271)
T TIGR02147 136 FADDPEELAKRCFPKI---SAEQVKESLDLLERLGLIKKNE----DGFYKQTDKA 183 (271)
T ss_pred CCCCHHHHHHHhCCCC---CHHHHHHHHHHHHHCCCeeECC----CCcEEeecce
Confidence 4457889999998 6 6778999999999999999886 7899988763
No 121
>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=92.10 E-value=0.15 Score=33.33 Aligned_cols=44 Identities=16% Similarity=0.200 Sum_probs=33.3
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.|++.|.. .+.++-++||..+|+ ++..++++|..|...|++...
T Consensus 17 ~Il~~L~~-~~~l~de~la~~~~l---~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 17 RILDALLR-KGELTDEDLAKKLGL---KPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHHHHHHH-H--B-HHHHHHTT-S----HHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHH-cCCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCCeEEE
Confidence 36788874 367999999999999 999999999999999999765
No 122
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=92.02 E-value=0.6 Score=31.63 Aligned_cols=78 Identities=14% Similarity=0.143 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcC-CCCCCcchHHHHHHHhhcCCceeecccC--C
Q 040869 14 QGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALD-IQPTKTTGLFRLMRLLVHSSCFNKTKVN--G 90 (131)
Q Consensus 14 ~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~-~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~ 90 (131)
-+.+.+++++.+-|..-+|+...+ ++.-..||-+.++ + .+..|.+-||.|...|++.+..-. .
T Consensus 11 c~~~~~l~~ig~kW~~lIl~~L~~-----------g~~RF~eL~r~i~~I---s~k~Ls~~Lk~Le~~Glv~R~~~~~~P 76 (120)
T COG1733 11 CPVEEALEVIGGKWTLLILRDLFD-----------GPKRFNELRRSIGGI---SPKMLSRRLKELEEDGLVERVVYPEEP 76 (120)
T ss_pred CCHHHHHHHHcCccHHHHHHHHhc-----------CCCcHHHHHHHcccc---CHHHHHHHHHHHHHCCCEEeeecCCCC
Confidence 345667777777777666554322 6788999999988 8 889999999999999999987421 1
Q ss_pred CCcceecchhccccc
Q 040869 91 QEEAYGLTAASTLLI 105 (131)
Q Consensus 91 ~~~~y~~t~~s~~L~ 105 (131)
..-.|++|+.++.|.
T Consensus 77 prveY~LT~~G~~L~ 91 (120)
T COG1733 77 PRVEYRLTEKGRDLL 91 (120)
T ss_pred ceeEEEEhhhHHHHH
Confidence 123599999988665
No 123
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=91.93 E-value=0.33 Score=35.49 Aligned_cols=45 Identities=16% Similarity=0.166 Sum_probs=38.0
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.|.+.+.+...+.|..|||+++++ .+.++++-+.+|+..|++...
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~i---S~~Tv~~~~~~~~~~~~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTI---SRTTARRYLEYCASRHLIIAE 210 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCc---cHHHHHHHHHHHHhCCeEEEE
Confidence 466667642236899999999999 999999999999999999875
No 124
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=91.80 E-value=0.21 Score=31.30 Aligned_cols=35 Identities=14% Similarity=0.298 Sum_probs=24.6
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
++..|++ |+|+|..+||.++|. +.+.+...|..+.
T Consensus 29 LLr~LA~-G~PVt~~~LA~a~g~---~~e~v~~~L~~~p 63 (77)
T PF12324_consen 29 LLRLLAK-GQPVTVEQLAAALGW---PVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHTT-TS-B-HHHHHHHHT-----HHHHHHHHHH-T
T ss_pred HHHHHHc-CCCcCHHHHHHHHCC---CHHHHHHHHHhCC
Confidence 6777885 899999999999999 7777777776654
No 125
>PRK01381 Trp operon repressor; Provisional
Probab=91.75 E-value=0.29 Score=32.17 Aligned_cols=42 Identities=12% Similarity=0.134 Sum_probs=35.8
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHS 80 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~ 80 (131)
.+.+++|+..|-+ +.+|..|||+.+|+ ....+.|.=|.|...
T Consensus 41 l~~R~~I~~~L~~--g~~sQREIa~~lGv---SiaTITRgsn~Lk~~ 82 (99)
T PRK01381 41 LGTRVRIVEELLR--GELSQREIKQELGV---GIATITRGSNSLKTA 82 (99)
T ss_pred HHHHHHHHHHHHc--CCcCHHHHHHHhCC---ceeeehhhHHHhccC
Confidence 3567899998873 78999999999999 889999988888654
No 126
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=91.43 E-value=0.47 Score=29.82 Aligned_cols=44 Identities=7% Similarity=0.133 Sum_probs=38.6
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|=|.|.. .+-.++.+||.+++. +++.++-+|..++.+|-+.+..
T Consensus 7 lRd~l~~-~gr~s~~~Ls~~~~~---p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 7 VRDLLAL-RGRMEAAQISQTLNT---PQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHH-cCcccHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEeec
Confidence 4567775 468999999999999 9999999999999999999764
No 127
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=91.25 E-value=0.17 Score=28.33 Aligned_cols=41 Identities=10% Similarity=0.268 Sum_probs=23.3
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
.++.+...+.. +.|..+||+.+|+ ++..++|+++.....|+
T Consensus 6 ~R~~ii~l~~~---G~s~~~ia~~lgv---s~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 6 RRAQIIRLLRE---GWSIREIAKRLGV---SRSTVYRWIKRYREEGL 46 (50)
T ss_dssp ----HHHHHHH---T--HHHHHHHHTS----HHHHHHHHT-------
T ss_pred HHHHHHHHHHC---CCCHHHHHHHHCc---CHHHHHHHHHHcccccc
Confidence 34556666653 6999999999999 99999999988766663
No 128
>PRK09954 putative kinase; Provisional
Probab=90.86 E-value=0.49 Score=37.31 Aligned_cols=44 Identities=18% Similarity=0.211 Sum_probs=38.9
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+.+|...|.+ .+.+|..|||+.+++ ....+.+.++.|...|++.
T Consensus 5 ~~~il~~l~~-~~~~s~~~la~~l~~---s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 5 EKEILAILRR-NPLIQQNEIADILQI---SRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHH-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCcC
Confidence 4568888886 468999999999999 9999999999999999985
No 129
>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=90.78 E-value=0.5 Score=30.33 Aligned_cols=41 Identities=15% Similarity=0.213 Sum_probs=34.5
Q ss_pred HHHHHhChHH-HHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869 33 KCAIELGIAD-IIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH 79 (131)
Q Consensus 33 ~~a~~L~ifd-~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~ 79 (131)
..+-++.|+. .|. +.+|..|||+.+|+ +...+.|+=|.|..
T Consensus 34 ~l~~R~~va~~lL~---~g~syreIa~~tgv---S~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 34 ALAQRWQVAKELLD---EGKSYREIAEETGV---SIATITRVSRCLKY 75 (87)
T ss_dssp HHHHHHHHHHHHHH---TTSSHHHHHHHHTS---THHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH---CCCCHHHHHHHhCC---CHHHHHHHHHHHHc
Confidence 3456788998 776 57999999999999 99999999998864
No 130
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=90.77 E-value=0.62 Score=30.20 Aligned_cols=48 Identities=10% Similarity=0.142 Sum_probs=41.9
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..+.|..+|.. -+|=.+.-||..+++ +...+.++++.|..+|++++..
T Consensus 8 l~~~IL~hl~~-~~~Dy~k~ia~~l~~---~~~~v~~~l~~Le~~GLler~~ 55 (92)
T PF10007_consen 8 LDLKILQHLKK-AGPDYAKSIARRLKI---PLEEVREALEKLEEMGLLERVE 55 (92)
T ss_pred hHHHHHHHHHH-HCCCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEec
Confidence 35677888875 368889999999999 9999999999999999999986
No 131
>PRK12423 LexA repressor; Provisional
Probab=90.64 E-value=0.64 Score=34.00 Aligned_cols=38 Identities=13% Similarity=0.220 Sum_probs=32.3
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+-+-|..|||+++|+. .+..+++-|+.|...|+++...
T Consensus 23 g~~Ps~~eia~~~g~~--s~~~v~~~l~~L~~~G~l~~~~ 60 (202)
T PRK12423 23 GQPPSLAEIAQAFGFA--SRSVARKHVQALAEAGLIEVVP 60 (202)
T ss_pred CCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCCCEEecC
Confidence 3467999999999941 6778999999999999999864
No 132
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=90.60 E-value=0.34 Score=26.81 Aligned_cols=24 Identities=13% Similarity=0.321 Sum_probs=17.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
...|..+||+.+|. ++..+.|.++
T Consensus 19 ~G~s~~~IA~~lg~---s~sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGR---SRSTVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT-----HHHHHHHHH
T ss_pred cCCCHHHHHHHHCc---CcHHHHHHHh
Confidence 46999999999999 9999999886
No 133
>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=90.40 E-value=0.48 Score=30.86 Aligned_cols=41 Identities=15% Similarity=0.140 Sum_probs=34.7
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH 79 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~ 79 (131)
.+.+.||+..|-+ +++|-.|||+++|+ ....+.|.=|.|..
T Consensus 41 l~~R~~i~~~Ll~--~~~tQrEIa~~lGi---S~atIsR~sn~lk~ 81 (94)
T TIGR01321 41 LGDRIRIVNELLN--GNMSQREIASKLGV---SIATITRGSNNLKT 81 (94)
T ss_pred HHHHHHHHHHHHh--CCCCHHHHHHHhCC---ChhhhhHHHhhccc
Confidence 4567899997763 68999999999999 88999998887763
No 134
>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=90.27 E-value=0.45 Score=28.37 Aligned_cols=43 Identities=14% Similarity=0.277 Sum_probs=34.5
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
|++.|-+ .|..|+.+|++.+++ +++.++.-|-.|...|++...
T Consensus 18 V~~~Ll~-~G~ltl~~i~~~t~l---~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 18 VGEVLLS-RGRLTLREIVRRTGL---SPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHH-C-SEEHHHHHHHHT-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHH-cCCcCHHHHHHHhCC---CHHHHHHHHHHHHHcCCeeee
Confidence 5666764 468999999999999 999999999999999988753
No 135
>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=90.20 E-value=0.38 Score=31.93 Aligned_cols=51 Identities=25% Similarity=0.364 Sum_probs=40.8
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCC-CCCcchHHHHHHHhhcCCceeecc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQ-PTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~-~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.++.|.++|.+.+ ++|+.||.+.++-. +-....+.-+|+-|+..|+++...
T Consensus 4 ~E~~IM~~lW~~~-~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~ 55 (115)
T PF03965_consen 4 LELEIMEILWESG-EATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK 55 (115)
T ss_dssp HHHHHHHHHHHHS-SEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHhCC-CCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee
Confidence 5677888887654 59999999998761 225788999999999999999875
No 136
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.19 E-value=0.67 Score=25.81 Aligned_cols=38 Identities=11% Similarity=0.267 Sum_probs=30.4
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
.|...+.+ + .|+.++|+++|+ +...+++.++.....|+
T Consensus 4 ~iv~~~~~--g-~s~~~~a~~~gi---s~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 4 QIVELYLE--G-ESVREIAREFGI---SRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHHc--C-CCHHHHHHHHCC---CHhHHHHHHHHHHhcCH
Confidence 34444442 3 499999999999 99999999999888774
No 137
>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=90.17 E-value=0.6 Score=32.88 Aligned_cols=47 Identities=13% Similarity=0.171 Sum_probs=37.4
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
.|++|++|||.+.|+ ..+.+---|-.+++.|-+.+... +|.-+|+..
T Consensus 4 ~Ga~T~eELA~~FGv---ttRkvaStLa~~ta~Grl~Rv~q-~gkfRy~iP 50 (155)
T PF07789_consen 4 EGAKTAEELAGKFGV---TTRKVASTLAMVTATGRLIRVNQ-NGKFRYCIP 50 (155)
T ss_pred cCcccHHHHHHHhCc---chhhhHHHHHHHHhcceeEEecC-CCceEEeCC
Confidence 589999999999999 88999999999999998887642 122346553
No 138
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=90.05 E-value=0.26 Score=35.74 Aligned_cols=45 Identities=13% Similarity=0.052 Sum_probs=39.7
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
-.|.+.|.. .+.++..+||+.+++ ++.+++|=|+.|...|++.+.
T Consensus 10 ~~Il~~l~~-~~~~~~~~La~~~~v---S~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 10 KALQELIEE-NPFITDEELAEKFGV---SIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHH-CCCEEHHHHHHHHCc---CHHHHHHHHHHHhcchHHHHH
Confidence 457778875 578999999999999 999999999999999998875
No 139
>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=89.82 E-value=0.85 Score=29.89 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=35.4
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
+...+|.+..+++.+|+.++|+.+|+ .+..|.++||- .|++...
T Consensus 11 Ka~~~d~~~~~~~~~ti~~~AK~L~i---~~~~l~~~Lr~---~g~l~~~ 54 (111)
T PF03374_consen 11 KAEFYDAFVDSDGLYTIREAAKLLGI---GRNKLFQWLRE---KGWLYRR 54 (111)
T ss_pred hhHHHHHHHcCCCCccHHHHHHHhCC---CHHHHHHHHHh---CCceEEC
Confidence 34567888776789999999999999 87777777764 8888874
No 140
>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=89.66 E-value=0.45 Score=36.44 Aligned_cols=37 Identities=19% Similarity=0.304 Sum_probs=33.6
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHH-HhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMR-LLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr-~L~~~gl~~~~~ 87 (131)
+++.++++||+.+|. ++..+.++++ .|+..|++....
T Consensus 253 ~~~~~~~~ia~~lg~---~~~~~~~~~e~~Li~~~li~~~~ 290 (305)
T TIGR00635 253 GGPVGLKTLAAALGE---DADTIEDVYEPYLLQIGFLQRTP 290 (305)
T ss_pred CCcccHHHHHHHhCC---CcchHHHhhhHHHHHcCCcccCC
Confidence 568999999999999 9999999999 799999997654
No 141
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=89.58 E-value=0.45 Score=30.48 Aligned_cols=36 Identities=19% Similarity=0.164 Sum_probs=33.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.-+|+..||+++++ .-+..+++||.|...|++....
T Consensus 40 K~ITps~lserlkI---~~SlAr~~Lr~L~~kG~Ik~V~ 75 (86)
T PRK09334 40 KIVTPYTLASKYGI---KISVAKKVLRELEKRGVLVLYS 75 (86)
T ss_pred cEEcHHHHHHHhcc---hHHHHHHHHHHHHHCCCEEEEe
Confidence 56999999999999 9999999999999999997653
No 142
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=89.47 E-value=0.79 Score=36.39 Aligned_cols=49 Identities=14% Similarity=0.097 Sum_probs=40.0
Q ss_pred CCCCCCHHHHHhh--cCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 47 HGRAITLSELVSA--LDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 47 ~~~~~s~~eLA~~--~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
.++|++..+||+. +++ ++.+++|-|..|...|++.+... ...+-+|..+
T Consensus 22 ~~~pv~s~~l~~~~~l~~---S~aTIR~dm~~Le~~G~l~~~h~---sagrIPT~kG 72 (339)
T PRK00082 22 TGEPVGSKTLSKRYGLGV---SSATIRNDMADLEELGLLEKPHT---SSGRIPTDKG 72 (339)
T ss_pred cCCCcCHHHHHHHhCCCC---ChHHHHHHHHHHHhCCCcCCCcC---CCCCCcCHHH
Confidence 3689999999977 888 89999999999999999998652 3445556554
No 143
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=89.38 E-value=0.48 Score=31.86 Aligned_cols=37 Identities=16% Similarity=0.121 Sum_probs=34.1
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..++|++|||+.+.+ .++.+.++|+-+...|.+.=.+
T Consensus 17 ~~~vtl~elA~~l~c---S~Rn~r~lLkkm~~~gWi~W~p 53 (115)
T PF12793_consen 17 PVEVTLDELAELLFC---SRRNARTLLKKMQEEGWITWQP 53 (115)
T ss_pred CcceeHHHHHHHhCC---CHHHHHHHHHHHHHCCCeeeeC
Confidence 357899999999999 9999999999999999999765
No 144
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=89.37 E-value=0.42 Score=34.52 Aligned_cols=36 Identities=19% Similarity=0.270 Sum_probs=33.7
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
++|+|++||++.+|. +.+.+..-||-|...|++...
T Consensus 39 ~~Pmtl~Ei~E~lg~---Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 39 RKPLTLDEIAEALGM---SKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred CCCccHHHHHHHHCC---CcchHHHHHHHHHhcchHHhh
Confidence 689999999999999 899999999999999999875
No 145
>PRK13239 alkylmercury lyase; Provisional
Probab=89.37 E-value=0.53 Score=34.95 Aligned_cols=41 Identities=12% Similarity=0.312 Sum_probs=33.3
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHS 80 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~ 80 (131)
+-.-|+..|++ |+|.|.++||+.+|. +.+.+.++|+.+...
T Consensus 23 ~~~~llr~la~-G~pvt~~~lA~~~~~---~~~~v~~~L~~l~~~ 63 (206)
T PRK13239 23 LLVPLLRLLAK-GRPVSVTTLAAALGW---PVEEVEAVLEAMPDT 63 (206)
T ss_pred HHHHHHHHHHc-CCCCCHHHHHHHhCC---CHHHHHHHHHhCCCe
Confidence 33446677874 899999999999999 999999988887643
No 146
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=89.31 E-value=0.54 Score=33.23 Aligned_cols=36 Identities=14% Similarity=0.153 Sum_probs=33.2
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
-|+|-+|||..+|+ .+..+.|+|+.|...|+++...
T Consensus 142 ~~~t~~~iA~~lG~---tretvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 142 LRLSHQAIAEAIGS---TRVTITRLLGDLRKKKLISIHK 177 (193)
T ss_pred CCCCHHHHHHHhCC---cHHHHHHHHHHHHHCCCEEecC
Confidence 36899999999999 9999999999999999998763
No 147
>PRK11642 exoribonuclease R; Provisional
Probab=88.84 E-value=0.88 Score=40.25 Aligned_cols=56 Identities=20% Similarity=0.275 Sum_probs=42.7
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCC-CCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQP-TKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~-~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
.|.+.|.+.+.|++..+|+++++++. .....|.+.|+.|...|.+.... .+.|...
T Consensus 23 ~Il~~l~~~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~----~~~~~~~ 79 (813)
T PRK11642 23 FILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTR----RQCYALP 79 (813)
T ss_pred HHHHHHHhcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcC----CceEecC
Confidence 36777765568999999999999932 12356999999999999998765 4556544
No 148
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=88.75 E-value=0.72 Score=33.09 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=32.7
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
++|-.+||+.+|+ .+..+.|+|+.|...|+++...
T Consensus 168 ~~t~~~lA~~lG~---tr~tvsR~l~~l~~~gii~~~~ 202 (211)
T PRK11753 168 KITRQEIGRIVGC---SREMVGRVLKMLEDQGLISAHG 202 (211)
T ss_pred CCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEecC
Confidence 7899999999999 9999999999999999998763
No 149
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=88.74 E-value=0.61 Score=34.21 Aligned_cols=35 Identities=14% Similarity=0.198 Sum_probs=32.9
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|+|-++||..+|+ .+..+.|+|+.|...|++....
T Consensus 184 ~lt~~~iA~~lG~---sr~tvsR~l~~l~~~g~I~~~~ 218 (235)
T PRK11161 184 TMTRGDIGNYLGL---TVETISRLLGRFQKSGMLAVKG 218 (235)
T ss_pred cccHHHHHHHhCC---cHHHHHHHHHHHHHCCCEEecC
Confidence 6899999999999 9999999999999999999773
No 150
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=88.71 E-value=0.9 Score=37.42 Aligned_cols=53 Identities=17% Similarity=0.283 Sum_probs=38.8
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
|-..|. .+|.|+.||++.+|+ +...+-|.|+.| .|++...... ..-.|+++.-
T Consensus 5 ~~~~L~--~g~~~~~eL~~~l~~---sq~~~s~~L~~L--~~~V~~~~~g-r~~~Y~l~~~ 57 (442)
T PRK09775 5 LTTLLL--QGPLSAAELAARLGV---SQATLSRLLAAL--GDQVVRFGKA-RATRYALLRP 57 (442)
T ss_pred HHHHHh--cCCCCHHHHHHHhCC---CHHHHHHHHHHh--hcceeEeccC-ceEEEEeccc
Confidence 445566 479999999999999 999999999999 7777665410 0123666543
No 151
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=88.60 E-value=0.86 Score=33.44 Aligned_cols=37 Identities=16% Similarity=0.137 Sum_probs=34.1
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|..++..+||+.+|+ +...++.-|+.|...|++...+
T Consensus 28 G~~L~e~eLae~lgV---SRtpVREAL~~L~~eGlv~~~~ 64 (224)
T PRK11534 28 DEKLRMSLLTSRYAL---GVGPLREALSQLVAERLVTVVN 64 (224)
T ss_pred CCcCCHHHHHHHHCC---ChHHHHHHHHHHHHCCCEEEeC
Confidence 567899999999999 9999999999999999998765
No 152
>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=88.36 E-value=0.18 Score=30.90 Aligned_cols=39 Identities=18% Similarity=0.440 Sum_probs=32.9
Q ss_pred CCCCCHHHHHhhc---CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSAL---DIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~---~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
++.+++.++|..+ +.+. ..+.+|-++.+|.+.|++++..
T Consensus 22 ~~~i~l~~ia~~l~~~~~k~-~~RRlYDI~NVLealgli~K~~ 63 (71)
T PF02319_consen 22 DKSISLNEIADKLISENVKT-QRRRLYDIINVLEALGLIEKQS 63 (71)
T ss_dssp CTEEEHHHHHHHCHHHCCHH-HCHHHHHHHHHHHHCTSEEEEE
T ss_pred CCcccHHHHHHHHccccccc-ccchhhHHHHHHHHhCceeecC
Confidence 3789999999999 7521 4578999999999999999864
No 153
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=88.34 E-value=0.7 Score=34.13 Aligned_cols=34 Identities=9% Similarity=0.168 Sum_probs=32.0
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
++|-.+||..+|+ .+..+.|+++.|...|++...
T Consensus 179 ~lt~~~IA~~lGi---sretlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 179 PMSRRDIADYLGL---TIETVSRALSQLQDRGLIGLS 212 (230)
T ss_pred cCCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEec
Confidence 6889999999999 999999999999999999865
No 154
>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=88.11 E-value=1 Score=35.74 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=36.5
Q ss_pred HHHhCCCCCCHHHHHhh--cCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 43 IIHSHGRAITLSELVSA--LDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 43 ~l~~~~~~~s~~eLA~~--~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+. .++|++..+|++. +++ ++.+++|-|..|...|++.+..
T Consensus 15 ~l~-~~~pv~s~~l~~~~~~~v---S~aTiR~d~~~Le~~G~l~~~h 57 (337)
T TIGR00331 15 YIK-TGQPVGSKTLLEKYNLGL---SSATIRNDMADLEDLGFIEKPH 57 (337)
T ss_pred HHh-cCCCcCHHHHHhhcCCCC---ChHHHHHHHHHHHHCCCccCCC
Confidence 444 3689999999999 888 8999999999999999999865
No 155
>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=87.99 E-value=1.5 Score=27.21 Aligned_cols=44 Identities=23% Similarity=0.264 Sum_probs=38.8
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
-.|...++. +..|.+||-+++|+ +...|-..|-.|+..|++.+.
T Consensus 8 ~~IL~~ls~--~c~TLeeL~ekTgi---~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 8 QKILIILSK--RCCTLEELEEKTGI---SKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHh--ccCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeeee
Confidence 356667774 48999999999999 999999999999999999986
No 156
>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=87.96 E-value=0.63 Score=30.93 Aligned_cols=36 Identities=22% Similarity=0.168 Sum_probs=33.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.-+|+..||+++++ .-+..+++||.|...|++....
T Consensus 58 K~ITp~~lserlkI---~~SlAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 58 KLITPSVLSERLKI---NGSLARKALRELESKGLIKPVS 93 (105)
T ss_dssp SCECHHHHHHHHCC---SCHHHHHHHHHHHHCCSSEEEE
T ss_pred cEeeHHHHHHhHhh---HHHHHHHHHHHHHHCCCEEEEe
Confidence 56999999999999 9999999999999999998763
No 157
>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=87.81 E-value=1.3 Score=28.65 Aligned_cols=69 Identities=13% Similarity=0.112 Sum_probs=47.6
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCC-----CCCCcchHHHHHHHhhcCCceeeccc--C-CC-CcceecchhccccccC
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDI-----QPTKTTGLFRLMRLLVHSSCFNKTKV--N-GQ-EEAYGLTAASTLLIKD 107 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~-----~~~~~~~l~RlLr~L~~~gl~~~~~~--~-~~-~~~y~~t~~s~~L~~~ 107 (131)
++=|.-.|. .+|.+--||.+.+.- -+.++..++++|+.|...|++..... . +. ...|..|+.++.+...
T Consensus 6 ~~~iL~~L~--~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~ 83 (100)
T TIGR03433 6 DLLILKTLS--LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAA 83 (100)
T ss_pred HHHHHHHHh--cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence 334555565 368999999988621 11277899999999999999997311 1 11 2459999999865543
No 158
>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=87.71 E-value=0.93 Score=32.87 Aligned_cols=37 Identities=16% Similarity=0.258 Sum_probs=34.2
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|..++-.+||+.+|+ +...++.-|+.|...|++...+
T Consensus 32 G~~L~e~~La~~lgV---SRtpVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 32 GAKLNESDIAARLGV---SRGPVREAFRALEEAGLVRNEK 68 (212)
T ss_pred CCEecHHHHHHHhCC---ChHHHHHHHHHHHHCCCEEEec
Confidence 567899999999999 9999999999999999998765
No 159
>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=87.66 E-value=0.9 Score=32.90 Aligned_cols=57 Identities=16% Similarity=0.155 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhChHHHHHhCCCC---CCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 28 SSMSLKCAIELGIADIIHSHGRA---ITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 28 ~~~aL~~a~~L~ifd~l~~~~~~---~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
...+|.+.+.+==.+-+.+.+.| .|-.+|+..+ |+ ++..+.|.++.|+..|++...+
T Consensus 45 ~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~---s~~tlrR~l~~LveaGLI~rrD 105 (177)
T PF03428_consen 45 ALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGM---SERTLRRHLARLVEAGLIVRRD 105 (177)
T ss_pred HHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCC---CHHHHHHHHHHHHHCCCeeecc
Confidence 34444444444433334322233 6889999999 99 9999999999999999999864
No 160
>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=87.60 E-value=0.91 Score=29.14 Aligned_cols=35 Identities=23% Similarity=0.329 Sum_probs=28.4
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
..|+..+. .+.|..+||+.+|+ +...++|+.|.+.
T Consensus 41 ~~I~~ll~---~G~S~~eIA~~LgI---SrsTIyRi~R~~n 75 (88)
T TIGR02531 41 LQVAKMLK---QGKTYSDIEAETGA---STATISRVKRCLN 75 (88)
T ss_pred HHHHHHHH---CCCCHHHHHHHHCc---CHHHHHHHHHhcc
Confidence 55666666 45899999999999 9999999887544
No 161
>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=87.56 E-value=0.98 Score=26.37 Aligned_cols=55 Identities=18% Similarity=0.220 Sum_probs=41.3
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
++.+|..+.+ .-|...-|+.+++ +++.+.|-++.|. ...+|... ++.+.+|+.++
T Consensus 3 ~l~~f~~v~~---~gs~~~AA~~l~i---s~~~vs~~i~~LE~~lg~~Lf~r~-----~~~~~lT~~G~ 60 (60)
T PF00126_consen 3 QLRYFLAVAE---TGSISAAAEELGI---SQSAVSRQIKQLEEELGVPLFERS-----GRGLRLTEAGE 60 (60)
T ss_dssp HHHHHHHHHH---HSSHHHHHHHCTS---SHHHHHHHHHHHHHHHTS-SEEEC-----SSSEEE-HHHH
T ss_pred HHHHHHHHHH---hCCHHHHHHHhhc---cchHHHHHHHHHHHHhCCeEEEEC-----CCCeeEChhhC
Confidence 4667778874 3489999999999 9999999998885 45688876 45688888753
No 162
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=87.53 E-value=0.75 Score=24.81 Aligned_cols=28 Identities=14% Similarity=0.236 Sum_probs=21.9
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVH 79 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~ 79 (131)
.++++++||..+|. ++..+.|+.+....
T Consensus 7 ~~~~l~~iA~~~g~---S~~~f~r~Fk~~~g 34 (42)
T PF00165_consen 7 QKLTLEDIAEQAGF---SPSYFSRLFKKETG 34 (42)
T ss_dssp SS--HHHHHHHHTS----HHHHHHHHHHHTS
T ss_pred CCCCHHHHHHHHCC---CHHHHHHHHHHHHC
Confidence 57999999999999 99999999886543
No 163
>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=87.46 E-value=0.64 Score=28.72 Aligned_cols=31 Identities=19% Similarity=0.301 Sum_probs=24.2
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
...|+.|||+.+++ ++..+.|+.+.|--.|+
T Consensus 33 ~~~si~elA~~~~v---S~sti~Rf~kkLG~~gf 63 (77)
T PF01418_consen 33 AFMSISELAEKAGV---SPSTIVRFCKKLGFSGF 63 (77)
T ss_dssp CT--HHHHHHHCTS----HHHHHHHHHHCTTTCH
T ss_pred HHccHHHHHHHcCC---CHHHHHHHHHHhCCCCH
Confidence 46999999999999 99999999998766664
No 164
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=87.44 E-value=1.3 Score=30.32 Aligned_cols=62 Identities=19% Similarity=0.280 Sum_probs=47.7
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCC-CcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPT-KTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~-~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
+.+..|.++|-. .+|.|+.||-+.++...+ ....+.-+|+-|+-.|++..... ++.|.-.|+
T Consensus 6 ~aE~eVM~ilW~-~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kd---gr~~~y~pL 68 (123)
T COG3682 6 AAEWEVMEILWS-RGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKD---GRAFRYSPL 68 (123)
T ss_pred HHHHHHHHHHHH-cCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhc---CCeeeeecc
Confidence 356678888875 469999999988876211 56689999999999999998763 566777775
No 165
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=87.21 E-value=1 Score=30.83 Aligned_cols=45 Identities=11% Similarity=0.183 Sum_probs=37.9
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
.--|+.|+|..+|+ +|-++.|--+-|...|++.... |.|.|-...
T Consensus 34 kLPSvRelA~~~~V---NpnTv~raY~eLE~eG~i~t~r---g~G~fV~~~ 78 (125)
T COG1725 34 KLPSVRELAKDLGV---NPNTVQRAYQELEREGIVETKR---GKGTFVTED 78 (125)
T ss_pred CCCcHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec---CeeEEEcCC
Confidence 45799999999999 9999999999999999998765 256665533
No 166
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=87.08 E-value=0.77 Score=30.33 Aligned_cols=46 Identities=20% Similarity=0.164 Sum_probs=38.0
Q ss_pred ChHHHHHh---CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 39 GIADIIHS---HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 39 ~ifd~l~~---~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+++.+.+ ...-+|...||.+.|+ +-+..+++||.|...|++....
T Consensus 45 e~~~ki~KEV~~~r~VTpy~la~r~gI---~~SvAr~vLR~LeeeGvv~lvs 93 (107)
T COG4901 45 ELLDKIRKEVPRERVVTPYVLASRYGI---NGSVARIVLRHLEEEGVVQLVS 93 (107)
T ss_pred HHHHHHHHhcccceeecHHHHHHHhcc---chHHHHHHHHHHHhCCceeeec
Confidence 35555543 1367999999999999 9999999999999999998764
No 167
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=86.96 E-value=0.83 Score=32.58 Aligned_cols=35 Identities=14% Similarity=0.104 Sum_probs=32.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
-++|-++||..+|+ .+..+.|+|+.|...|++...
T Consensus 148 ~~~t~~~iA~~lG~---tretvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 148 IYATHDELAAAVGS---VRETVTKVIGELSREGYIRSG 182 (202)
T ss_pred ecCCHHHHHHHhCc---cHHHHHHHHHHHHHCCCEEcC
Confidence 36899999999999 999999999999999999855
No 168
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=86.76 E-value=1.3 Score=32.71 Aligned_cols=37 Identities=19% Similarity=0.233 Sum_probs=35.1
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|.+++-.+||+.+|+ +...++.-|+.|++.|++...+
T Consensus 37 G~~l~e~~La~~~gv---SrtPVReAL~rL~~eGlv~~~p 73 (230)
T COG1802 37 GERLSEEELAEELGV---SRTPVREALRRLEAEGLVEIEP 73 (230)
T ss_pred CCCccHHHHHHHhCC---CCccHHHHHHHHHHCCCeEecC
Confidence 678999999999999 9999999999999999999875
No 169
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=86.74 E-value=1.3 Score=32.14 Aligned_cols=45 Identities=20% Similarity=0.231 Sum_probs=38.8
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
..|++++.+ .+-+|-+|||..+|+ ....++|+|+.|...|++...
T Consensus 21 ~~v~~~l~~-kge~tDeela~~l~i---~~~~vrriL~~L~e~~li~~~ 65 (176)
T COG1675 21 VLVVDALLE-KGELTDEELAELLGI---KKNEVRRILYALYEDGLISYR 65 (176)
T ss_pred hHHHHHHHh-cCCcChHHHHHHhCc---cHHHHHHHHHHHHhCCceEEE
Confidence 347788874 247999999999999 999999999999999999854
No 170
>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=86.27 E-value=0.79 Score=27.95 Aligned_cols=60 Identities=10% Similarity=0.159 Sum_probs=41.1
Q ss_pred HHHHHhCCCCCCHHHHHhhcCCC-----CCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchhcc
Q 040869 41 ADIIHSHGRAITLSELVSALDIQ-----PTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAAST 102 (131)
Q Consensus 41 fd~l~~~~~~~s~~eLA~~~~~~-----~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~s~ 102 (131)
.-+|.. +|++.-||.+.+.-. ..++..+++.|+.|...|+++..... .+ ...|..|+.++
T Consensus 2 L~~L~~--~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~ 70 (75)
T PF03551_consen 2 LGLLSE--GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGR 70 (75)
T ss_dssp HHHHHH--S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHH
T ss_pred hhhhcc--CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHH
Confidence 344553 678888888766421 12678899999999999999976432 11 23499999876
No 171
>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=86.23 E-value=0.85 Score=26.73 Aligned_cols=40 Identities=23% Similarity=0.284 Sum_probs=32.8
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
.-++.|++.|-+ .+.+++.|||..+|+ ....+..-+..|.
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~ela~~l~~---S~rti~~~i~~L~ 44 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLKELAKKLNI---SERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHHHHHHHCTS----HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHHHHHHHHCC---CHHHHHHHHHHHH
Confidence 346778888876 678999999999999 8888888887775
No 172
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=86.03 E-value=1.9 Score=33.26 Aligned_cols=55 Identities=16% Similarity=0.107 Sum_probs=45.5
Q ss_pred hCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-ccc
Q 040869 46 SHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLI 105 (131)
Q Consensus 46 ~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~ 105 (131)
+.++++--+|||..++- +|-.++-.|..|.++|+++-.+. ..|.|.+|-.+. .|.
T Consensus 21 ~~~r~IKgeeIA~~l~r---npGTVRNqmq~LkaLgLVegvpG--PkGGY~PT~kAYe~L~ 76 (294)
T COG2524 21 RKKRPIKGEEIAEVLNR---NPGTVRNQMQSLKALGLVEGVPG--PKGGYKPTSKAYEALS 76 (294)
T ss_pred hcCCCcchHHHHHHHcc---CcchHHHHHHHHHhcCccccccC--CCCCccccHHHHHHhc
Confidence 44679999999999999 99999999999999999997641 158899997654 443
No 173
>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=85.48 E-value=0.75 Score=28.55 Aligned_cols=34 Identities=15% Similarity=0.071 Sum_probs=29.8
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
..+|..|||+.+|+ ++..+...++.+-..|.+..
T Consensus 31 eGlS~kEIAe~LGI---S~~TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 31 AGKTASEIAEELGR---TEQTVRNHLKGETKAGGLVK 64 (73)
T ss_pred cCCCHHHHHHHHCc---CHHHHHHHHhcCcccchHHH
Confidence 56999999999999 99999999998888876653
No 174
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=84.99 E-value=1.4 Score=38.22 Aligned_cols=50 Identities=16% Similarity=0.255 Sum_probs=41.4
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
....|.+|+|+.+|+ ++..++|.|......|++.+.+.....|+|..++.
T Consensus 614 k~twt~eelse~l~i---p~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~iEs 663 (765)
T KOG2165|consen 614 KNTWTLEELSESLGI---PVPALRRRLSFWIQKGVLREEPIISDTGTLTVIES 663 (765)
T ss_pred cccccHHHHHHHhCC---CHHHHHHHHHHHHHcCeeecCCCCCCCceeeeccc
Confidence 357999999999999 99999999999999999998752222477777763
No 175
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=84.96 E-value=1.3 Score=32.50 Aligned_cols=35 Identities=17% Similarity=0.238 Sum_probs=32.6
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.++|..|||+++++ .+.+++..++.|+..|++.+.
T Consensus 177 ~g~s~~eIA~~l~i---S~~Tv~~~~~~~~~~~~~~~~ 211 (239)
T PRK10430 177 YEFSTDELANAVNI---SRVSCRKYLIWLVNCHILFTS 211 (239)
T ss_pred CCcCHHHHHHHhCc---hHHHHHHHHHHHHhCCEEEEE
Confidence 67999999999999 999999999999999999665
No 176
>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=84.92 E-value=1.7 Score=29.24 Aligned_cols=42 Identities=14% Similarity=0.226 Sum_probs=35.6
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|.+... .|.|+.|||..+++ +...++-|+--|...|++.-..
T Consensus 48 Il~lC~---~~~SVAEiAA~L~l---PlgVvrVLvsDL~~~G~v~v~~ 89 (114)
T PF05331_consen 48 ILELCR---RPLSVAEIAARLGL---PLGVVRVLVSDLADAGLVRVRA 89 (114)
T ss_pred HHHHHC---CCccHHHHHHhhCC---CchhhhhhHHHHHhCCCEEEeC
Confidence 445444 59999999999999 8888888999999999998765
No 177
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=84.80 E-value=1.3 Score=33.10 Aligned_cols=43 Identities=9% Similarity=0.149 Sum_probs=38.4
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
-|=.|||++.|+ +..+++|-|+.|+..|++.+.. |.|+|-..+
T Consensus 32 PsE~eLa~~f~V---SR~TvRkAL~~L~~eGli~r~~---G~GtfV~~~ 74 (236)
T COG2188 32 PSERELAEQFGV---SRMTVRKALDELVEEGLIVRRQ---GKGTFVASP 74 (236)
T ss_pred CCHHHHHHHHCC---cHHHHHHHHHHHHHCCcEEEEe---cCeeEEcCc
Confidence 466799999999 9999999999999999999875 378888877
No 178
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=84.65 E-value=2 Score=31.50 Aligned_cols=37 Identities=16% Similarity=0.213 Sum_probs=33.9
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|..++..+||+.+|+ +...++.-|+.|...|++...+
T Consensus 32 G~~L~e~~La~~lgV---SRtpVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 32 GARLITKNLAEQLGM---SITPVREALLRLVSVNALSVAP 68 (221)
T ss_pred CCccCHHHHHHHHCC---CchhHHHHHHHHHHCCCEEecC
Confidence 567889999999999 9999999999999999998765
No 179
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=84.49 E-value=2.1 Score=23.93 Aligned_cols=35 Identities=11% Similarity=0.230 Sum_probs=27.4
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
+--|...+. ...|..++|+.+|+ +...+.|+++..
T Consensus 17 ~~~i~~~~~---~~~s~~~vA~~~~v---s~~TV~ri~~~~ 51 (52)
T PF13542_consen 17 EQYILKLLR---ESRSFKDVARELGV---SWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHh---hcCCHHHHHHHHCC---CHHHHHHHHHhh
Confidence 334566665 23799999999999 999999998754
No 180
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=84.48 E-value=2.7 Score=30.69 Aligned_cols=57 Identities=19% Similarity=0.216 Sum_probs=42.1
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC---CCCcceecchhc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQEEAYGLTAAS 101 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~---~~~~~y~~t~~s 101 (131)
|.+..+|+- .+|+|-.||++..|+ +. ..+++.|...|++.+.+.. +.+-.|..|+..
T Consensus 93 LEtLaiIay-~qPiTr~eI~~irGv---~~---~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F 152 (188)
T PRK00135 93 LEVLAIIAY-KQPITRIEIDEIRGV---NS---DGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEF 152 (188)
T ss_pred HHHHHHHHH-cCCcCHHHHHHHHCC---CH---HHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHH
Confidence 446677764 479999999999999 64 8899999999999875321 113447777653
No 181
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=84.33 E-value=2.2 Score=31.11 Aligned_cols=47 Identities=17% Similarity=0.188 Sum_probs=38.1
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
++-.|.|.|.+.|..+|+-+||+++|+ +...+.|-|=-|-..|.+.-
T Consensus 5 ~~~~i~~~l~~~~~~~~a~~i~k~l~i---~k~~vNr~LY~L~~~~~v~~ 51 (183)
T PHA02701 5 CASLILTLLSSSGDKLPAKRIAKELGI---SKHEANRCLYRLLESDAVSC 51 (183)
T ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCc---cHHHHHHHHHHHhhcCcEec
Confidence 456799999876646999999999999 88888887777777776643
No 182
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=84.28 E-value=1.9 Score=36.32 Aligned_cols=42 Identities=14% Similarity=0.468 Sum_probs=33.9
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHS 80 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~ 80 (131)
-+|-..|...+++.|+++||+++|.. ++...++.|||.|++.
T Consensus 466 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~i~~~~~~n 507 (528)
T PRK14096 466 KKVEELLKEDGGELSIEEIAAALGAP-EQVETIYKILRHLAAN 507 (528)
T ss_pred HHHHHHHhccCCCCCHHHHHHHcCCC-ccHHHHHHHHHHHhcC
Confidence 44666675556899999999999983 3677899999999986
No 183
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=84.06 E-value=2.2 Score=23.55 Aligned_cols=26 Identities=15% Similarity=0.198 Sum_probs=21.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
...|..|||+.+|+ ++..+++.++.+
T Consensus 17 ~g~s~~eia~~l~i---s~~tv~~~~~~~ 42 (58)
T smart00421 17 EGLTNKEIAERLGI---SEKTVKTHLSNI 42 (58)
T ss_pred cCCCHHHHHHHHCC---CHHHHHHHHHHH
Confidence 35899999999999 888888776654
No 184
>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=84.00 E-value=1.6 Score=26.04 Aligned_cols=29 Identities=14% Similarity=0.310 Sum_probs=22.8
Q ss_pred HHHHHhCCCCCCHHHHHhhcCCCCCCcchHHH
Q 040869 41 ADIIHSHGRAITLSELVSALDIQPTKTTGLFR 72 (131)
Q Consensus 41 fd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~R 72 (131)
|++--+++|.++..|||+++|+ ++..+++
T Consensus 13 ~e~y~~~~g~i~lkdIA~~Lgv---s~~tIr~ 41 (60)
T PF10668_consen 13 FEIYKESNGKIKLKDIAEKLGV---SESTIRK 41 (60)
T ss_pred HHHHHHhCCCccHHHHHHHHCC---CHHHHHH
Confidence 4545445689999999999999 8777764
No 185
>PRK10736 hypothetical protein; Provisional
Probab=83.77 E-value=2.1 Score=34.55 Aligned_cols=51 Identities=4% Similarity=-0.041 Sum_probs=42.3
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
.|.+.|. ..|+++++|+.++|+ +...+..+|-.|.-.|++.+.. ++.|..-
T Consensus 312 ~v~~~l~--~~~~~iD~L~~~~~l---~~~~v~~~L~~LEl~G~v~~~~----g~~~~~~ 362 (374)
T PRK10736 312 ELLANVG--DEVTPVDVVAERAGQ---PVPEVVTQLLELELAGWIAAVP----GGYVRLR 362 (374)
T ss_pred HHHHhcC--CCCCCHHHHHHHHCc---CHHHHHHHHHHHHhCCcEEEcC----CcEEEEe
Confidence 4556554 368999999999999 9999999999999999999986 5666553
No 186
>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=83.70 E-value=0.88 Score=25.56 Aligned_cols=21 Identities=10% Similarity=0.351 Sum_probs=14.1
Q ss_pred CHHHHHhhcCCCCCCcchHHHHHH
Q 040869 52 TLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 52 s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
|+.|||+.+|+ +...+.|+|+
T Consensus 1 Ti~dIA~~agv---S~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGV---SKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTS---SHHHHHHHHT
T ss_pred CHHHHHHHHCc---CHHHHHHHHh
Confidence 56788888887 5565555553
No 187
>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=83.52 E-value=1.3 Score=23.98 Aligned_cols=22 Identities=23% Similarity=0.498 Sum_probs=19.9
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+|..|+|+.+|+ ++..++++++
T Consensus 2 lt~~e~a~~lgi---s~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGV---SKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCC---CHHHHHHHHH
Confidence 689999999999 9999998875
No 188
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=83.42 E-value=6.1 Score=25.03 Aligned_cols=56 Identities=13% Similarity=0.128 Sum_probs=34.5
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHH---HHHhhcCCceeecccCCCCcceecchhccccccCcc
Q 040869 50 AITLSELVSALDIQPTKTTGLFRL---MRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKP 109 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~Rl---Lr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~~~ 109 (131)
.+|-+|....+.-.+..+..-.|+ +-+|...|+++... .|.|.+|+.++.+...+|
T Consensus 34 ~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~----rG~~~iT~~G~~~l~~~p 92 (92)
T PF14338_consen 34 GLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERPK----RGIWRITEKGRKALAEHP 92 (92)
T ss_pred CCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCCC----CCceEECHhHHHHHhhCc
Confidence 455555555543100011223333 56788999998766 799999999996655544
No 189
>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=83.41 E-value=9.1 Score=26.59 Aligned_cols=75 Identities=13% Similarity=0.107 Sum_probs=51.3
Q ss_pred HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcC---CCCCCcchHHHHHHHhhcCCceeecccC--CCC--cceecchhc
Q 040869 29 SMSLKCAIELGIADIIHSHGRAITLSELVSALD---IQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQE--EAYGLTAAS 101 (131)
Q Consensus 29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~---~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~~--~~y~~t~~s 101 (131)
.+..+-.+++=|.-.|.+ +|+.--+|.+.+. .-..++..|+++|+-|...|++...... .++ ..|.+|+.+
T Consensus 18 ~ql~kg~l~~~IL~~L~~--~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~G 95 (138)
T TIGR02719 18 NGAPKNFLVPFLLLCLKD--WNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAG 95 (138)
T ss_pred HHHHHHHHHHHHHHHHcc--CCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHH
Confidence 445666666667777763 6778877777653 2122778899999999999999864211 112 349999999
Q ss_pred cccc
Q 040869 102 TLLI 105 (131)
Q Consensus 102 ~~L~ 105 (131)
+...
T Consensus 96 r~~L 99 (138)
T TIGR02719 96 EQYL 99 (138)
T ss_pred HHHH
Confidence 8543
No 190
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=83.32 E-value=1.6 Score=26.01 Aligned_cols=29 Identities=28% Similarity=0.409 Sum_probs=24.6
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSS 81 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g 81 (131)
++|+++||+.+|+ ++..+.|+++......
T Consensus 1 ~~~~~~la~~~~~---s~~~l~~~f~~~~~~s 29 (84)
T smart00342 1 PLTLEDLAEALGM---SPRHLQRLFKKETGTT 29 (84)
T ss_pred CCCHHHHHHHhCC---CHHHHHHHHHHHhCcC
Confidence 4789999999999 9999999998775544
No 191
>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=83.11 E-value=1.8 Score=31.96 Aligned_cols=42 Identities=14% Similarity=0.183 Sum_probs=37.0
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
-|=.|||++.|+ +..+++|-|+.|+..|++.... |.|+|-..
T Consensus 25 PsE~eLa~~~gV---SR~TVR~Al~~L~~eGli~r~~---G~GTfV~~ 66 (233)
T TIGR02404 25 PSEHELMDQYGA---SRETVRKALNLLTEAGYIQKIQ---GKGSIVLN 66 (233)
T ss_pred cCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeC---CceEEEec
Confidence 478899999999 9999999999999999999876 37888743
No 192
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=82.88 E-value=1.8 Score=31.70 Aligned_cols=35 Identities=11% Similarity=0.217 Sum_probs=32.3
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+.|-.+||+.+|+ .++.+.|+|+-|...|+++...
T Consensus 169 ~~t~~~lA~~lG~---sretvsR~L~~L~~~G~I~~~~ 203 (226)
T PRK10402 169 HEKHTQAAEYLGV---SYRHLLYVLAQFIQDGYLKKSK 203 (226)
T ss_pred cchHHHHHHHHCC---cHHHHHHHHHHHHHCCCEEeeC
Confidence 5788999999999 9999999999999999999763
No 193
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=82.65 E-value=2.4 Score=33.26 Aligned_cols=58 Identities=17% Similarity=0.302 Sum_probs=42.6
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
+.|..+|..... +|+.+||+.+++ +.+.++|=++.|...|+--+...+ .++.|.+-+-
T Consensus 11 ~~ii~~L~~~~~-vta~~lA~~~~V---S~RTi~RDi~~L~~~gvPI~~e~G-~~~gy~~~~~ 68 (311)
T COG2378 11 LQIIQILRAKET-VTAAELADEFEV---SVRTIYRDIATLRAAGVPIEGERG-KGGGYRLRPG 68 (311)
T ss_pred HHHHHHHHhCcc-chHHHHHHhcCC---CHHHHHHHHHHHHHCCCCeEeecC-CCccEEEccC
Confidence 445666664334 999999999999 999999999999999988665421 0244555443
No 194
>PF12728 HTH_17: Helix-turn-helix domain
Probab=82.59 E-value=1.4 Score=24.62 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=20.5
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
+|++|+|+.+|+ +...++++++.
T Consensus 2 lt~~e~a~~l~i---s~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGI---SRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHHc
Confidence 689999999999 99999988863
No 195
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=82.33 E-value=1.5 Score=34.21 Aligned_cols=47 Identities=17% Similarity=0.231 Sum_probs=38.8
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHH-HhhcCCceeecccCCCCcceecchhcc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMR-LLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr-~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
+++.+++.||..+|. ++..+..+++ +|...|++.... .|+ ..|+.+.
T Consensus 274 ~~~~~~~~~a~~lg~---~~~~~~~~~e~~Li~~~li~~~~----~gr-~~~~~~~ 321 (328)
T PRK00080 274 GGPVGLDTLAAALGE---ERDTIEDVYEPYLIQQGFIQRTP----RGR-VATPKAY 321 (328)
T ss_pred CCceeHHHHHHHHCC---CcchHHHHhhHHHHHcCCcccCC----chH-HHHHHHH
Confidence 579999999999999 9999999999 999999998664 343 4455544
No 196
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=82.27 E-value=3.7 Score=25.79 Aligned_cols=51 Identities=20% Similarity=0.264 Sum_probs=41.5
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
+.++|-++||+++|+ ....+-.-+..|...|+=-+... ...|.+......+
T Consensus 17 ~~~~SGe~La~~Lgi---SRtaVwK~Iq~Lr~~G~~I~s~~---~kGY~L~~~~~ll 67 (79)
T COG1654 17 GNFVSGEKLAEELGI---SRTAVWKHIQQLREEGVDIESVR---GKGYLLPQLPDLL 67 (79)
T ss_pred CCcccHHHHHHHHCc---cHHHHHHHHHHHHHhCCceEecC---CCceeccCccccC
Confidence 579999999999999 99999999999999997665541 4468887765554
No 197
>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=82.10 E-value=2.1 Score=26.95 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=26.9
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
..|.+.|.+ +.+|+.+||+..|+ ....+.|.|
T Consensus 9 ~~I~e~l~~--~~~ti~dvA~~~gv---S~~TVsr~L 40 (80)
T TIGR02844 9 LEIGKYIVE--TKATVRETAKVFGV---SKSTVHKDV 40 (80)
T ss_pred HHHHHHHHH--CCCCHHHHHHHhCC---CHHHHHHHh
Confidence 456777875 78999999999999 889998865
No 198
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=82.01 E-value=2.3 Score=26.63 Aligned_cols=58 Identities=14% Similarity=0.175 Sum_probs=40.2
Q ss_pred HhChHHHHHh--CCCCCCHHHHHhhcCCCCCCcchHHHHH-HHhhcCCceeecccCCCCcceecchhcc
Q 040869 37 ELGIADIIHS--HGRAITLSELVSALDIQPTKTTGLFRLM-RLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 37 ~L~ifd~l~~--~~~~~s~~eLA~~~~~~~~~~~~l~RlL-r~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
+.++...|.+ .++|+.++.||..+|- ++..+.-+. -+|...|++.+++ .|+ ..|+.+.
T Consensus 10 D~~yL~~l~~~f~ggPvGl~tlA~~l~e---d~~Tie~v~EPyLiq~G~I~RT~----rGR-~~T~~a~ 70 (76)
T PF05491_consen 10 DRRYLKTLIENFKGGPVGLDTLAAALGE---DKETIEDVIEPYLIQIGFIQRTP----RGR-VATPKAY 70 (76)
T ss_dssp HHHHHHHHHHCSTTS-B-HHHHHHHTTS----HHHHHHTTHHHHHHTTSEEEET----TEE-EE-HHHH
T ss_pred HHHHHHHHHHHcCCCCeeHHHHHHHHCC---CHhHHHHHhhHHHHHhhhHhhCc----cHH-HhHHHHH
Confidence 3445566654 3799999999999999 999887554 5799999999987 566 5555543
No 199
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=81.95 E-value=1.8 Score=34.19 Aligned_cols=35 Identities=20% Similarity=0.242 Sum_probs=33.0
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.++|-+|||+++|+ ....+.|+|......|+++-.
T Consensus 25 ~gltQ~eIA~~Lgi---SR~~v~rlL~~Ar~~GiV~I~ 59 (321)
T COG2390 25 EGLTQSEIAERLGI---SRATVSRLLAKAREEGIVKIS 59 (321)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCeEEEE
Confidence 57999999999999 999999999999999999865
No 200
>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=81.84 E-value=1 Score=25.83 Aligned_cols=32 Identities=22% Similarity=0.361 Sum_probs=22.7
Q ss_pred hChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHH
Q 040869 38 LGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFR 72 (131)
Q Consensus 38 L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~R 72 (131)
+.+++.|...| .-+|..+||+.+|+ ++..+++
T Consensus 15 ~r~L~~l~~~G~~~vSS~~La~~~gi---~~~qVRK 47 (50)
T PF06971_consen 15 LRYLEQLKEEGVERVSSQELAEALGI---TPAQVRK 47 (50)
T ss_dssp HHHHHHHHHTT-SEE-HHHHHHHHTS----HHHHHH
T ss_pred HHHHHHHHHcCCeeECHHHHHHHHCC---CHHHhcc
Confidence 34556666545 56999999999999 8887765
No 201
>PHA02591 hypothetical protein; Provisional
Probab=81.83 E-value=2.7 Score=26.45 Aligned_cols=32 Identities=13% Similarity=0.287 Sum_probs=26.1
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
+...|.+ .++|.++||+.+|+ +...+.+.++-
T Consensus 51 vA~eL~e--qGlSqeqIA~~LGV---sqetVrKYL~~ 82 (83)
T PHA02591 51 VTHELAR--KGFTVEKIASLLGV---SVRKVRRYLES 82 (83)
T ss_pred HHHHHHH--cCCCHHHHHHHhCC---CHHHHHHHHhc
Confidence 4455653 67999999999999 99999988864
No 202
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=81.82 E-value=1.2 Score=25.82 Aligned_cols=31 Identities=23% Similarity=0.443 Sum_probs=21.3
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
|-+.+.+ ..+|..+||+.+|+ +...+.+++.
T Consensus 2 L~~~m~~--~~it~~~La~~~gi---s~~tl~~~~~ 32 (63)
T PF13443_consen 2 LKELMAE--RGITQKDLARKTGI---SRSTLSRILN 32 (63)
T ss_dssp HHHHHHH--TT--HHHHHHHHT-----HHHHHHHHT
T ss_pred HHHHHHH--cCCCHHHHHHHHCc---CHHHHHHHHh
Confidence 3455664 56899999999999 8888888876
No 203
>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=81.69 E-value=2.2 Score=31.45 Aligned_cols=43 Identities=9% Similarity=0.126 Sum_probs=37.4
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
-|=.|||++.|+ +..++++-|..|+..|++.... |.|+|-..+
T Consensus 33 PsE~eLa~~~~V---SR~TvR~Al~~L~~eGli~r~~---G~GtfV~~~ 75 (238)
T TIGR02325 33 PAEMQLAERFGV---NRHTVRRAIAALVERGLLRAEQ---GRGTFVAAR 75 (238)
T ss_pred cCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CCEEEECCC
Confidence 377899999999 9999999999999999999876 378887543
No 204
>PRK13558 bacterio-opsin activator; Provisional
Probab=81.56 E-value=1.4 Score=37.40 Aligned_cols=44 Identities=18% Similarity=0.198 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 27 LSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 27 ~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
..-.+|.+|.+.|-|+ .+ +..|.+|||+.+|+ .+..+...||..
T Consensus 611 ~q~e~l~~a~~~gyf~-~p---r~~~~~e~a~~l~i---s~~t~~~~lr~a 654 (665)
T PRK13558 611 RQLTALQKAYVSGYFE-WP---RRVEGEELAESMGI---SRSTFHQHLRAA 654 (665)
T ss_pred HHHHHHHHHHHcCCCC-CC---ccCCHHHHHHHhCC---CHHHHHHHHHHH
Confidence 4567899999999998 43 67999999999999 888877777654
No 205
>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=81.48 E-value=3 Score=28.33 Aligned_cols=49 Identities=6% Similarity=-0.048 Sum_probs=43.2
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
.|.+.++||..++- +...+..-|.++...|+++..+ +|.|..+...+..
T Consensus 52 ipy~~e~LA~~~~~---~~~~V~~AL~~f~k~glIe~~e----d~~i~i~~~~~~~ 100 (121)
T PF09681_consen 52 IPYTAEMLALEFDR---PVDTVRLALAVFQKLGLIEIDE----DGVIYIPNWEKHQ 100 (121)
T ss_pred CCCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec----CCeEEeecHHHHh
Confidence 69999999999999 9999999999999999999876 7888877765544
No 206
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.37 E-value=2.5 Score=29.41 Aligned_cols=40 Identities=23% Similarity=0.295 Sum_probs=34.1
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
-|++.|-. .+.+|-++||..+|+ +...++++|..|..-++
T Consensus 5 ~v~d~L~~-~~~~~dedLa~~l~i---~~n~vRkiL~~L~ed~~ 44 (147)
T smart00531 5 LVLDALMR-NGCVTEEDLAELLGI---KQKQLRKILYLLYDEKL 44 (147)
T ss_pred eehHHHHh-cCCcCHHHHHHHhCC---CHHHHHHHHHHHHhhhc
Confidence 47787765 358999999999999 99999999999999443
No 207
>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=81.36 E-value=3.9 Score=23.87 Aligned_cols=46 Identities=15% Similarity=0.221 Sum_probs=32.5
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCccee
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYG 96 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~ 96 (131)
+.|.+-. -.-+|+.-+|+.+|+ .+....|+++-|. + .|-. |.++|.
T Consensus 4 Lidll~~-~P~Vsa~mva~~L~v---T~~~A~~li~eLg---~-rEiT---Gr~R~R 49 (54)
T PF11972_consen 4 LIDLLLS-RPLVSAPMVAKELGV---TPQAAQRLIAELG---L-REIT---GRGRYR 49 (54)
T ss_pred HHHHHHh-CccccHHHHHHHhCC---CHHHHHHHHHHhh---c-eeec---CCcccc
Confidence 4566653 234899999999999 8999999886654 4 4432 256675
No 208
>PRK14999 histidine utilization repressor; Provisional
Probab=81.28 E-value=2.5 Score=31.46 Aligned_cols=45 Identities=16% Similarity=0.197 Sum_probs=38.4
Q ss_pred CCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 49 RAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 49 ~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
..+ |=.|||++.|+ +..++++-|+.|+..|++.... |.|+|-..+
T Consensus 34 ~~LPsE~eLa~~~gV---SR~TVR~Al~~L~~eGli~r~~---GkGTfV~~~ 79 (241)
T PRK14999 34 DRIPSEAELVAQYGF---SRMTINRALRELTDEGWLVRLQ---GVGTFVAEP 79 (241)
T ss_pred CcCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CcEEEECCC
Confidence 345 88999999999 9999999999999999999875 378887543
No 209
>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=81.22 E-value=1.8 Score=24.11 Aligned_cols=26 Identities=23% Similarity=0.425 Sum_probs=21.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
.+.|..|||+.+|+ +...+.++.+..
T Consensus 19 ~~~t~~eIa~~lg~---s~~~V~~~~~~a 44 (50)
T PF04545_consen 19 EGLTLEEIAERLGI---SRSTVRRILKRA 44 (50)
T ss_dssp ST-SHHHHHHHHTS---CHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCC---cHHHHHHHHHHH
Confidence 67999999999999 889888887643
No 210
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=81.19 E-value=3 Score=28.10 Aligned_cols=33 Identities=12% Similarity=0.060 Sum_probs=27.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
.++|+++||+.+|+ ++..+.|+.+.-+...+-+
T Consensus 24 ~~~sl~~lA~~~g~---S~~~l~r~Fk~~~G~s~~~ 56 (127)
T PRK11511 24 SPLSLEKVSERSGY---SKWHLQRMFKKETGHSLGQ 56 (127)
T ss_pred CCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHH
Confidence 68999999999999 9999999998776655443
No 211
>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=80.93 E-value=2.5 Score=31.12 Aligned_cols=45 Identities=16% Similarity=0.206 Sum_probs=38.3
Q ss_pred CCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 49 RAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 49 ~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
..+ |=.|||++.|+ +..++++-|..|+..|++.... |.|+|-..+
T Consensus 23 ~~LPsE~eLa~~~~V---SR~TVR~Al~~L~~eGli~r~~---G~GtfV~~~ 68 (230)
T TIGR02018 23 HRIPSEHELVAQYGC---SRMTVNRALRELTDAGLLERRQ---GVGTFVAEP 68 (230)
T ss_pred CcCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CCEEEEccC
Confidence 345 88899999999 9999999999999999999876 368887543
No 212
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=80.88 E-value=3.4 Score=26.68 Aligned_cols=34 Identities=12% Similarity=0.170 Sum_probs=28.1
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
..++++++||+.+|+ ++..+.|+.+......+-+
T Consensus 19 ~~~~~~~~lA~~~~~---S~~~l~r~f~~~~g~s~~~ 52 (107)
T PRK10219 19 DQPLNIDVVAKKSGY---SKWYLQRMFRTVTHQTLGD 52 (107)
T ss_pred CCCCCHHHHHHHHCC---CHHHHHHHHHHHHCcCHHH
Confidence 368999999999999 9999999998876555443
No 213
>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=80.87 E-value=1.5 Score=26.72 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=27.4
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
|..-|..|||+.+|+ ++..+..+|........+...
T Consensus 18 gr~Pt~eEiA~~lgi---s~~~v~~~l~~~~~~~Sl~~~ 53 (78)
T PF04539_consen 18 GREPTDEEIAEELGI---SVEEVRELLQASRRPVSLDLP 53 (78)
T ss_dssp SS--BHHHHHHHHTS----HHHHHHHHHHHSCCEESSHC
T ss_pred CCCCCHHHHHHHHcc---cHHHHHHHHHhCCCCeEEeee
Confidence 578999999999999 999999999987665555543
No 214
>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=80.70 E-value=1.9 Score=23.13 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=19.8
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
+|..|+|+.+|+ ++..+++..+.
T Consensus 1 ~s~~e~a~~lgv---s~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGV---SPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHHc
Confidence 478999999999 88988888774
No 215
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=80.61 E-value=3.1 Score=30.98 Aligned_cols=45 Identities=13% Similarity=0.193 Sum_probs=37.6
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
|..+ +-.+||+.+|+ +...++--|+.|...|++...+. .|.|-..
T Consensus 28 G~~LPsE~eLa~~~gV---SRtpVREAL~~L~~eGlV~~~~~---~G~~V~~ 73 (251)
T PRK09990 28 GQALPSERRLCEKLGF---SRSALREGLTVLRGRGIIETAQG---RGSFVAR 73 (251)
T ss_pred CCcCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeCC---CeeEEec
Confidence 5678 88999999999 99999999999999999997751 4555443
No 216
>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=80.58 E-value=2.9 Score=27.45 Aligned_cols=35 Identities=9% Similarity=0.170 Sum_probs=32.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.-+|.+++++.+|+ ++..+.+.+..|...|++...
T Consensus 53 d~Is~sq~~e~tg~---~~~~V~~al~~Li~~~vI~~~ 87 (100)
T PF04492_consen 53 DRISNSQIAEMTGL---SRDHVSKALNELIRRGVIIRD 87 (100)
T ss_pred ceeeHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeC
Confidence 46999999999999 999999999999999999766
No 217
>PF13551 HTH_29: Winged helix-turn helix
Probab=80.42 E-value=2.6 Score=27.03 Aligned_cols=27 Identities=19% Similarity=0.399 Sum_probs=26.0
Q ss_pred CHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869 52 TLSELVSALDIQPTKTTGLFRLMRLLVHSS 81 (131)
Q Consensus 52 s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g 81 (131)
|..++|+.+|+ ++..++|.++....-|
T Consensus 14 ~~~~ia~~lg~---s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGI---SRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCc---CHHHHHHHHHHHHccc
Confidence 79999999999 9999999999999988
No 218
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=80.37 E-value=3.1 Score=31.10 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=38.4
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
|..+ |-.+||+.+|+ +...++--|+.|.+.|+++..+ +.|.|-...
T Consensus 31 G~~LpsE~eLa~~lgV---SRtpVREAL~~L~~eGlv~~~~---~~G~~V~~~ 77 (254)
T PRK09464 31 GEKLPPERELAKQFDV---SRPSLREAIQRLEAKGLLLRRQ---GGGTFVQSS 77 (254)
T ss_pred CCcCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec---CceeEEecC
Confidence 4567 89999999999 9999999999999999999765 256666543
No 219
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=80.19 E-value=3.2 Score=31.06 Aligned_cols=45 Identities=18% Similarity=0.230 Sum_probs=37.4
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
|..+ |-.+||+++|+ +...++.-|+.|.+.|++...+ +.|.|-..
T Consensus 30 G~~LpsE~eLa~~~gV---SRtpVREAL~~L~~eGlV~~~~---~~G~~V~~ 75 (257)
T PRK10225 30 GERLPPEREIAEMLDV---TRTVVREALIMLEIKGLVEVRR---GAGIYVLD 75 (257)
T ss_pred CCcCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec---CCEEEEeC
Confidence 5678 68999999999 9999999999999999998765 14555544
No 220
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=80.14 E-value=3.2 Score=30.65 Aligned_cols=45 Identities=13% Similarity=0.165 Sum_probs=37.9
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
|..+ |-.+||+++|+ +...++.-|+.|...|++...+ |.|.|-.+
T Consensus 28 G~~LPsE~eLae~~gV---SRt~VReAL~~L~~eGlv~~~~---g~G~~V~~ 73 (239)
T PRK04984 28 GSILPAERELSELIGV---TRTTLREVLQRLARDGWLTIQH---GKPTKVNN 73 (239)
T ss_pred CCcCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeC---CCeeEeCC
Confidence 4567 78999999999 9999999999999999999765 25666543
No 221
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=80.01 E-value=2.7 Score=31.23 Aligned_cols=45 Identities=20% Similarity=0.287 Sum_probs=38.1
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
|..+ |=.|||+..|+ +..++++-|..|+..|++.... |.|+|-..
T Consensus 26 G~~LPsE~eL~~~~~V---SR~TvR~Al~~L~~eGli~r~~---G~GtfV~~ 71 (240)
T PRK09764 26 GDALPTESALQTEFGV---SRVTVRQALRQLVEQQILESIQ---GSGTYVKE 71 (240)
T ss_pred CCcCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CceeEEcc
Confidence 3455 77999999999 9999999999999999999875 36778643
No 222
>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=79.91 E-value=2.7 Score=24.74 Aligned_cols=46 Identities=17% Similarity=0.179 Sum_probs=33.9
Q ss_pred CCCCHHHHHhhcCCCCCCcch-HHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 49 RAITLSELVSALDIQPTKTTG-LFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~-l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
.+++.+++.++.|. +... ....+..+...|++..+ ++++.+|+.++
T Consensus 19 ~Gi~~~~~~~~~g~---~~~~~~~~~l~~l~~~Gll~~~-----~~~l~lT~~G~ 65 (66)
T PF06969_consen 19 EGIDLSEFEQRFGI---DFAEEFQKELEELQEDGLLEID-----GGRLRLTEKGR 65 (66)
T ss_dssp SEEEHHHHHHHTT-----THHH-HHHHHHHHHTTSEEE------SSEEEE-TTTG
T ss_pred CCcCHHHHHHHHCc---CHHHHHHHHHHHHHHCCCEEEe-----CCEEEECcccC
Confidence 46889999999998 6443 47778899999999987 68999998765
No 223
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=79.88 E-value=6.5 Score=23.89 Aligned_cols=55 Identities=16% Similarity=0.251 Sum_probs=46.1
Q ss_pred HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..++....++.|...+.+. .+.++.+|+..++. +...+.+-|..|...|++....
T Consensus 19 ~~~l~~~~r~~il~~l~~~-~~~~~~~l~~~~~~---~~~~v~~hL~~L~~~glv~~~~ 73 (110)
T COG0640 19 LKALADPTRLEILSLLAEG-GELTVGELAEALGL---SQSTVSHHLKVLREAGLVELRR 73 (110)
T ss_pred HHHhCCHHHHHHHHHHHhc-CCccHHHHHHHHCC---ChhHHHHHHHHHHHCCCeEEEe
Confidence 3455556788888888742 57899999999999 9999999999999999999854
No 224
>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=79.78 E-value=3.9 Score=22.57 Aligned_cols=33 Identities=15% Similarity=0.214 Sum_probs=24.4
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
.++..+. ..+|..+||+.+++ ++..+++.++.+
T Consensus 7 ~i~~~~~---~~~s~~eia~~l~~---s~~tv~~~~~~~ 39 (57)
T cd06170 7 EVLRLLA---EGKTNKEIADILGI---SEKTVKTHLRNI 39 (57)
T ss_pred HHHHHHH---cCCCHHHHHHHHCC---CHHHHHHHHHHH
Confidence 3454443 35899999999999 888877776643
No 225
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=79.50 E-value=14 Score=27.85 Aligned_cols=53 Identities=23% Similarity=0.264 Sum_probs=43.7
Q ss_pred HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
++-.-.+.+|+..+..+ .+.++.|+.+.++. +..+++=.+|.|.+.++++...
T Consensus 97 v~~ns~R~~Iy~~i~~n-PG~~lsEl~~nl~i---~R~TlRyhlriLe~~~li~a~~ 149 (240)
T COG3398 97 VFLNSKRDGIYNYIKPN-PGFSLSELRANLYI---NRSTLRYHLRILESNPLIEAGR 149 (240)
T ss_pred hHhhhhHHHHHHHhccC-CCccHHHHHHhcCC---ChHHHHHHHHHHHhCcchhhhc
Confidence 34445567788888753 56999999999999 9999999999999999998654
No 226
>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=79.42 E-value=2.7 Score=24.93 Aligned_cols=36 Identities=11% Similarity=0.214 Sum_probs=29.2
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+-++++.||.+.|+ -.+.+-.-||-|.+.|+++...
T Consensus 3 g~lvas~iAd~~Gi---TRSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 3 GRLVASKIADRVGI---TRSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp EEE-HHHHHHHHT-----HHHHHHHHHHHHHTTSEEEEE
T ss_pred ceehHHHHHHHhCc---cHHHHHHHHHHHHhcCceeecc
Confidence 45789999999999 8889999999999999999653
No 227
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=79.22 E-value=3.4 Score=30.88 Aligned_cols=45 Identities=13% Similarity=0.147 Sum_probs=37.3
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
|..+ +-.|||+++|+ +...++.-|+.|.+.|++...+ +.|.|-..
T Consensus 23 G~~LpsE~eLae~~gV---SRtpVREAL~~Le~~GlV~~~~---~~G~~V~~ 68 (253)
T PRK10421 23 GMKLPAERQLAMQLGV---SRNSLREALAKLVSEGVLLSRR---GGGTFIRW 68 (253)
T ss_pred CCcCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEeC---CCeEEEec
Confidence 4567 68999999999 9999999999999999998765 15666544
No 228
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=78.72 E-value=3.4 Score=31.19 Aligned_cols=41 Identities=7% Similarity=0.067 Sum_probs=35.3
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSS 81 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g 81 (131)
+-.|.+.|.+ .+.+++.|||+.+|+ ++.+++|=|+.|...+
T Consensus 9 ~~~I~~~l~~-~~~v~v~eLa~~~~V---S~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 9 IGQLLQALKR-SDKLHLKDAAALLGV---SEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHH-cCCCcHHHHHHHhCC---CHHHHHHHHHHhhcCe
Confidence 4457888876 478999999999999 9999999999998654
No 229
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=78.70 E-value=3.3 Score=31.15 Aligned_cols=42 Identities=10% Similarity=0.064 Sum_probs=36.8
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
-+=.|||+++|+ +...++--|+.|.+.|++.-.. |.|+|-.+
T Consensus 35 P~EreLae~fgV---SR~~vREAl~~L~a~Glve~r~---G~Gt~V~~ 76 (241)
T COG2186 35 PSERELAERFGV---SRTVVREALKRLEAKGLVEIRQ---GSGTFVRP 76 (241)
T ss_pred CCHHHHHHHHCC---CcHHHHHHHHHHHHCCCeeecC---CCceEecC
Confidence 457899999999 9999999999999999999875 37888865
No 230
>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=78.53 E-value=3.9 Score=30.16 Aligned_cols=45 Identities=13% Similarity=0.165 Sum_probs=37.4
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
|..+ |-.+||+.+|+ +...++.-|+.|...|+++..+ +.|.|-..
T Consensus 27 G~~LpsE~~La~~lgV---SRtpVREAL~~Le~eGlV~~~~---~~G~~V~~ 72 (235)
T TIGR02812 27 GSILPAERELSELIGV---TRTTLREVLQRLARDGWLTIQH---GKPTKVNN 72 (235)
T ss_pred CCcCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEeC---CCccEecC
Confidence 4568 89999999999 9999999999999999999765 14555443
No 231
>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=78.52 E-value=4.6 Score=35.15 Aligned_cols=56 Identities=25% Similarity=0.431 Sum_probs=41.6
Q ss_pred ChHHHHHh-CCCCCCHHHHHhhcCCCC-CCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 39 GIADIIHS-HGRAITLSELVSALDIQP-TKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 39 ~ifd~l~~-~~~~~s~~eLA~~~~~~~-~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
.|.+.|.+ .+.|++..+|+++++++. .+...+.++|+.|...|.+.... .+.|...
T Consensus 6 ~il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~~----~~~~~~~ 63 (709)
T TIGR02063 6 LILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNR----RGLYALP 63 (709)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcC----CceEecC
Confidence 36677764 348999999999999932 13456999999999999998755 4555433
No 232
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=78.49 E-value=2.2 Score=32.29 Aligned_cols=45 Identities=16% Similarity=0.164 Sum_probs=35.1
Q ss_pred HHhChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869 36 IELGIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF 83 (131)
Q Consensus 36 ~~L~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~ 83 (131)
.+-.|.+.|-++. ..+|+.|||+++++ ++..+-|+.|.|--.|+-
T Consensus 17 ~e~~Ia~yil~n~~~v~~~si~~lA~~~~v---S~aTv~Rf~kklG~~gf~ 64 (284)
T PRK11302 17 SERKVAEVILASPQTAIHSSIATLAKMANV---SEPTVNRFCRSLDTKGFP 64 (284)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhCC---CHHHHHHHHHHcCCCCHH
Confidence 3445666665433 35899999999999 999999999998877764
No 233
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=78.45 E-value=4.7 Score=23.09 Aligned_cols=35 Identities=6% Similarity=0.217 Sum_probs=24.9
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
--++.|...+.. |+ +..+||...|+ +...+..++.
T Consensus 10 ~eK~~iI~~~e~--g~-s~~~ia~~fgv---~~sTv~~I~K 44 (53)
T PF04218_consen 10 EEKLEIIKRLEE--GE-SKRDIAREFGV---SRSTVSTILK 44 (53)
T ss_dssp HHHHHHHHHHHC--TT--HHHHHHHHT-----CCHHHHHHH
T ss_pred HHHHHHHHHHHc--CC-CHHHHHHHhCC---CHHHHHHHHH
Confidence 345677777762 44 99999999999 9999998875
No 234
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=78.07 E-value=4.1 Score=30.26 Aligned_cols=44 Identities=14% Similarity=0.141 Sum_probs=37.6
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
--|=.+||+..|+ +..++++-|..|+..|++.... |.|+|-..+
T Consensus 35 LPsE~eLa~~~~V---SR~TVR~Al~~L~~eGli~r~~---G~GtfV~~~ 78 (241)
T PRK10079 35 LPAEQQLAARYEV---NRHTLRRAIDQLVEKGWVQRRQ---GVGVLVLMR 78 (241)
T ss_pred CCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CCEEEEecC
Confidence 3477899999999 9999999999999999999876 378887543
No 235
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=77.96 E-value=3.8 Score=30.43 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=37.7
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
--|=.|||+..|+ +..++++-|..|+..|++.... |.|+|-..+
T Consensus 33 LPsE~eLa~~~~V---SR~TvR~Al~~L~~eGli~r~~---G~GTfV~~~ 76 (241)
T PRK11402 33 IPTENELCTQYNV---SRITIRKAISDLVADGVLIRWQ---GKGTFVQSQ 76 (241)
T ss_pred CcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CceeEECCC
Confidence 4577899999999 9999999999999999999876 378887443
No 236
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=77.89 E-value=2.6 Score=31.95 Aligned_cols=43 Identities=12% Similarity=0.215 Sum_probs=33.8
Q ss_pred HhChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 37 ELGIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 37 ~L~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
+-+|.+.|-++. .-+|+.|||+++++ ++..+.|+.|.|--.|+
T Consensus 14 e~~ia~yil~n~~~v~~~si~elA~~~~v---S~aTv~Rf~kklG~~Gf 59 (278)
T PRK11557 14 DRKLADYLLLQPDTARHLSSQQLANEAGV---SQSSVVKFAQKLGYKGF 59 (278)
T ss_pred HHHHHHHHHhCHHHHHhcCHHHHHHHhCC---CHHHHHHHHHHcCCCCH
Confidence 445666665432 35999999999999 99999999999877775
No 237
>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=77.84 E-value=3.4 Score=23.76 Aligned_cols=36 Identities=17% Similarity=0.258 Sum_probs=27.0
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
.+..|+..+. .+.+..|||+.+++ .+..++..++.+
T Consensus 7 ~E~~vl~~l~---~G~~~~eIA~~l~i---s~~tV~~~~~~i 42 (58)
T PF00196_consen 7 RELEVLRLLA---QGMSNKEIAEELGI---SEKTVKSHRRRI 42 (58)
T ss_dssp HHHHHHHHHH---TTS-HHHHHHHHTS---HHHHHHHHHHHH
T ss_pred HHHHHHHHHH---hcCCcchhHHhcCc---chhhHHHHHHHH
Confidence 4667888887 47999999999999 888776555443
No 238
>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=77.83 E-value=2.8 Score=28.40 Aligned_cols=46 Identities=13% Similarity=0.141 Sum_probs=40.1
Q ss_pred HHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccCc
Q 040869 55 ELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDK 108 (131)
Q Consensus 55 eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~~ 108 (131)
+||+.++. +.+-|.-++.++...|+++.. +|-..+|+.++.+++.+
T Consensus 2 ~La~~l~~---eiDdL~p~~eAaelLgf~~~~-----~Gdi~LT~~G~~f~~a~ 47 (120)
T PF09821_consen 2 QLADELHL---EIDDLLPIVEAAELLGFAEVE-----EGDIRLTPLGRRFAEAD 47 (120)
T ss_pred chHHHhCC---cHHHHHHHHHHHHHcCCeeec-----CCcEEeccchHHHHHCC
Confidence 58889999 999999999999999999976 57889999999877543
No 239
>PF13814 Replic_Relax: Replication-relaxation
Probab=77.53 E-value=3.5 Score=29.27 Aligned_cols=58 Identities=19% Similarity=0.169 Sum_probs=43.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC------CCCcceecchhcccccc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN------GQEEAYGLTAASTLLIK 106 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~------~~~~~y~~t~~s~~L~~ 106 (131)
+.+|..+|+.....+...+..++|.|+-|...|++...... ..+..|.+|+.+..++.
T Consensus 8 r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~ 71 (191)
T PF13814_consen 8 RFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLA 71 (191)
T ss_pred cCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHH
Confidence 68999999999988322223899999999999999876421 12457999999875543
No 240
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=77.17 E-value=3.1 Score=24.49 Aligned_cols=44 Identities=11% Similarity=0.108 Sum_probs=28.3
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec-ccCCCCcceecchhc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT-KVNGQEEAYGLTAAS 101 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~-~~~~~~~~y~~t~~s 101 (131)
.|..|+|+.+|+ ++..+++.. ..|++... ....|...|..+.+-
T Consensus 1 ~s~~eva~~~gv---s~~tlr~~~----~~gli~~~~~~~~g~r~y~~~dl~ 45 (70)
T smart00422 1 YTIGEVAKLAGV---SVRTLRYYE----RIGLLPPPIRTEGGYRLYSDEDLE 45 (70)
T ss_pred CCHHHHHHHHCc---CHHHHHHHH----HCCCCCCCccCCCCCEecCHHHHH
Confidence 478999999999 888776664 48887643 111123446555553
No 241
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=77.03 E-value=3.3 Score=32.57 Aligned_cols=35 Identities=20% Similarity=0.172 Sum_probs=32.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
..+|=+|||+++|+ +...+.|+|......|+++-.
T Consensus 28 ~g~tQ~eIA~~lgi---SR~~VsRlL~~Ar~~GiV~I~ 62 (318)
T PRK15418 28 DGLTQSEIGERLGL---TRLKVSRLLEKGRQSGIIRVQ 62 (318)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHHHHHHHcCcEEEE
Confidence 56999999999999 999999999999999999864
No 242
>PRK03837 transcriptional regulator NanR; Provisional
Probab=76.75 E-value=5.3 Score=29.40 Aligned_cols=45 Identities=13% Similarity=0.161 Sum_probs=37.3
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
|..+ +-.+||+++|+ +...++.-|+.|...|+++..+ |.|.|-..
T Consensus 34 G~~Lp~E~~Lae~~gV---SRt~VREAL~~L~~eGlv~~~~---~~G~~V~~ 79 (241)
T PRK03837 34 GDQLPSERELMAFFGV---GRPAVREALQALKRKGLVQISH---GERARVSR 79 (241)
T ss_pred CCCCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec---CCceeEec
Confidence 5568 89999999999 9999999999999999999865 14554433
No 243
>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=76.64 E-value=2.3 Score=23.48 Aligned_cols=22 Identities=9% Similarity=0.427 Sum_probs=19.2
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRL 73 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~Rl 73 (131)
..+|..+||+++|+ ++..+++-
T Consensus 15 ~~~s~~~Ia~~~gv---s~~~~y~~ 36 (47)
T PF00440_consen 15 EAVSIRDIARRAGV---SKGSFYRY 36 (47)
T ss_dssp TTSSHHHHHHHHTS---CHHHHHHH
T ss_pred HhCCHHHHHHHHcc---chhhHHHH
Confidence 67999999999999 88888763
No 244
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=75.90 E-value=3 Score=29.16 Aligned_cols=31 Identities=19% Similarity=0.432 Sum_probs=20.5
Q ss_pred HHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 42 DIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 42 d~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+.+...++..|.+|||+.+|+ ++..|||...
T Consensus 26 e~~~~~~~r~T~~eiAee~Gi---s~~tLYrWr~ 56 (142)
T PF13022_consen 26 ELMPENGERRTQAEIAEEVGI---SRSTLYRWRQ 56 (142)
T ss_dssp HHS------S-HHHHHHHHTS----HHHHHHHHH
T ss_pred HHhhhccccchHHHHHHHhCC---CHHHHHHHHh
Confidence 444444577999999999999 9999999885
No 245
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=75.53 E-value=3.2 Score=29.68 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=23.8
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
.++|..|||+.+|+ ++..++|-++..-
T Consensus 150 ~Gls~~EIA~~lgi---S~~tV~r~l~~aR 176 (185)
T PF07638_consen 150 EGLSVEEIAERLGI---SERTVRRRLRRAR 176 (185)
T ss_pred CCCCHHHHHHHHCc---CHHHHHHHHHHHH
Confidence 46999999999999 9999999888654
No 246
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=75.42 E-value=2.1 Score=32.90 Aligned_cols=46 Identities=22% Similarity=0.263 Sum_probs=35.4
Q ss_pred HHhChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 36 IELGIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 36 ~~L~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
.+-+|.+.|-++. .-.|+.|||+++|+ ++..+-|+.|.|--.|+=+
T Consensus 19 ~er~iA~yil~~~~~~~~~si~elA~~a~V---S~aTv~Rf~~kLGf~Gf~e 67 (281)
T COG1737 19 SERKIADYILANPDEVALLSIAELAERAGV---SPATVVRFARKLGFEGFSE 67 (281)
T ss_pred HHHHHHHHHHhCHHHHHHHHHHHHHHHhCC---CHHHHHHHHHHcCCCCHHH
Confidence 3445666665332 35899999999999 9999999999998888643
No 247
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=74.85 E-value=4.5 Score=30.95 Aligned_cols=60 Identities=22% Similarity=0.161 Sum_probs=48.3
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
-.|.+|..+.+ ..|.+.-|+++++ ..+.+.|-++.|.. .-+|.+. +..+.+|+.++.|.+
T Consensus 5 ~~L~~f~~v~e---~gs~s~AA~~L~i---SQpavS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~ 67 (308)
T PRK10094 5 ETLRTFIAVAE---TGSFSKAAERLCK---TTATISYRIKLLEENTGVALFFRT-----TRSVTLTAAGEHLLS 67 (308)
T ss_pred HHHHHHHHHHH---hCCHHHHHHHhcC---CHHHHHHHHHHHHHHhCCEEEeeC-----CCceeECHhHHHHHH
Confidence 35678888884 4689999999999 88899998888864 4588877 577999999987754
No 248
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=74.24 E-value=8.7 Score=23.71 Aligned_cols=30 Identities=30% Similarity=0.406 Sum_probs=20.1
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
|-+.+. ...+|-.|+|+.+|+ +.+.+.|++
T Consensus 23 i~~~~~--~~~ltQ~e~A~~lgi---sq~~vS~l~ 52 (80)
T PF13744_consen 23 IRELRE--ERGLTQAELAERLGI---SQPRVSRLE 52 (80)
T ss_dssp HHHHHH--CCT--HHHHHHHHTS----HHHHHHHH
T ss_pred HHHHHH--HcCCCHHHHHHHHCC---ChhHHHHHH
Confidence 666666 367999999999999 666655555
No 249
>smart00351 PAX Paired Box domain.
Probab=73.73 E-value=6.7 Score=26.47 Aligned_cols=47 Identities=4% Similarity=0.095 Sum_probs=37.8
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.-.+..|..... +..|..+||+++|+ ++..++++++-....|.+...
T Consensus 20 ~~~R~riv~~~~---~G~s~~~iA~~~gv---s~~tV~kwi~r~~~~G~~~pk 66 (125)
T smart00351 20 DEERQRIVELAQ---NGVRPCDISRQLCV---SHGCVSKILGRYYETGSIRPG 66 (125)
T ss_pred HHHHHHHHHHHH---cCCCHHHHHHHHCc---CHHHHHHHHHHHHHcCCcCCc
Confidence 334556666554 35799999999999 999999999999999987764
No 250
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=73.61 E-value=6.5 Score=29.36 Aligned_cols=46 Identities=9% Similarity=0.049 Sum_probs=37.5
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
|..+ |-.+||+.+|+ +...++--|+.|...|+++..+ +.|.|-...
T Consensus 29 G~~LpsE~eLae~~gV---SRtpVREAL~~L~~eGlV~~~~---~~G~~V~~~ 75 (253)
T PRK11523 29 GDKLPAERFIADEKNV---SRTVVREAIIMLEVEGYVEVRK---GSGIHVVSN 75 (253)
T ss_pred CCCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CCeeEEecC
Confidence 5678 57899999999 9999999999999999998765 145555443
No 251
>PRK13824 replication initiation protein RepC; Provisional
Probab=73.32 E-value=5 Score=32.76 Aligned_cols=35 Identities=14% Similarity=0.107 Sum_probs=31.3
Q ss_pred CCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeeccc
Q 040869 51 ITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKV 88 (131)
Q Consensus 51 ~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~ 88 (131)
.|-.+|+.++ |. .+..|+|.++.|+..|++...++
T Consensus 83 pSN~~La~r~~Gm---s~~tlrRhla~LveaGLI~rrDS 118 (404)
T PRK13824 83 PSNAQLSLRAHGM---AGATLRRHLAALVEAGLIIRRDS 118 (404)
T ss_pred hhHHHHHHHHcCC---CHHHHHHHHHHHHHCCCeEeecC
Confidence 6788999985 99 99999999999999999988653
No 252
>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=73.24 E-value=2.9 Score=23.42 Aligned_cols=25 Identities=20% Similarity=0.312 Sum_probs=19.6
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
..+|..|+|+++|+ ++..+.|+.+-
T Consensus 8 ~gls~~~la~~~gi---s~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGI---SRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS----HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCC---CcchhHHHhcC
Confidence 56999999999999 88888888763
No 253
>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=72.91 E-value=6.6 Score=25.49 Aligned_cols=64 Identities=13% Similarity=0.128 Sum_probs=47.4
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
++.+|..+.+ .-|...-|+.+|+ +++.+.|-++.|.. .-+|.+.....+++.+.+|+.++.|..
T Consensus 6 ~l~~~~av~~---~gSis~AA~~L~i---S~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~~ 72 (99)
T TIGR00637 6 RVALLKAIAR---MGSISQAAKDAGI---SYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLIQ 72 (99)
T ss_pred HHHHHHHHHH---hCCHHHHHHHHCC---CHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHHH
Confidence 5667888874 4678999999999 89999998888853 446887631000357999999997753
No 254
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=72.81 E-value=4 Score=31.18 Aligned_cols=44 Identities=18% Similarity=0.279 Sum_probs=34.5
Q ss_pred HhChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869 37 ELGIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF 83 (131)
Q Consensus 37 ~L~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~ 83 (131)
+-.|.+.|-++. ..+|+.+||+++++ ++..+.|+.|.|--.|+-
T Consensus 30 e~~Ia~yil~~~~~v~~~si~~lA~~~~v---S~aTi~Rf~kkLGf~gf~ 76 (292)
T PRK11337 30 ESRVVEWLLKPGDLSEATALKDIAEALAV---SEAMIVKVAKKLGFSGFR 76 (292)
T ss_pred HHHHHHHHHhCHHHHHhcCHHHHHHHhCC---ChHHHHHHHHHcCCCCHH
Confidence 455666665432 35899999999999 999999999998777753
No 255
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=72.80 E-value=6.8 Score=29.65 Aligned_cols=60 Identities=12% Similarity=0.091 Sum_probs=48.2
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
-+|.+|-.+.+ ..|...-|+++++ ..+.+.|-++.|.. .-+|.+. ++.+.+|+.++.|..
T Consensus 7 ~~L~~F~~v~e---~gs~s~AA~~L~i---sqpavS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~ 69 (296)
T PRK11062 7 NHLYYFWMVCK---EGSVVGAAEALFL---TPQTITGQIKALEERLQGKLFKRK-----GRGLEPTELGELVFR 69 (296)
T ss_pred HHHHHHHHHHh---cCCHHHHHHHhCC---ChHHHHHHHHHHHHHcCccceeec-----CCceeECHhHHHHHH
Confidence 36778888884 5789999999999 88888888888854 4588877 577999999987654
No 256
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=72.74 E-value=6.2 Score=29.58 Aligned_cols=60 Identities=17% Similarity=0.130 Sum_probs=48.3
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccccC
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
++.+|..+.+ .-|...-|+++++ .++.+.|-++.|.. ..+|.+. +..+.+|+.++.|.+.
T Consensus 5 ~l~~f~~v~~---~gs~s~AA~~L~i---sqpavS~~I~~LE~~lG~~LF~R~-----~r~~~lT~~G~~l~~~ 67 (275)
T PRK03601 5 LLKTFLEVSR---TRHFGRAAESLYL---TQSAVSFRIRQLENQLGVNLFTRH-----RNNIRLTAAGERLLPY 67 (275)
T ss_pred HHHHHHHHHH---cCCHHHHHHHhCC---ChHHHHHHHHHHHHHhCCceEEEC-----CCceEECHhHHHHHHH
Confidence 5678888884 4678999999999 88888888888754 5688887 4779999999977654
No 257
>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=72.70 E-value=5.7 Score=33.82 Aligned_cols=56 Identities=7% Similarity=0.014 Sum_probs=43.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccCcccC
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYC 111 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~~~~s 111 (131)
.|....|+++.++. ++..+.++++.|+..|.+.+-. ++.|-+..+.+++..+.+-+
T Consensus 487 ~~~~~~~~~~~~~~---~~~~~~~~l~~l~~~g~~~~~~----~~~~~~~~~~~~~~~~~~~~ 542 (581)
T TIGR00475 487 KGAWVREFAEEVNG---DEKVMLKRVRKAGHRGGETLIV----KDRLLKKYINELKEEGGTFN 542 (581)
T ss_pred CCCCHHHHHhhhCC---CHHHHHHHHHHHHhCCCEEEEe----CCeEHHHHHHHHHhcCCcCc
Confidence 68999999999999 9999999999999999777765 56776655555554444333
No 258
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=72.66 E-value=8.1 Score=26.19 Aligned_cols=49 Identities=8% Similarity=0.007 Sum_probs=42.6
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
-|.+.+.||..++- +...++.-|.++...|+++..+ +|.|..+.....-
T Consensus 50 ipy~~e~LA~~~~~---~~~~V~~Al~~f~k~glIe~~d----~g~i~i~~~~~~~ 98 (119)
T TIGR01714 50 APYNAEMLATMFNR---NVGDIRITLQTLESLGLIEKKN----NGDIFLENWEKHV 98 (119)
T ss_pred CCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec----CCcEEehhHHHHc
Confidence 68999999999999 9999999999999999999886 6778777765443
No 259
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=72.58 E-value=8 Score=26.17 Aligned_cols=69 Identities=16% Similarity=0.242 Sum_probs=49.9
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCC--C---CCCcchHHHHHHHhhcCCceeecccC-CC---Ccceecchhccccc
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDI--Q---PTKTTGLFRLMRLLVHSSCFNKTKVN-GQ---EEAYGLTAASTLLI 105 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~--~---~~~~~~l~RlLr~L~~~gl~~~~~~~-~~---~~~y~~t~~s~~L~ 105 (131)
.+++-|+..|.. .|.+--||.+.+.- . ..++..++.+|+.|...|++...... ++ ...|.+|+.++...
T Consensus 9 ~l~~~iL~~L~~--~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l 86 (138)
T COG1695 9 SLELLILSLLSE--KPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEEL 86 (138)
T ss_pred hHHHHHHHHHhc--CCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHH
Confidence 355667777774 48999999887653 1 23788999999999999999965322 11 25699999998443
No 260
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.55 E-value=4.3 Score=26.19 Aligned_cols=25 Identities=16% Similarity=0.321 Sum_probs=22.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
.++|.++||++++. .+..+.++|..
T Consensus 22 ~~LS~~~iA~~Ln~---t~~~lekil~~ 46 (97)
T COG4367 22 CPLSDEEIATALNW---TEVKLEKILQV 46 (97)
T ss_pred ccccHHHHHHHhCC---CHHHHHHHHHH
Confidence 58999999999999 88999999854
No 261
>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=72.52 E-value=5.2 Score=30.92 Aligned_cols=58 Identities=24% Similarity=0.303 Sum_probs=42.5
Q ss_pred HHHhCCCCCCHHHHHh---hcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 43 IIHSHGRAITLSELVS---ALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 43 ~l~~~~~~~s~~eLA~---~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
++...++.+++.+|.+ .+|+ ++..++-.|.-|+..|+++.... +....|.+|+.++..
T Consensus 10 ~~~~~gg~i~~~~Li~l~~~~gi---~~~~vr~al~RL~~~G~l~~~~~-grr~~Y~LT~~g~~~ 70 (280)
T TIGR02277 10 AIRPRGGAIWLGSLIEFLAGLGI---NERLVRTAVSRLVAQGWLQSERK-GRRSFYSLTDKGRRR 70 (280)
T ss_pred hccCCCCceeHHHHHHHHHhcCC---CcchHHHHHHHHHHCCCEEeeec-CCCCEEEECHHHHHH
Confidence 3444456777776554 5677 99999999999999999987641 113679999998743
No 262
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=72.29 E-value=4.4 Score=32.11 Aligned_cols=45 Identities=16% Similarity=0.321 Sum_probs=35.8
Q ss_pred hHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 40 IADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 40 ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
|..+|..+| .++-..+|..++++ +...+.|+|+.|.+.+++.+..
T Consensus 89 vy~~I~~ag~~GIw~~~i~~~t~l---~~~~~~k~lk~Le~k~lIK~vk 134 (327)
T PF05158_consen 89 VYQLIEEAGNKGIWTKDIKKKTNL---HQTQLTKILKSLESKKLIKSVK 134 (327)
T ss_dssp HHHHHHHHTTT-EEHHHHHHHCT-----HHHHHHHHHHHHHTTSEEEE-
T ss_pred HHHHHHHhCCCCCcHHHHHHHcCC---CHHHHHHHHHHHHhCCCEEEec
Confidence 566666544 67999999999999 9999999999999999999864
No 263
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=71.87 E-value=6.5 Score=29.53 Aligned_cols=60 Identities=15% Similarity=0.214 Sum_probs=48.4
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhccccccC
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
.|.+|-.+.+ .-|...-|+++++ .++.+.|-++.|. ..-+|.+. ++.+.+|+.++.|.+.
T Consensus 5 ~L~~f~~v~~---~gs~s~AA~~L~i---sQ~avSr~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~~ 67 (296)
T PRK09906 5 HLRYFVAVAE---ELNFTKAAEKLHT---AQPSLSQQIKDLENCVGVPLLVRD-----KRKVALTAAGEVFLQD 67 (296)
T ss_pred HHHHHHHHHh---hCCHHHHHHHhCC---CCcHHHHHHHHHHHHhCCeeeeeC-----CCcceEcHhHHHHHHH
Confidence 5678888884 3589999999999 8888888888885 45688887 5779999999977654
No 264
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=71.84 E-value=6 Score=29.90 Aligned_cols=61 Identities=11% Similarity=0.114 Sum_probs=48.6
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhccccccC
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
-.|.+|..+.+ .-|...-|+++++ ..+.+.|-++.|. ...+|.+. ++.+.+|+.++.|.+.
T Consensus 8 ~~L~~f~~v~~---~gs~s~AA~~L~i---sQ~avS~~i~~LE~~lG~~LF~R~-----~r~~~lT~~G~~l~~~ 71 (302)
T PRK09791 8 HQIRAFVEVAR---QGSIRGASRMLNM---SQPALTKSIQELEEGLAAQLFFRR-----SKGVTLTDAGESFYQH 71 (302)
T ss_pred HHHHHHHHHHH---cCCHHHHHHHhCC---ChHHHHHHHHHHHHHhCCeEEEEc-----CCCceECccHHHHHHH
Confidence 45778888885 3489999999999 8888888888885 45688886 5779999999877643
No 265
>PF14502 HTH_41: Helix-turn-helix domain
Probab=71.79 E-value=11 Score=21.40 Aligned_cols=36 Identities=14% Similarity=0.232 Sum_probs=32.6
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+-.|++|+++++++ ..-.+..-|+.|...|.+.-..
T Consensus 5 Ri~tI~e~~~~~~v---s~GtiQ~Alk~Le~~gaI~Le~ 40 (48)
T PF14502_consen 5 RIPTISEYSEKFGV---SRGTIQNALKFLEENGAIKLES 40 (48)
T ss_pred ccCCHHHHHHHhCc---chhHHHHHHHHHHHCCcEEeee
Confidence 56789999999999 8899999999999999988765
No 266
>cd00131 PAX Paired Box domain
Probab=71.35 E-value=1.9 Score=29.42 Aligned_cols=55 Identities=9% Similarity=0.187 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 26 HLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 26 ~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
|...+++-.-.+..|..... ...|..+||+.+++ ....++|++.-....|=+...
T Consensus 12 ~~m~~~lS~d~R~rIv~~~~---~G~s~~~iA~~~~V---s~~tV~r~i~r~~e~G~v~pk 66 (128)
T cd00131 12 FVNGRPLPDSIRQRIVELAQ---SGIRPCDISRQLRV---SHGCVSKILNRYYETGSIRPG 66 (128)
T ss_pred ccCCCcCCHHHHHHHHHHHH---cCCCHHHHHHHHCc---CHHHHHHHHHHHHHcCCcCCC
Confidence 33344455556667776665 46899999999999 999999999999988876654
No 267
>PF13309 HTH_22: HTH domain
Probab=71.20 E-value=3.8 Score=24.49 Aligned_cols=38 Identities=18% Similarity=0.251 Sum_probs=27.9
Q ss_pred HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
-.+++..-+-|+|. + .-+++.+|+++|+ +...+||-||
T Consensus 27 ~~iV~~L~~~G~F~-l-----Kgav~~vA~~L~i---S~~TVY~YLr 64 (64)
T PF13309_consen 27 KEIVRQLYEKGIFL-L-----KGAVEYVAEKLGI---SRATVYRYLR 64 (64)
T ss_pred HHHHHHHHHCCCcc-c-----CcHHHHHHHHHCC---CHHHHHHHcC
Confidence 34455555666664 2 3468999999999 9999999875
No 268
>smart00753 PAM PCI/PINT associated module.
Probab=71.19 E-value=15 Score=22.53 Aligned_cols=51 Identities=12% Similarity=0.147 Sum_probs=38.8
Q ss_pred HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.....+..++..... -..++.++||+.+++ +.+.+.+++.-+...|.+.-.
T Consensus 7 ~~~~~~~~l~~l~~~-y~~i~~~~i~~~~~l---~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00753 7 QRKIRLTNLLQLSEP-YSSISLSDLAKLLGL---SVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHhHH-hceeeHHHHHHHhCc---CHHHHHHHHHHHHHCCCeEEE
Confidence 344445555554442 367999999999999 888899999999999988753
No 269
>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=71.19 E-value=15 Score=22.53 Aligned_cols=51 Identities=12% Similarity=0.147 Sum_probs=38.8
Q ss_pred HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
.....+..++..... -..++.++||+.+++ +.+.+.+++.-+...|.+.-.
T Consensus 7 ~~~~~~~~l~~l~~~-y~~i~~~~i~~~~~l---~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00088 7 QRKIRLTNLLQLSEP-YSSISLSDLAKLLGL---SVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHhHH-hceeeHHHHHHHhCc---CHHHHHHHHHHHHHCCCeEEE
Confidence 344445555554442 367999999999999 888899999999999988753
No 270
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=71.18 E-value=6.2 Score=30.11 Aligned_cols=61 Identities=10% Similarity=0.160 Sum_probs=49.0
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.-+|.+|..+.+ ..|...-|+++++ ..+.+.|-++.|.. ..+|.+. +....+|+.++.|.+
T Consensus 9 ~~~L~~F~av~e---~gs~s~AA~~L~i---SQpavS~~I~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~~ 72 (312)
T PRK10341 9 TQHLVVFQEVIR---SGSIGSAAKELGL---TQPAVSKIINDIEDYFGVELIVRK-----NTGVTLTPAGQVLLS 72 (312)
T ss_pred HHHHHHHHHHHH---cCCHHHHHHHhCC---ChHHHHHHHHHHHHHhCCeEEEEc-----CCCceEChhHHHHHH
Confidence 346778888884 6789999999999 88888888888854 4588887 577999999987664
No 271
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=71.14 E-value=4.8 Score=29.46 Aligned_cols=30 Identities=20% Similarity=0.170 Sum_probs=27.9
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
++|-.+||..+|+ .++.+.|+++.|...|+
T Consensus 173 ~~t~~~iA~~lG~---tretvsR~l~~L~~~gl 202 (236)
T PRK09392 173 PYEKRVLASYLGM---TPENLSRAFAALASHGV 202 (236)
T ss_pred eCCHHHHHHHhCC---ChhHHHHHHHHHHhCCe
Confidence 5677899999999 99999999999999996
No 272
>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=70.86 E-value=4.7 Score=22.61 Aligned_cols=24 Identities=21% Similarity=0.418 Sum_probs=16.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
...|..|||+.+|+ ++..+.+.++
T Consensus 25 ~g~s~~eIa~~l~~---s~~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGI---SESTVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS----HHHHHHHHH
T ss_pred HCcCHHHHHHHHCc---CHHHHHHHHH
Confidence 57999999999999 8888776654
No 273
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=70.74 E-value=7.6 Score=29.54 Aligned_cols=59 Identities=19% Similarity=0.147 Sum_probs=47.4
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
+|..|-.+.+ ..|...-|+++++ ..+.+.|-++.|. ..-+|.+. +..+.+|+.++.|..
T Consensus 5 ~L~~F~~v~~---~~S~s~AA~~L~i---sQ~avS~~I~~LE~~lg~~LF~R~-----~r~v~lT~~G~~l~~ 66 (305)
T PRK11233 5 RLKYFVKIVD---IGSLTQAAEVLHI---AQPALSQQVATLEGELNQQLLIRT-----KRGVTPTEAGKILYT 66 (305)
T ss_pred HHHHHHHHHH---cCCHHHHHHHhCC---CchHHHHHHHHHHHHhCCceEEeC-----CCCceECHhHHHHHH
Confidence 4677888874 4589999999999 8888888888885 45588887 577999999986654
No 274
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=70.32 E-value=7.3 Score=25.13 Aligned_cols=59 Identities=15% Similarity=0.164 Sum_probs=34.8
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC---CCCcceecchh
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQEEAYGLTAA 100 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~---~~~~~y~~t~~ 100 (131)
+|=|.-.|.. +.. ++..|-+.+|. +.+.+.+.+.+|...|+--+-... ...|.|..+.-
T Consensus 10 rlyla~li~~-~~~-nvp~L~~~TGm---PrRT~Qd~i~aL~~~~I~~~Fvq~G~R~~~GyY~i~~W 71 (90)
T PF09904_consen 10 RLYLAYLIDS-GER-NVPALMEATGM---PRRTIQDTIKALPELGIECEFVQDGERNNAGYYRISDW 71 (90)
T ss_dssp HHHHHHHHHH-S-B--HHHHHHHH------HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE-
T ss_pred HHHHHHHHhc-CCc-cHHHHHHHhCC---CHhHHHHHHHHhhcCCeEEEEEecCccCCCCcEEeeec
Confidence 4445556664 334 99999999999 999999999999999975552110 11466776643
No 275
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=70.21 E-value=7.8 Score=28.90 Aligned_cols=59 Identities=10% Similarity=0.113 Sum_probs=47.0
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.|.+|-.+.+ ..|...-|+++++ ..+.+.|-++.|.. ..+|.+. ++.+.+|+.++.|.+
T Consensus 7 ~L~~f~~v~e---~~s~t~AA~~L~i---sqpavS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~ 68 (290)
T PRK10837 7 QLEVFAEVLK---SGSTTQASVMLAL---SQSAVSAALTDLEGQLGVQLFDRV-----GKRLVVNEHGRLLYP 68 (290)
T ss_pred HHHHHHHHHH---cCCHHHHHHHhCC---CccHHHHHHHHHHHHhCCccEeec-----CCeEEECHhHHHHHH
Confidence 4677878874 4589999999999 88888888888754 5688886 577999999987764
No 276
>PF14557 AphA_like: Putative AphA-like transcriptional regulator
Probab=70.09 E-value=11 Score=27.27 Aligned_cols=68 Identities=15% Similarity=0.123 Sum_probs=51.4
Q ss_pred HHHHHHhChHHHHHhCCCCCCHHHHHhhcCC------CCCCcchHHHHHHHhhcCCceeecccC--CCCcceecchhcc
Q 040869 32 LKCAIELGIADIIHSHGRAITLSELVSALDI------QPTKTTGLFRLMRLLVHSSCFNKTKVN--GQEEAYGLTAAST 102 (131)
Q Consensus 32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~------~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~~~~y~~t~~s~ 102 (131)
-+-+++|++.-.|+ .+|.+++++|+.+.- -| ....+.--|..|...|+++..... ...-.|..|+-++
T Consensus 8 pre~v~L~vLG~la--~~p~~~~~va~~vrh~~sr~~gp-s~~Ll~~sie~Lr~eGlve~~~g~g~e~~a~l~iT~~Gr 83 (175)
T PF14557_consen 8 PREAVRLCVLGTLA--RGPRRYEEVAGAVRHFASRIWGP-SLDLLGTSIELLREEGLVEAVDGEGMEDNALLAITDAGR 83 (175)
T ss_pred HHHHHHHHHHHHHh--cCCcCHHHHHHHHHHhccccccC-chhhhhhHHHHHHhcCCcccccccCCCccceeeeCcchH
Confidence 45678888888888 489999999998752 22 677788888999999999977322 1245688888765
No 277
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=69.98 E-value=3.6 Score=27.16 Aligned_cols=40 Identities=15% Similarity=0.395 Sum_probs=28.6
Q ss_pred hHHHHHh--CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869 40 IADIIHS--HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHS 80 (131)
Q Consensus 40 ifd~l~~--~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~ 80 (131)
|++.++. .|.-.|+.+||+-.|. |..++.+.|+|..|..-
T Consensus 11 v~~vv~~IP~GkV~TYGdIA~laG~-p~~ARqVG~il~~l~~~ 52 (103)
T COG3695 11 VLDVVAAIPEGKVSTYGDIAKLAGL-PRAARQVGRILKHLPEG 52 (103)
T ss_pred HHHHHHhCCCCceeeHHHHHHHhCC-ChhHHHHHHHHhhCCCC
Confidence 4444442 2567999999999999 11378899999976543
No 278
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=69.84 E-value=3.9 Score=24.61 Aligned_cols=11 Identities=9% Similarity=0.323 Sum_probs=7.0
Q ss_pred CHHHHHhhcCC
Q 040869 52 TLSELVSALDI 62 (131)
Q Consensus 52 s~~eLA~~~~~ 62 (131)
|..|||+++|+
T Consensus 2 t~~~iA~~~gv 12 (70)
T smart00354 2 TIKDVARLAGV 12 (70)
T ss_pred CHHHHHHHHCC
Confidence 45666666666
No 279
>PRK15482 transcriptional regulator MurR; Provisional
Probab=69.81 E-value=5.3 Score=30.44 Aligned_cols=45 Identities=16% Similarity=0.300 Sum_probs=34.9
Q ss_pred HhChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 37 ELGIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 37 ~L~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+-.|.+.|-++. .-+|+.|||+++|+ ++..+-|+.+.|--.|+-+
T Consensus 18 e~~Ia~yIl~n~~~v~~~si~elA~~~~v---S~aTv~Rf~kkLGf~Gf~e 65 (285)
T PRK15482 18 EQKIADFLRANVSELKSVSSRKMAKQLGI---SQSSIVKFAQKLGAQGFTE 65 (285)
T ss_pred HHHHHHHHHhCHHHHHhcCHHHHHHHhCC---CHHHHHHHHHHhCCCCHHH
Confidence 445666665432 45999999999999 9999999999987777633
No 280
>PRK04217 hypothetical protein; Provisional
Probab=69.38 E-value=6 Score=26.44 Aligned_cols=25 Identities=12% Similarity=0.222 Sum_probs=21.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
..+|.+|||+.+|+ +...+++.++.
T Consensus 57 eGlS~~EIAk~LGI---S~sTV~r~L~R 81 (110)
T PRK04217 57 EGLTQEEAGKRMGV---SRGTVWRALTS 81 (110)
T ss_pred cCCCHHHHHHHHCc---CHHHHHHHHHH
Confidence 56899999999999 88988887764
No 281
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=69.37 E-value=2.5 Score=25.56 Aligned_cols=50 Identities=20% Similarity=0.236 Sum_probs=34.7
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+=.|.+.|.+.+ +.++..||...|++- +...+.|+|-.|...|.+....
T Consensus 5 ~ee~Il~~L~~~g-~~~a~~ia~~~~L~~-~kk~VN~~LY~L~k~g~v~k~~ 54 (66)
T PF02295_consen 5 LEEKILDFLKELG-GSTATAIAKALGLSV-PKKEVNRVLYRLEKQGKVCKEG 54 (66)
T ss_dssp HHHHHHHHHHHHT-SSEEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEC
T ss_pred HHHHHHHHHHhcC-CccHHHHHHHhCcch-hHHHHHHHHHHHHHCCCEeeCC
Confidence 3456788887655 555555655555400 5788999999999999998753
No 282
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=69.28 E-value=20 Score=27.07 Aligned_cols=44 Identities=11% Similarity=0.213 Sum_probs=38.6
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
||+.|...+|-+.++-||.++|+ -.+.+---||-|.+.|+++..
T Consensus 194 I~eELdG~EG~lvASkiADrvGI---TRSVIVNALRKlESAGvIeSR 237 (261)
T COG4465 194 IFEELDGNEGLLVASKIADRVGI---TRSVIVNALRKLESAGVIESR 237 (261)
T ss_pred HHHhcCCccceeeehhhhhhhCc---hHHHHHHHHHHhhhcCceeec
Confidence 67777766688999999999999 888888999999999999865
No 283
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=69.06 E-value=6.4 Score=31.29 Aligned_cols=31 Identities=26% Similarity=0.314 Sum_probs=26.4
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSS 81 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g 81 (131)
+.|+|+++||+..|+ +++.+.|+-+.-....
T Consensus 234 e~plsl~~LA~~~~~---S~R~leRlF~~~lG~s 264 (328)
T COG4977 234 EEPLSLEELADRAGL---SRRQLERLFRAELGVS 264 (328)
T ss_pred cCCcCHHHHHHHhCC---CHHHHHHHHHHHhCCC
Confidence 489999999999999 9999999988655443
No 284
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=68.98 E-value=5.2 Score=33.56 Aligned_cols=37 Identities=16% Similarity=0.221 Sum_probs=34.0
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+..+|++|||+.+.| .++..+++|+.+...|.+.=.+
T Consensus 21 ~~~~~l~~la~~l~c---s~R~~~~~l~~~~~~gwl~w~~ 57 (552)
T PRK13626 21 SQETTLNELAELLNC---SRRHMRTLLNTMQQRGWLTWQA 57 (552)
T ss_pred cceeeHHHHHHHhcC---ChhHHHHHHHHHHHCCCeeeec
Confidence 357999999999999 9999999999999999999764
No 285
>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=68.94 E-value=9.2 Score=28.16 Aligned_cols=59 Identities=15% Similarity=0.160 Sum_probs=47.2
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccccC
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
|..|..+.+ .-|...-|+++++ .++.+.|-++.|.. .-+|.+. ++...+|+.++.|...
T Consensus 2 l~~f~~v~~---~gs~~~AA~~L~i---sqsavS~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~~ 63 (279)
T TIGR03339 2 LKAFHAVAR---CGSFTRAAERLGL---SQPTVTDQVRKLEERYGVELFHRN-----GRRLELTDAGHRLLPI 63 (279)
T ss_pred chhhHHHHh---cCCHHHHHHHhcC---CchHHHHHHHHHHHHhCCccEEEc-----CCeEEEChhHHHHHHH
Confidence 567888884 4589999999999 88888888888853 4588887 5779999999877643
No 286
>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=68.66 E-value=5.5 Score=24.35 Aligned_cols=47 Identities=19% Similarity=0.308 Sum_probs=32.6
Q ss_pred CCCCCCHHHHHh---hcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc---ceecchh
Q 040869 47 HGRAITLSELVS---ALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE---AYGLTAA 100 (131)
Q Consensus 47 ~~~~~s~~eLA~---~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~---~y~~t~~ 100 (131)
.+++++..+|.+ .+|+ ++..++--|--|+..|+++... .| .|.+|+-
T Consensus 17 ~g~~i~~~~Li~ll~~~Gv---~e~avR~alsRl~~~G~L~~~r----~Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 17 RGGWIWVASLIRLLAAFGV---SESAVRTALSRLVRRGWLESER----RGRRSYYRLTER 69 (70)
T ss_dssp TTS-EEHHHHHHHHCCTT-----HHHHHHHHHHHHHTTSEEEEC----CCTEEEEEE-HH
T ss_pred CCCceeHHHHHHHHHHcCC---ChHHHHHHHHHHHHcCceeeee----cCccceEeeCCC
Confidence 356677666554 5677 8889998899999999999876 34 5888864
No 287
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=68.32 E-value=12 Score=27.30 Aligned_cols=46 Identities=11% Similarity=0.192 Sum_probs=36.4
Q ss_pred HHHHHhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869 33 KCAIELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSS 81 (131)
Q Consensus 33 ~~a~~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g 81 (131)
+.-....|.+.|...+ ..+|..|||+..|+ ++..++|=|+.+...|
T Consensus 14 r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v---~~~tirrDl~~l~~~G 60 (213)
T PRK05472 14 RLPLYYRYLKELKEEGVERVSSKELAEALGV---DSAQIRKDLSYFGEFG 60 (213)
T ss_pred HhHHHHHHHHHHHHcCCcEEeHHHHHHHhCc---CHHHHHHHHHHHHhcC
Confidence 4455667888888633 37999999999999 8889999888886555
No 288
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=68.13 E-value=7.8 Score=29.47 Aligned_cols=61 Identities=10% Similarity=0.109 Sum_probs=49.1
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccccC
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
-+|.+|-.+.+ .-|...-|+++++ ..+.+.|-++.|.. ..+|.+. ++.+.+|+.++.|.+.
T Consensus 11 ~~L~~F~~va~---~gs~s~AA~~L~i---sQpavS~~I~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~~ 74 (302)
T TIGR02036 11 SKMHTFEVAAR---HQSFSLAAEELSL---TPSAISHRINQLEEELGIQLFVRS-----HRKVELTHEGKRIYWA 74 (302)
T ss_pred HHHHHHHHHHH---hCCHHHHHHHHCC---CHHHHHHHHHHHHHHhCCceEEEC-----CCceeECHhHHHHHHH
Confidence 45778888874 5678999999999 88999999998864 5588877 5889999999877643
No 289
>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=67.98 E-value=10 Score=23.85 Aligned_cols=49 Identities=12% Similarity=0.124 Sum_probs=37.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
+-+..+.|++..|+ +...+...|.-|...+++..... .-..|++|-.+-
T Consensus 23 E~VP~~~I~~~s~l---~~~~~~~~L~~L~~~kLv~~~~~--~Y~GYrLT~~GY 71 (82)
T PF09202_consen 23 EWVPLELIEKISGL---SEGEVEKRLKRLVKLKLVSRRNK--PYDGYRLTFLGY 71 (82)
T ss_dssp SSEEHHHHHHHHT-----HHHHHHHHHHHHHTTSEEEE-S--SS-EEEE-HHHH
T ss_pred ccCCHHHHHHHhCc---CHHHHHHHHHHHHhcCCccccCC--CcceEEEeecch
Confidence 57889999999999 89999999999999999998531 135688887764
No 290
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=67.92 E-value=17 Score=22.39 Aligned_cols=34 Identities=21% Similarity=0.359 Sum_probs=25.3
Q ss_pred hHHHHHhCC-CCCCHHHHHhhcC-CCCCCcc-hHHHHHHH
Q 040869 40 IADIIHSHG-RAITLSELVSALD-IQPTKTT-GLFRLMRL 76 (131)
Q Consensus 40 ifd~l~~~~-~~~s~~eLA~~~~-~~~~~~~-~l~RlLr~ 76 (131)
+.+.|.+.+ .|+|++||...++ + +.. .+.++|+.
T Consensus 14 aV~ymK~r~~~Plt~~EIl~~ls~~---d~~~~~~~~L~~ 50 (75)
T cd07977 14 IVDYMKKRHQHPLTLDEILDYLSLL---DIGPKLKEWLKS 50 (75)
T ss_pred HHHHHHhcCCCCccHHHHHHHHhcc---CccHHHHHHHHh
Confidence 456787767 8999999999999 7 544 34456653
No 291
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=67.86 E-value=12 Score=28.23 Aligned_cols=66 Identities=12% Similarity=0.114 Sum_probs=49.7
Q ss_pred HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
|+=...-.|++.|.+ ++..|.-+||...|+ +..++.=-+..|...|+..++... ..-.|..||.-.
T Consensus 171 Lkn~~~k~I~~eiq~-~~~~t~~~ia~~l~l---s~aTV~~~lk~l~~~Gii~~~~~G-r~iiy~in~s~~ 236 (240)
T COG3398 171 LKNETSKAIIYEIQE-NKCNTNLLIAYELNL---SVATVAYHLKKLEELGIIPEDREG-RSIIYSINPSIE 236 (240)
T ss_pred hhchhHHHHHHHHhc-CCcchHHHHHHHcCc---cHHHHHHHHHHHHHcCCCcccccC-ceEEEEeCHHHH
Confidence 444444568888875 567999999999999 999999999999999999998620 012377776533
No 292
>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=67.79 E-value=6.9 Score=20.90 Aligned_cols=26 Identities=12% Similarity=0.227 Sum_probs=22.0
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
...|..+||+.+|+ +...+++.++..
T Consensus 25 ~~~~~~~ia~~~~~---s~~~i~~~~~~~ 50 (55)
T cd06171 25 EGLSYEEIAEILGI---SRSTVRQRLHRA 50 (55)
T ss_pred cCCCHHHHHHHHCc---CHHHHHHHHHHH
Confidence 45899999999999 889888887653
No 293
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=67.53 E-value=8.9 Score=27.98 Aligned_cols=44 Identities=16% Similarity=0.166 Sum_probs=35.9
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
++.+.|.. ++..|+.+||+++|+ +...+.|.|=-|...|.+...
T Consensus 17 ~~~~~l~~-~~~~~a~~i~~~l~~---~k~~vNr~LY~l~~~~~v~~~ 60 (183)
T PHA03103 17 KEVKNLGL-GEGITAIEISRKLNI---EKSEVNKQLYKLQREGMVYMS 60 (183)
T ss_pred HHHHHhcc-CCCccHHHHHHHhCC---CHHHHHHHHHHHHhcCceecC
Confidence 34556653 678999999999999 888899999888888877654
No 294
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=67.42 E-value=7.6 Score=29.29 Aligned_cols=60 Identities=13% Similarity=0.102 Sum_probs=48.4
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
-+|.+|..+.+ .-|...-|+++++ ..+.+.|-++.|.. .-+|.+. +....+|+.++.|..
T Consensus 5 ~~L~~f~~va~---~gs~s~AA~~L~i---sQpavS~~I~~LE~~lG~~LF~R~-----~r~~~lT~~G~~l~~ 67 (301)
T PRK14997 5 NDFAWFVHVVE---EGGFAAAGRALDE---PKSKLSRRIAQLEERLGVRLIQRT-----TRQFNVTEVGQTFYE 67 (301)
T ss_pred HHHHHHHHHHH---cCCHHHHHHHhCC---CHHHHHHHHHHHHHHhCCEeeeec-----cCcceEcHhHHHHHH
Confidence 46788888884 5789999999999 88888888888854 4578877 477999999987654
No 295
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=67.18 E-value=8 Score=29.29 Aligned_cols=59 Identities=19% Similarity=0.245 Sum_probs=48.3
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
+|.+|..+.+ ..|...-|+++++ ..+.+.|-++.|.. .-+|.+. +..+.+|+.++.|.+
T Consensus 6 ~L~~f~~v~e---~~s~s~AA~~L~i---sQpavS~~I~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~~ 67 (300)
T PRK11074 6 SLEVVDAVAR---TGSFSAAAQELHR---VPSAVSYTVRQLEEWLAVPLFERR-----HRDVELTPAGEWFVK 67 (300)
T ss_pred HHHHHHHHHH---hCCHHHHHHHhCC---CHHHHHHHHHHHHHHhCCeeEEeC-----CCCceECccHHHHHH
Confidence 5778988984 4589999999999 88999999888864 4588887 577999999987764
No 296
>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=67.06 E-value=7.8 Score=29.16 Aligned_cols=59 Identities=17% Similarity=0.217 Sum_probs=47.1
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.+.+|-.+.+ ..|...-|+++++ ..+.+.|-++.|. ..-+|.+. ++.+.+|+.++.|.+
T Consensus 7 ~l~~f~~v~~---~gS~s~AA~~L~i---sq~avS~~I~~LE~~lg~~LF~R~-----~~~~~lT~~G~~l~~ 68 (300)
T TIGR02424 7 HLQCFVEVAR---QGSVKRAAEALHI---TQPAVSKTLRELEEILGTPLFERD-----RRGIRLTRYGELFLR 68 (300)
T ss_pred HHHHHHHHHH---hCCHHHHHHHhCC---ChHHHHHHHHHHHHHhCCeEEEEc-----CCCccccHhHHHHHH
Confidence 4667777874 4689999999999 8888888888875 45588887 577999999987764
No 297
>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=66.92 E-value=6.4 Score=21.31 Aligned_cols=27 Identities=15% Similarity=0.170 Sum_probs=20.6
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+|..|+|+.+|+ ++..++ .....|++.
T Consensus 1 ~~~~e~a~~~gv---~~~tlr----~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGV---SPSTLR----YYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCc---CHHHHH----HHHHCCCCC
Confidence 478999999999 777555 446777766
No 298
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=66.73 E-value=10 Score=28.35 Aligned_cols=60 Identities=17% Similarity=0.167 Sum_probs=47.3
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
-.|.+|..+.+ .-|...-|+++++ .++.+.|-++.|. ...+|.+. ++.+.+|+.++.|.+
T Consensus 10 ~~l~~f~~v~~---~gs~t~AA~~L~i---tq~avS~~i~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~~ 72 (294)
T PRK09986 10 KLLRYFLAVAE---ELHFGRAAARLNI---SQPPLSIHIKELEDQLGTPLFIRH-----SRSVVLTHAGKILME 72 (294)
T ss_pred HHHHHHHHHHH---hcCHHHHHHHhCC---CCCHHHHHHHHHHHHhCCeeEeeC-----CCceeECHhHHHHHH
Confidence 46778888874 4588999999999 8888888888875 45688887 477999999986653
No 299
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=66.56 E-value=24 Score=21.78 Aligned_cols=56 Identities=16% Similarity=0.255 Sum_probs=32.1
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcc-hHHHHHHHhhcCCceeecccCCCCcceec
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTT-GLFRLMRLLVHSSCFNKTKVNGQEEAYGL 97 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~-~l~RlLr~L~~~gl~~~~~~~~~~~~y~~ 97 (131)
|.+.|.. .+..|++||++++|.+|+..+ .+.++++-=..+.+..+... ++..+|..
T Consensus 15 li~mL~r-p~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i~s~k~~-g~~r~YrI 71 (72)
T PF11994_consen 15 LIAMLRR-PEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTITSEKVD-GGGRRYRI 71 (72)
T ss_pred HHHHHcC-CCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEEEeeecC-CCeeeEee
Confidence 5666764 577999999999999443222 34555544334444444331 11345654
No 300
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=66.36 E-value=8.8 Score=29.53 Aligned_cols=60 Identities=15% Similarity=0.049 Sum_probs=47.8
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
-+|.+|-.+.+ ..|...-|+++++ ..+.+.|-++.|. ..-+|.+. +..+.+|+.++.|..
T Consensus 14 ~~L~~F~~v~e---~gs~s~AA~~L~i---SQpavS~~I~~LE~~lG~~LF~R~-----~~~~~LT~~G~~l~~ 76 (310)
T PRK15092 14 DLLRTFVAVAD---LNTFAAAAAAVCR---TQSAVSQQMQRLEQLVGKELFARH-----GRNKLLTEHGIQLLG 76 (310)
T ss_pred HHHHHHHHHHH---cCCHHHHHHHhCC---ChHHHHHHHHHHHHHhCcceEEEC-----CCCceECHhHHHHHH
Confidence 35677888874 5788999999999 8888888888885 45588887 467899999997754
No 301
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=66.14 E-value=10 Score=28.87 Aligned_cols=31 Identities=10% Similarity=0.185 Sum_probs=26.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
.++|+++||+.+|+ ++..+.|+.+..+...+
T Consensus 20 ~~~~l~~lA~~~~~---S~~~l~r~F~~~~g~s~ 50 (289)
T PRK15121 20 QPLSLDNVAAKAGY---SKWHLQRMFKDVTGHAI 50 (289)
T ss_pred CCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCH
Confidence 68999999999999 99999988877654443
No 302
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=66.12 E-value=10 Score=27.83 Aligned_cols=35 Identities=20% Similarity=0.185 Sum_probs=27.2
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
+--|..|+..++ .+.|..|||+++++ ++..+...+
T Consensus 135 SpRErEVLrLLA---qGkTnKEIAe~L~I---S~rTVkth~ 169 (198)
T PRK15201 135 SVTERHLLKLIA---SGYHLSETAALLSL---SEEQTKSLR 169 (198)
T ss_pred CHHHHHHHHHHH---CCCCHHHHHHHhCC---CHHHHHHHH
Confidence 345677888887 57999999999999 777765444
No 303
>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=66.08 E-value=11 Score=26.18 Aligned_cols=34 Identities=21% Similarity=0.421 Sum_probs=26.1
Q ss_pred hHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 40 IADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 40 ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
|-+.|.+++ ...|+.||++.+|+ ++..+.+++|-
T Consensus 35 V~~yLr~~p~~~ati~eV~e~tgV---s~~~I~~~Ire 69 (137)
T TIGR03826 35 VYKFLRKHENRQATVSEIVEETGV---SEKLILKFIRE 69 (137)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHCc---CHHHHHHHHHc
Confidence 445555433 35899999999999 99988888874
No 304
>PRK00118 putative DNA-binding protein; Validated
Probab=66.05 E-value=6.7 Score=25.93 Aligned_cols=35 Identities=9% Similarity=0.258 Sum_probs=26.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH--------HhhcCCceeec
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR--------LLVHSSCFNKT 86 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr--------~L~~~gl~~~~ 86 (131)
...|..|||+.+|+ ++..+++.++ .+...|+++..
T Consensus 32 eg~S~~EIAe~lGI---S~~TV~r~L~RArkkLr~~~~~~~~~~~~ 74 (104)
T PRK00118 32 DDYSLGEIAEEFNV---SRQAVYDNIKRTEKLLEDYEEKLHLYEKF 74 (104)
T ss_pred cCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHHHHHChHHHH
Confidence 57999999999999 8888776654 34566777654
No 305
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=65.89 E-value=7.8 Score=29.23 Aligned_cols=39 Identities=21% Similarity=0.271 Sum_probs=27.6
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
...++.+.+.|.....-.|+.||++.+|+ ++..|.|-.+
T Consensus 7 ~~~~~~~v~~lr~lk~~~ty~el~~~~g~---p~~~l~RYv~ 45 (238)
T PRK08558 7 VRLQLRAVRVLRSLKKTYTYEELSSITGL---PESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHHHhcccCHHHHHHHHCC---CHHHHHHHHc
Confidence 44566667777544467899999999999 6666665443
No 306
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=65.73 E-value=9.9 Score=27.67 Aligned_cols=35 Identities=9% Similarity=0.060 Sum_probs=27.0
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
+--|..|+..+. .+.|..|||+++++ .+.++..-+
T Consensus 139 T~RE~eVL~lla---~G~snkeIA~~L~i---S~~TVk~h~ 173 (207)
T PRK15411 139 SRTESSMLRMWM---AGQGTIQISDQMNI---KAKTVSSHK 173 (207)
T ss_pred CHHHHHHHHHHH---cCCCHHHHHHHcCC---CHHHHHHHH
Confidence 455677888887 57999999999999 777755433
No 307
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=65.69 E-value=9.2 Score=27.62 Aligned_cols=24 Identities=25% Similarity=0.452 Sum_probs=21.6
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
...|+.+||+.+|+ +...++|++.
T Consensus 171 ~g~s~~~iak~lgi---s~~Tv~r~~k 194 (200)
T PRK13413 171 KGTSKSEIARKLGV---SRTTLARFLK 194 (200)
T ss_pred CCCCHHHHHHHHCC---CHHHHHHHHH
Confidence 35899999999999 9999999886
No 308
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=65.20 E-value=6.9 Score=29.32 Aligned_cols=59 Identities=12% Similarity=0.179 Sum_probs=47.3
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.|.+|..+.+ .-|.+.-|+++++ .++.+.|-+..|.. .-+|.+. +..+.+|+.++.|..
T Consensus 5 ~L~~f~~v~~---~gs~s~AA~~L~i---tqpavS~~Ik~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~~ 66 (291)
T TIGR03418 5 ALRVFESAAR---LASFTAAARELGS---TQPAVSQQVKRLEEELGTPLFERG-----HRGIELTEDGQRLFE 66 (291)
T ss_pred HHHHHHHHHH---hCCHHHHHHHhCC---CHHHHHHHHHHHHHHhCcHHhhcC-----CCceeEcHhHHHHHH
Confidence 5678888884 4589999999999 88888888888753 4588876 577999999997764
No 309
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=64.91 E-value=18 Score=25.09 Aligned_cols=65 Identities=20% Similarity=0.226 Sum_probs=44.4
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcC---C--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALD---I--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~---~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L 104 (131)
.+=|..+|.+ + .+--+|.+.+. . -+.++..+|.+|+-|...|++...........|..|+.++..
T Consensus 45 ~l~IL~lL~~--~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~ 114 (135)
T PRK09416 45 LLAILQLLMN--E-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKM 114 (135)
T ss_pred HHHHHHHHhC--C-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHH
Confidence 3446666663 4 78888877643 1 122778999999999999999864311113569999999843
No 310
>PRK10632 transcriptional regulator; Provisional
Probab=64.72 E-value=11 Score=28.83 Aligned_cols=59 Identities=12% Similarity=0.228 Sum_probs=47.4
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
+|.+|-.+. +..|...-|+++++ ..+.+.|-++.|. ..-+|.+. +..+.+|+.++.|..
T Consensus 6 ~L~~F~~v~---e~gS~t~AA~~L~i---sQpavS~~I~~LE~~lg~~Lf~R~-----~r~i~lT~~G~~l~~ 67 (309)
T PRK10632 6 RMSVFAKVV---EFGSFTAAARQLQM---SVSSISQTVSKLEDELQVKLLNRS-----TRSIGLTEAGRIYYQ 67 (309)
T ss_pred HHHHHHHHH---hcCCHHHHHHHhCC---CHHHHHHHHHHHHHHhCCeeeccc-----CCCceechhHHHHHH
Confidence 467888887 36789999999999 8888888888875 45588877 577999999987754
No 311
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=64.66 E-value=11 Score=28.09 Aligned_cols=59 Identities=15% Similarity=0.220 Sum_probs=47.1
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
+|.+|..+.+ .-|.+.-|+++++ ..+.+.|-+..|.. .-+|.+. +..+.+|+.++.|.+
T Consensus 5 ~L~~f~~v~~---~gs~s~AA~~L~i---sqsavS~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~ 66 (296)
T PRK11242 5 HIRYFLAVAE---HGNFTRAAEALHV---SQPTLSQQIRQLEESLGVQLFDRS-----GRTVRLTDAGEVYLR 66 (296)
T ss_pred HHHHHHHHHH---hCCHHHHHHHcCC---CchHHHHHHHHHHHHhCCeeEeEc-----CCceeechhHHHHHH
Confidence 5678888884 4589999999999 88888888887753 5688887 577999999987754
No 312
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=64.62 E-value=12 Score=28.50 Aligned_cols=62 Identities=19% Similarity=0.233 Sum_probs=46.8
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhccccccC
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
+|..|-.+.+ ...|.+.-|+++++ .++.+.|-++.|. ..-+|.+.. .+.+.+|+.++.|.+.
T Consensus 5 ~L~~F~~v~~--~~~s~s~AA~~L~i---sq~avSr~I~~LE~~lg~~LF~R~~----~~~~~lT~~G~~l~~~ 69 (309)
T PRK12682 5 QLRFVREAVR--RNLNLTEAAKALHT---SQPGVSKAIIELEEELGIEIFIRHG----KRLKGLTEPGKAVLDV 69 (309)
T ss_pred HHHHHHHHHH--ccCCHHHHHHHhcC---ccHHHHHHHHHHHHHhCCeeEEECC----CCcCccCHhHHHHHHH
Confidence 4667777774 34689999999999 8888888888885 455888764 3334899999977654
No 313
>PHA00542 putative Cro-like protein
Probab=64.57 E-value=10 Score=23.59 Aligned_cols=24 Identities=13% Similarity=0.285 Sum_probs=20.4
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
..+|..++|+.+|+ +...+.|+.+
T Consensus 30 ~glTq~elA~~lgI---s~~tIsr~e~ 53 (82)
T PHA00542 30 AGWSQEQIADATDV---SQPTICRIYS 53 (82)
T ss_pred CCCCHHHHHHHHCc---CHHHHHHHHc
Confidence 56999999999999 7787877765
No 314
>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=64.14 E-value=11 Score=27.60 Aligned_cols=41 Identities=5% Similarity=0.050 Sum_probs=35.4
Q ss_pred CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 52 TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 52 s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
|-.|||++.|+ +...+++=|+.|...|++.+.. |.|+|-..
T Consensus 27 sE~eLa~~~~V---sr~Tvr~Al~~L~~eGli~~~~---g~Gt~V~~ 67 (231)
T TIGR03337 27 SERDLGERFNT---TRVTIREALQQLEAEGLIYRED---RRGWFVSP 67 (231)
T ss_pred CHHHHHHHHCC---CHHHHHHHHHHHHHCCeEEEeC---CCEEEECC
Confidence 78899999999 8899999999999999999875 25677543
No 315
>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=64.07 E-value=20 Score=22.28 Aligned_cols=53 Identities=13% Similarity=0.098 Sum_probs=39.1
Q ss_pred HHHHHHHHHhChHHHHH-hCCCCCCHHHHHhhcC-CCCCCcchHHHHHHHhhcCCcee
Q 040869 29 SMSLKCAIELGIADIIH-SHGRAITLSELVSALD-IQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 29 ~~aL~~a~~L~ifd~l~-~~~~~~s~~eLA~~~~-~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
....+..++=.|+.... +..+.+|.++.-+.+. . |...+.|+..+|...|++.
T Consensus 31 ~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~---d~~~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 31 TPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGI---DVNKIRRIYDFLERWGLIN 85 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSS---SHHHHHHHHHHHHHTTSSS
T ss_pred ChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHcccc---CHHHHHHHHHHHHHcCccC
Confidence 34466677777777642 2357899999988888 8 9999999999999999874
No 316
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=64.05 E-value=11 Score=27.99 Aligned_cols=40 Identities=18% Similarity=0.309 Sum_probs=30.5
Q ss_pred ChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869 39 GIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSS 81 (131)
Q Consensus 39 ~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g 81 (131)
.+++.|...+ .-+|..|||+++|+ ++..++|=+-++-..|
T Consensus 20 R~le~l~a~~v~rvsS~els~~~~v---dsatIRrDfSYFG~lG 60 (211)
T COG2344 20 RVLERLHASGVERVSSKELSEALGV---DSATIRRDFSYFGELG 60 (211)
T ss_pred HHHHHHHHcCCceecHHHHHHHhCC---CHHHHhhhhHHHHhcC
Confidence 4567776545 56999999999999 9999988776654444
No 317
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=63.79 E-value=12 Score=28.42 Aligned_cols=59 Identities=20% Similarity=0.256 Sum_probs=47.2
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
-.|++|..+.+ .-|...-|+++++ .++.+.|-++.|.. .-+|.+. +..+.+|+.++.|.
T Consensus 8 ~~L~~f~~v~e---~gs~s~AA~~L~i---sqpavS~~i~~LE~~lg~~Lf~R~-----~r~~~lT~~G~~l~ 69 (305)
T CHL00180 8 DQLRILKAIAT---EGSFKKAAESLYI---SQPAVSLQIKNLEKQLNIPLFDRS-----KNKASLTEAGELLL 69 (305)
T ss_pred HHHHHHHHHHH---cCCHHHHHHHhcC---CChHHHHHHHHHHHHhCCEEEEec-----CCCceECHhHHHHH
Confidence 35778888884 4589999999999 88889988888853 4588877 46799999998774
No 318
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=63.76 E-value=9.8 Score=22.91 Aligned_cols=33 Identities=15% Similarity=0.346 Sum_probs=20.6
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcc-hHHHHHH
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTT-GLFRLMR 75 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~-~l~RlLr 75 (131)
+.+.|.+.+.|+|++||...+.+ +.. .+..+|+
T Consensus 10 ~VeymK~r~~Plt~~eI~d~l~~---d~~~~~~~~Lk 43 (65)
T PF02186_consen 10 AVEYMKKRDHPLTLEEILDYLSL---DIGKKLKQWLK 43 (65)
T ss_dssp HHHHHHHH-S-B-HHHHHHHHTS---SS-HHHHHHHH
T ss_pred HHHHHHhcCCCcCHHHHHHHHcC---CCCHHHHHHHH
Confidence 45667665799999999999998 544 3444444
No 319
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=63.62 E-value=10 Score=28.84 Aligned_cols=61 Identities=15% Similarity=0.142 Sum_probs=49.1
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccccC
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
-+|++|-.+.+ ..|...-|+++++ ..+.+.|-++.|.. .-+|.+. ++.+.+|+.++.|.+.
T Consensus 7 ~~L~~f~av~~---~gS~s~AAe~L~i---sqsavS~~Ik~LE~~lg~~Lf~R~-----~~~v~LT~~G~~l~~~ 70 (309)
T PRK11013 7 RHIEIFHAVMT---AGSLTEAARLLHT---SQPTVSRELARFEKVIGLKLFERV-----RGRLHPTVQGLRLFEE 70 (309)
T ss_pred HHHHHHHHHHH---hCcHHHHHHHHCC---CcHHHHHHHHHHHHHhCceeeeec-----CCCcccCHHHHHHHHH
Confidence 45778888884 4589999999999 88899998888864 4588877 4679999999977653
No 320
>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=63.59 E-value=9.2 Score=22.09 Aligned_cols=25 Identities=28% Similarity=0.336 Sum_probs=21.1
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
-++..|.|+++|+ ....|.|+.|.+
T Consensus 15 hlp~~eAA~~Lgv---~~T~LKr~CR~~ 39 (52)
T PF02042_consen 15 HLPIKEAAKELGV---SVTTLKRRCRRL 39 (52)
T ss_pred CCCHHHHHHHhCC---CHHHHHHHHHHc
Confidence 3778999999999 889999988843
No 321
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=63.49 E-value=5.3 Score=25.39 Aligned_cols=28 Identities=18% Similarity=0.102 Sum_probs=19.7
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHS 80 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~ 80 (131)
+.|-.|||+++|- ++..+.+.|+.+..-
T Consensus 3 G~tq~eIA~~lGk---s~s~Vs~~l~Ll~lP 30 (93)
T PF08535_consen 3 GWTQEEIAKRLGK---SRSWVSNHLALLDLP 30 (93)
T ss_dssp T--HHHHHHHTT-----HHHHHHHHGGGS--
T ss_pred CCCHHHHHHHHCC---CHHHHHHHHHHHcCC
Confidence 5789999999999 999999999877533
No 322
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=63.35 E-value=11 Score=28.77 Aligned_cols=61 Identities=10% Similarity=0.113 Sum_probs=48.4
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccccC
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
-+|.+|..+.+ .-|...-|+++++ ..+.+-|-++.|.. .-+|.+. ++.+.+|+.++.|...
T Consensus 17 ~~L~~f~~va~---~gs~s~AA~~L~i---SQpavS~~I~~LE~~lG~~LF~R~-----~r~~~LT~~G~~l~~~ 80 (311)
T PRK10086 17 SKLHTFEVAAR---HQSFALAADELSL---TPSAVSHRINQLEEELGIKLFVRS-----HRKVELTEEGKRVFWA 80 (311)
T ss_pred HHHHHHHHHHH---cCCHHHHHHHHCC---CHHHHHHHHHHHHHHhCCeeEEEc-----CCCcccCHhHHHHHHH
Confidence 34667777874 5688999999999 88899988888864 4588887 5789999999877643
No 323
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=62.84 E-value=16 Score=29.38 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=36.3
Q ss_pred CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869 48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL 97 (131)
Q Consensus 48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~ 97 (131)
|..+ |..+||+++|+ +...+.+-++.|.+.|++..... .|.|-.
T Consensus 26 g~~lps~r~la~~~~v---sr~tv~~a~~~L~~~g~i~~~~~---~G~~v~ 70 (431)
T PRK15481 26 GDSLPPVRELASELGV---NRNTVAAAYKRLVTAGLAQSQGR---NGTVIR 70 (431)
T ss_pred CCcCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeCC---CceEEc
Confidence 4456 88999999999 99999999999999999986641 465554
No 324
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=62.66 E-value=4.4 Score=32.01 Aligned_cols=36 Identities=8% Similarity=0.273 Sum_probs=33.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.-+.+++.|.++|+ ..+.+|-|...|.+.|++.+..
T Consensus 43 dlvgLddaA~KlgV---ErRRIYDiVNvlEsig~var~~ 78 (388)
T KOG2578|consen 43 DLVGLDDAARKLGV---ERRRIYDIVNVLESIGAVARRG 78 (388)
T ss_pred ceechhhHHHhcCc---hHHHHHHHHHHHHHHHHHHhcc
Confidence 45889999999999 9999999999999999999875
No 325
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=62.36 E-value=11 Score=26.21 Aligned_cols=43 Identities=26% Similarity=0.352 Sum_probs=33.1
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
...+|.+.++.+.++..|+|+.+++ -+..|.++|| ..|++-..
T Consensus 35 v~f~D~v~~~~gli~~re~AK~lki---ge~~l~~~L~---e~~~l~~~ 77 (135)
T COG3645 35 VEFADAVVEASGLILFRELAKLLKI---GENRLFAWLR---ENKYLIKR 77 (135)
T ss_pred hHHHHHHhcCccceeHHHHHHHHcc---CHHHHHHHHH---HCCEEEEc
Confidence 4568888877788999999999999 7666666555 66776655
No 326
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=62.31 E-value=11 Score=22.71 Aligned_cols=38 Identities=13% Similarity=0.265 Sum_probs=30.3
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSS 81 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g 81 (131)
|.+.|.. .+++|+.||++.+++ +...+..-+--|+..+
T Consensus 13 Vw~~L~~-~~~~s~~el~k~~~l---~~~~~~~AiGWLarE~ 50 (65)
T PF10771_consen 13 VWQLLNE-NGEWSVSELKKATGL---SDKEVYLAIGWLAREN 50 (65)
T ss_dssp HHHHHCC-SSSEEHHHHHHHCT----SCHHHHHHHHHHHCTT
T ss_pred HHHHHhh-CCCcCHHHHHHHhCc---CHHHHHHHHHHHhccC
Confidence 7788874 479999999999999 7787877777777665
No 327
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=61.83 E-value=8.6 Score=23.11 Aligned_cols=54 Identities=19% Similarity=0.367 Sum_probs=29.4
Q ss_pred HHHHHhCCCCCCHHHHHhhcC---C-CC--CCc-chHH-HHHHHhh-cCCceeecccCCCCcceecc
Q 040869 41 ADIIHSHGRAITLSELVSALD---I-QP--TKT-TGLF-RLMRLLV-HSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 41 fd~l~~~~~~~s~~eLA~~~~---~-~~--~~~-~~l~-RlLr~L~-~~gl~~~~~~~~~~~~y~~t 98 (131)
.++|.+.++|+|+.||.++.. . +. .+| ..+. +|-+.+. .-+.|...+ +++|++-
T Consensus 8 ~~vL~~~~~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg----~~~~~L~ 70 (72)
T PF05066_consen 8 YEVLEEAGRPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIKNEDSRFVKVG----PGRWGLR 70 (72)
T ss_dssp HHHHHHH-S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH-T-SS-EESS----SSEEE-G
T ss_pred HHHHHhcCCCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcccCCCCEEEeC----CCcEEee
Confidence 456666678999999988753 2 11 122 3444 5555555 667777775 6777653
No 328
>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=61.72 E-value=19 Score=22.37 Aligned_cols=52 Identities=17% Similarity=0.186 Sum_probs=39.4
Q ss_pred HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
.+...+....+-.+...-..++.++||+.+++ +...+..++.-+...|.+.-
T Consensus 41 ~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~---~~~~vE~~l~~~I~~~~i~~ 92 (105)
T PF01399_consen 41 QLKEKIRRRNLRQLSKPYSSISISEIAKALQL---SEEEVESILIDLISNGLIKA 92 (105)
T ss_dssp HHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSSEE
T ss_pred HHHHHHHHHHHHHHHHHhcccchHHHHHHhcc---chHHHHHHHHHHHHCCCEEE
Confidence 34444444444445443478999999999999 99999999999999998874
No 329
>PRK09492 treR trehalose repressor; Provisional
Probab=61.66 E-value=2.7 Score=31.80 Aligned_cols=23 Identities=9% Similarity=0.307 Sum_probs=19.3
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
..|..|||++.|+ +..++.|+|+
T Consensus 4 ~~ti~dIA~~agV---S~~TVSrvLn 26 (315)
T PRK09492 4 KLTIKDIARLSGV---GKSTVSRVLN 26 (315)
T ss_pred CCcHHHHHHHhCC---CHHHHhHHhC
Confidence 4799999999999 7777777776
No 330
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=61.62 E-value=14 Score=28.22 Aligned_cols=61 Identities=21% Similarity=0.270 Sum_probs=46.2
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
++.+|-.+.+ ...|...-|+++++ .++.+.|-++.|. ..-+|.+.. .+...+|+.++.|..
T Consensus 5 ~l~~f~~v~~--~~~s~s~AA~~L~i---SQ~avSr~I~~LE~~lg~~LF~R~~----~~~~~lT~~G~~l~~ 68 (316)
T PRK12679 5 QLKIIREAAR--QDYNLTEVANMLFT---SQSGVSRHIRELEDELGIEIFIRRG----KRLLGMTEPGKALLV 68 (316)
T ss_pred HHHHHHHHHH--cCCCHHHHHHHhcC---CchHHHHHHHHHHHHhCCEEEEECC----CcccccCHhHHHHHH
Confidence 5677888874 34689999999999 8888888888775 455888764 333689999997754
No 331
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=61.35 E-value=14 Score=31.19 Aligned_cols=36 Identities=22% Similarity=0.357 Sum_probs=30.0
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
+..|++.|. .+++|.++||+.+|+ +.++++|=+..+
T Consensus 6 ~~~iL~~L~--~~~~t~~~LA~~l~V---S~RTIr~dI~~i 41 (584)
T PRK09863 6 ELKIVDLLE--QQDRSGGELAQQLGV---SRRTIVRDIAYI 41 (584)
T ss_pred HHHHHHHHH--cCCCCHHHHHHHhCC---CHHHHHHHHHHH
Confidence 456777775 378999999999999 999999888755
No 332
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.22 E-value=14 Score=23.95 Aligned_cols=39 Identities=21% Similarity=0.253 Sum_probs=32.6
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
.|-++.|...|. .+.|+.+|...+|+ +...+.|+-|.|-
T Consensus 43 laqRlqVa~mL~---eg~tY~~I~~eTGa---StaTIsRVkRcl~ 81 (100)
T COG4496 43 LAQRLQVAKMLK---EGRTYRDIEDETGA---STATISRVKRCLN 81 (100)
T ss_pred HHHHHHHHHHHH---cCCCcchhhhccCc---chhhHHHHHHHHH
Confidence 355688888887 46899999999999 8899999988774
No 333
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=61.22 E-value=8 Score=28.67 Aligned_cols=43 Identities=19% Similarity=0.197 Sum_probs=34.1
Q ss_pred ChHHHH-HhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 39 GIADII-HSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 39 ~ifd~l-~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
.|.+.+ ....+++|+.+|++.+|+ ++....-.|..+...|++-
T Consensus 178 ~il~~~~~~~~g~vt~~~l~~~~~w---s~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 178 RILELAEEENGGGVTASELAEKLGW---SVERAKEALEELEREGLLW 221 (223)
T ss_dssp HHHHHH--TTTSEEEHHHHHHHHTB----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHhhcCCCCCHHHHHHHhCC---CHHHHHHHHHHHHhCCCEe
Confidence 445555 334689999999999999 9999999999999999874
No 334
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=61.08 E-value=15 Score=27.73 Aligned_cols=42 Identities=14% Similarity=0.245 Sum_probs=32.6
Q ss_pred hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+.+.|..+ .+++|+++||+++|+ ++..+.|+.+--+...+.+
T Consensus 188 ~~~~i~~~~~~~isl~~lA~~~~l---S~~~l~r~Fk~~~G~tp~~ 230 (290)
T PRK10572 188 ACQYISDHLASEFDIESVAQHVCL---SPSRLAHLFRQQLGISVLR 230 (290)
T ss_pred HHHHHHhcccCCCCHHHHHHHHCC---CHHHHHHHHHHHHCcCHHH
Confidence 44555432 378999999999999 9999999998877666544
No 335
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=60.82 E-value=15 Score=27.80 Aligned_cols=60 Identities=13% Similarity=0.122 Sum_probs=47.1
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
-.+.+|-.+.+ .-|...-|+++++ ..+.+.|-++.|.. .-+|.+. +..+.+|+.++.|..
T Consensus 14 ~~l~~F~av~e---~gS~t~AA~~L~i---SQpavS~~I~~LE~~lG~~Lf~R~-----~r~~~lT~~G~~l~~ 76 (303)
T PRK10082 14 KWLYDFLTLEK---CRNFSQAAVSRNV---SQPAFSRRIRALEQAIGVELFNRQ-----VTPLQLSEQGKIFHS 76 (303)
T ss_pred HHHHHHHHHHh---cCCHHHHHHHhCC---ChHHHHHHHHHHHHHcCCEEEEec-----CCCCccCHHHHHHHH
Confidence 35667777873 5689999999999 88889998888864 4478877 467999999986654
No 336
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=60.72 E-value=14 Score=27.77 Aligned_cols=61 Identities=11% Similarity=0.136 Sum_probs=48.0
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccccC
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
-.+.+|..+.+ .-|...-|+++++ .++.+.|-++.|.. .-+|.+. +..+.+|+.++.|...
T Consensus 9 ~~l~~f~~v~~---~gs~s~AA~~L~i---sq~avS~~i~~LE~~lg~~Lf~R~-----~r~l~lT~~G~~l~~~ 72 (297)
T PRK11139 9 NALRAFEAAAR---HLSFTRAAEELFV---TQAAVSHQIKALEDFLGLKLFRRR-----NRSLLLTEEGQRYFLD 72 (297)
T ss_pred HHHHHHHHHHH---hCCHHHHHHHhCC---ChHHHHHHHHHHHHHhCchheEec-----CCceeECHhHHHHHHH
Confidence 35677888874 4689999999999 88888888888854 4588877 5779999999877643
No 337
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=60.49 E-value=8.6 Score=29.22 Aligned_cols=46 Identities=15% Similarity=0.267 Sum_probs=40.9
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
+-+|..|.|+..++ ++..++.++--|...|.+.+-. .|+|.--|+-
T Consensus 29 kiiTirdvae~~ev---~~n~lr~lasrLekkG~LeRi~----rG~YlI~~lp 74 (269)
T COG5340 29 KIITIRDVAETLEV---APNTLRELASRLEKKGWLERIL----RGRYLIIPLP 74 (269)
T ss_pred ceEEeHHhhhhccC---CHHHHHHHHhhhhhcchhhhhc----CccEEEeecC
Confidence 67999999999999 9999999999999999999987 7888877653
No 338
>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=60.48 E-value=9 Score=21.21 Aligned_cols=24 Identities=8% Similarity=0.041 Sum_probs=19.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
..+|..++|+++|+ ++..+.++.+
T Consensus 14 ~gltq~~lA~~~gv---s~~~vs~~e~ 37 (58)
T TIGR03070 14 LGLTQADLADLAGV---GLRFIRDVEN 37 (58)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHHC
Confidence 56899999999999 7777776653
No 339
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=60.33 E-value=12 Score=31.11 Aligned_cols=45 Identities=22% Similarity=0.285 Sum_probs=38.7
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.++..+.+ .+++|..+|+..+++ +...+.|.+..|+..|++....
T Consensus 406 ~il~~~~e-n~~~T~~~L~~~l~i---s~~~i~r~i~~Lv~~g~~~~~g 450 (467)
T COG2865 406 KILELIKE-NGKVTARELREILGI---SSETIRRRIANLVKRGLLKQLG 450 (467)
T ss_pred HHHHHHhh-ccccCHHHHHHHhCc---chhhHHHHHHHHhcccHHHHhC
Confidence 35555654 468999999999999 9999999999999999999864
No 340
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=60.11 E-value=13 Score=30.25 Aligned_cols=51 Identities=14% Similarity=0.201 Sum_probs=42.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
.++..+++.++.|. +.......++.+...|++..+ ++++.+|+.++.+.+.
T Consensus 360 ~gl~~~~~~~~~g~---~~~~~~~~l~~l~~~gll~~~-----~~~l~lT~~G~~~~d~ 410 (430)
T PRK08208 360 QGLDLADYRQRFGS---DPLRDFPELELLIDRGWLEQN-----GGRLRLTEEGLALSDA 410 (430)
T ss_pred CCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEE-----CCEEEECcchhhHHHH
Confidence 56888999999998 766677889999999999987 5889999998877643
No 341
>PRK13503 transcriptional activator RhaS; Provisional
Probab=60.06 E-value=15 Score=27.32 Aligned_cols=42 Identities=10% Similarity=0.179 Sum_probs=31.4
Q ss_pred hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+.+.|.+. ..++|+++||+.+++ ++..+.|+.+......+.+
T Consensus 176 ~~~~I~~~~~~~~tl~~lA~~~~l---S~~~l~r~Fk~~~G~S~~~ 218 (278)
T PRK13503 176 LLAWLEDHFAEEVNWEALADQFSL---SLRTLHRQLKQQTGLTPQR 218 (278)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCC---CHHHHHHHHHHHhCcCHHH
Confidence 44455433 268999999999999 9999999987766555444
No 342
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=60.00 E-value=25 Score=25.60 Aligned_cols=57 Identities=18% Similarity=0.209 Sum_probs=41.7
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCC---CCcceecchh
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNG---QEEAYGLTAA 100 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~---~~~~y~~t~~ 100 (131)
.+.+.-+|+ -..|+|-.||-+--|+ +. .++++.|...|++.+.+..+ .+-.|..|+.
T Consensus 94 alEtLAiIA-Y~QPiTR~eI~~iRGv---~~---~~~i~~L~e~glI~~~g~~~~~Grp~ly~tT~~ 153 (184)
T COG1386 94 ALETLAIIA-YKQPVTRSEIEEIRGV---AV---SQVISTLLERGLIREVGRRDTPGRPYLYGTTEK 153 (184)
T ss_pred HHHHHHHHH-HcCCccHHHHHHHhCc---cH---HHHHHHHHHCCCeEecCCCCCCCCceeeeccHH
Confidence 345666676 2479999999999888 44 45999999999999875321 1345777774
No 343
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=59.97 E-value=22 Score=25.05 Aligned_cols=46 Identities=13% Similarity=0.279 Sum_probs=39.3
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcC--CCCCCcchHHHHHHHhhcCCceeecc
Q 040869 39 GIADIIHSHGRAITLSELVSALD--IQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~--~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
-|++.|....+|.|+.+|..-++ + ....+.+.|..|+..|-+....
T Consensus 5 ~Il~y~~~qNRPys~~di~~nL~~~~---~K~~v~k~Ld~L~~~g~i~~K~ 52 (169)
T PF07106_consen 5 AILEYMKEQNRPYSAQDIFDNLHNKV---GKTAVQKALDSLVEEGKIVEKE 52 (169)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHhhc---cHHHHHHHHHHHHhCCCeeeee
Confidence 47788876679999999999884 6 7788999999999999888764
No 344
>PRK15340 transcriptional regulator InvF; Provisional
Probab=59.97 E-value=30 Score=25.81 Aligned_cols=43 Identities=12% Similarity=0.050 Sum_probs=33.6
Q ss_pred ChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 39 GIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 39 ~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+|...|-.. ....++++||+.+|+ +++.+.|+.+..+...+-.
T Consensus 113 ~l~~~Ll~~~~~~~sleeLA~~~gv---S~r~f~RlFk~~~G~tpk~ 156 (216)
T PRK15340 113 WLVGYLLAQSTSGNTMRMLGEDYGV---SYTHFRRLCSRALGGKAKS 156 (216)
T ss_pred HHHHHHHhCccCCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHH
Confidence 455555432 378999999999999 9999999999887777543
No 345
>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=59.89 E-value=14 Score=24.57 Aligned_cols=33 Identities=21% Similarity=0.349 Sum_probs=24.8
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
..-+|..|||+.+|+ +...+.+.|. .+|+-.+.
T Consensus 69 ~pd~tl~Ela~~l~V---s~~ti~~~Lk---rlg~t~KK 101 (119)
T PF01710_consen 69 NPDATLRELAERLGV---SPSTIWRALK---RLGITRKK 101 (119)
T ss_pred CCCcCHHHHHHHcCC---CHHHHHHHHH---HcCchhcc
Confidence 356999999999999 8887776554 45665544
No 346
>PRK05660 HemN family oxidoreductase; Provisional
Probab=59.72 E-value=13 Score=29.74 Aligned_cols=50 Identities=8% Similarity=0.164 Sum_probs=41.4
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.++...++.++.|. +.......++.|...|++..+ ++++.+|+.++.+.+
T Consensus 320 ~G~~~~~~~~~~g~---~~~~~~~~l~~l~~~gl~~~~-----~~~~~lt~~G~~~~d 369 (378)
T PRK05660 320 EAAPRADFEAYTGL---PESVIRPQLDEALAQGYLTET-----ADHWQITEHGKLFLN 369 (378)
T ss_pred cCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEe-----CCEEEECcchhHHHH
Confidence 46788899999998 666667788999999999976 578999999887764
No 347
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=59.54 E-value=14 Score=27.87 Aligned_cols=60 Identities=15% Similarity=0.138 Sum_probs=47.4
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhccccccC
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
.|.+|-.+.+ .-|...-|+++++ .++.+.|-++.|. ..-+|.+. +..+.+|+.++.|...
T Consensus 5 ~L~~f~~v~~---~gS~s~AA~~L~i---tQpavS~~i~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~~~ 67 (305)
T PRK11151 5 DLEYLVALAE---HRHFRRAADSCHV---SQPTLSGQIRKLEDELGVMLLERT-----SRKVLFTQAGLLLVDQ 67 (305)
T ss_pred HHHHHHHHHH---hCCHHHHHHHhCC---CchHHHHHHHHHHHHhCchheeeC-----CCceeECccHHHHHHH
Confidence 4677888874 3589999999999 8888888888775 45588886 5789999999877643
No 348
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=59.34 E-value=17 Score=25.22 Aligned_cols=29 Identities=17% Similarity=0.492 Sum_probs=21.2
Q ss_pred hHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHH
Q 040869 40 IADIIHSHG-RAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 40 ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
.++.+.+.+ ..+|+.||+++.|+ +..+.|
T Consensus 12 ~~~Ll~~k~~~~ITV~~I~~~Agv---sR~TFY 41 (176)
T TIGR02366 12 FKDLMEVQAFSKISVSDIMSTAQI---RRQTFY 41 (176)
T ss_pred HHHHHHHCCCccCCHHHHHHHhCC---CHHHHH
Confidence 345565544 67999999999999 655544
No 349
>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=59.30 E-value=3.1 Score=31.60 Aligned_cols=22 Identities=9% Similarity=0.341 Sum_probs=18.7
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
.|..|||+..|+ +..++.|.|+
T Consensus 2 ~ti~dIA~~agV---S~sTVSr~Ln 23 (311)
T TIGR02405 2 LTIKDIARLAGV---GKSTVSRVLN 23 (311)
T ss_pred CcHHHHHHHhCC---CHHHHHHHhC
Confidence 588999999999 8888888885
No 350
>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=59.28 E-value=7.3 Score=21.92 Aligned_cols=22 Identities=18% Similarity=0.596 Sum_probs=18.7
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
++..|+++.+|+ +...++|+++
T Consensus 4 l~~~ev~~~~g~---s~~ti~~~~k 25 (51)
T PF05930_consen 4 LRIKEVAELLGV---SRSTIYRLIK 25 (51)
T ss_dssp E-HHHHHHHHSS----HHHHHHHHH
T ss_pred ccHHHHHHHHCC---CHHHHHHHHh
Confidence 578999999999 9999999998
No 351
>PRK00441 argR arginine repressor; Provisional
Probab=59.27 E-value=17 Score=25.42 Aligned_cols=52 Identities=23% Similarity=0.257 Sum_probs=35.6
Q ss_pred ChHHHHHhCCCCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 39 GIADIIHSHGRAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
.|.+.|.+ .+..|..||++.+ ++ ....++|-|+.|....+-..++ .-+|+..
T Consensus 8 ~I~~ll~~-~~~~~q~eL~~~L~~~G~~v---SqaTisRDl~~L~lvKv~~~~G----~~~Y~l~ 64 (149)
T PRK00441 8 KILEIINS-KEIETQEELAEELKKMGFDV---TQATVSRDIKELKLIKVLSNDG----KYKYATI 64 (149)
T ss_pred HHHHHHHH-cCCCcHHHHHHHHHhcCCCc---CHHHHHHHHHHcCcEEeECCCC----CEEEEeC
Confidence 35677765 4688999999997 77 7888998888765444333332 4467763
No 352
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=58.88 E-value=14 Score=28.41 Aligned_cols=60 Identities=13% Similarity=0.170 Sum_probs=47.6
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
-+|.+|..+.+ .-|...-|+++++ ....+.+-++.|. ...+|.+. +....+|+.++.|..
T Consensus 5 ~~L~~f~av~~---~gs~s~AA~~L~i---SqpaVS~~Ik~LE~~lg~~LF~R~-----~r~v~lT~~G~~l~~ 67 (317)
T PRK15421 5 KHLKTLQALRN---CGSLAAAAATLHQ---TQSALSHQFSDLEQRLGFRLFVRK-----SQPLRFTPQGEILLQ 67 (317)
T ss_pred HHHHHHHHHHH---cCCHHHHHHHhCC---CHHHHHHHHHHHHHHhCCEEEEec-----CCCceECHhHHHHHH
Confidence 35778888885 3489999999999 8888888888885 35588887 466899999987764
No 353
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=58.52 E-value=16 Score=26.75 Aligned_cols=41 Identities=20% Similarity=0.272 Sum_probs=32.2
Q ss_pred HHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 41 ADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 41 fd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
...|..+..+.+.++||..+|. ++..++|+...-..+...+
T Consensus 88 ~~~ie~~~~~~~le~la~~lg~---sp~~~~R~FK~~~G~Tp~~ 128 (187)
T COG2169 88 CRLIEQNPEKRWLEELADELGV---SPSTLHRLFKAITGMTPKE 128 (187)
T ss_pred HHHHHcCCCcccHHHHHHHhCC---ChHHHHHHHHHHhCCCHHH
Confidence 3445555688999999999999 9999999988766555444
No 354
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=58.40 E-value=16 Score=26.15 Aligned_cols=48 Identities=15% Similarity=0.216 Sum_probs=38.1
Q ss_pred HHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 43 IIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 43 ~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
.|......+|+.|+|.+.|+ +...-+.-|..|-+.|-+++. ..+|++.
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~ 164 (166)
T PRK15466 117 LLTSVRQGMTAGEVAAHFGW---PLEKARNALEQLFSAGTLRKR-----SSRYRLK 164 (166)
T ss_pred HHHHHHccccHHHHHHHhCC---cHHHHHHHHHHHHhccchhhc-----ccccccc
Confidence 34433468999999999999 888888888888889988876 4677764
No 355
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=58.30 E-value=3.3 Score=29.49 Aligned_cols=24 Identities=13% Similarity=0.444 Sum_probs=0.0
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
.|+|..|||..+|+ +++++.|.++
T Consensus 48 ~PLt~~~iA~~lgl---~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADELGL---HESTVSRAVK 71 (160)
T ss_dssp ---------------------------
T ss_pred cCCCHHHHHHHhCC---CHhHHHHHHc
Confidence 69999999999999 9999999876
No 356
>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=58.07 E-value=10 Score=22.20 Aligned_cols=24 Identities=8% Similarity=0.313 Sum_probs=19.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
.+.++.|||+.+|+ ++..++.-.+
T Consensus 12 ~G~~~~eIA~~Lg~---~~~TV~~W~~ 35 (58)
T PF06056_consen 12 QGWSIKEIAEELGV---PRSTVYSWKD 35 (58)
T ss_pred cCCCHHHHHHHHCC---ChHHHHHHHH
Confidence 46899999999999 8777776543
No 357
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=58.00 E-value=14 Score=26.38 Aligned_cols=26 Identities=15% Similarity=0.383 Sum_probs=19.8
Q ss_pred HHhCC-CCCCHHHHHhhcCCCCCCcchHHH
Q 040869 44 IHSHG-RAITLSELVSALDIQPTKTTGLFR 72 (131)
Q Consensus 44 l~~~~-~~~s~~eLA~~~~~~~~~~~~l~R 72 (131)
+.+.| ..+|.++||+++|+ ++..+|+
T Consensus 24 f~~~G~~~~ti~~Ia~~agv---sk~t~Y~ 50 (213)
T PRK09975 24 FALRGVSNTTLNDIADAANV---TRGAIYW 50 (213)
T ss_pred HHHcCcccCCHHHHHHHcCC---CHHHHHH
Confidence 44334 57999999999999 7777664
No 358
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=57.70 E-value=12 Score=26.40 Aligned_cols=27 Identities=15% Similarity=0.318 Sum_probs=20.1
Q ss_pred HHHhCC-CCCCHHHHHhhcCCCCCCcchHHH
Q 040869 43 IIHSHG-RAITLSELVSALDIQPTKTTGLFR 72 (131)
Q Consensus 43 ~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~R 72 (131)
.+.+.| ...|..+||+++|+ ++..+++
T Consensus 20 lf~e~G~~~~s~~~IA~~agv---s~~~lY~ 47 (202)
T TIGR03613 20 TFSRFGFHGTSLEQIAELAGV---SKTNLLY 47 (202)
T ss_pred HHHHhCcccCCHHHHHHHhCC---CHHHHHH
Confidence 444445 67999999999999 6666653
No 359
>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=57.65 E-value=15 Score=21.63 Aligned_cols=45 Identities=16% Similarity=0.135 Sum_probs=26.7
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
.+..|+|+.+|+ ++..|+..-+. .|++.......|...|....+-
T Consensus 1 ~~i~e~A~~~gV---s~~tlr~ye~~---~gl~~~~r~~~g~R~yt~~di~ 45 (68)
T cd04763 1 YTIGEVALLTGI---KPHVLRAWERE---FGLLKPQRSDGGHRLFNDADID 45 (68)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHHh---cCCCCCCcCCCCCcccCHHHHH
Confidence 368999999999 88776655332 2666432211123456655543
No 360
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.53 E-value=26 Score=30.92 Aligned_cols=52 Identities=15% Similarity=0.165 Sum_probs=44.5
Q ss_pred HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
...++.+.||....+ ...+|.+||.+.+++ ....+.|+|+-|+...+.....
T Consensus 605 ~~s~~q~~vfll~n~-~e~lt~eei~e~T~l---~~~dl~~~L~sl~~ak~~~l~~ 656 (773)
T COG5647 605 TFSVYQLLVFLLFND-HEELTFEEILELTKL---STDDLKRVLQSLSCAKLVVLLK 656 (773)
T ss_pred HHHHHHHHHHHHhcC-ccceeHHHHHhhcCC---ChhhHHHHHHHHHhhheeeecc
Confidence 356678889988874 468999999999999 8999999999999999887654
No 361
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=57.45 E-value=23 Score=27.67 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 25 SHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 25 ~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+||....+... .+....+|+.+|++.+|+ .++ -++.+|..+|++....
T Consensus 207 ~YW~~~il~~L---------~~~~~~isi~~is~~T~i---~~~---Dii~tL~~l~~l~~~~ 254 (290)
T PLN03238 207 SYWTRVLLEQL---------RDVKGDVSIKDLSLATGI---RGE---DIVSTLQSLNLIKYWK 254 (290)
T ss_pred HHHHHHHHHHH---------HhcCCCccHHHHHHHhCC---CHH---HHHHHHHHCCcEEEEC
Confidence 56776665555 223468999999999999 444 3788889999998653
No 362
>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=57.33 E-value=18 Score=27.17 Aligned_cols=55 Identities=20% Similarity=0.167 Sum_probs=38.6
Q ss_pred HHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 42 DIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 42 d~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
+.|.++ ..++|++++|+.+++ ++..+.|+.+..+...+.+-- ..+++..+.+.|.
T Consensus 193 ~~I~~~~~~~~sl~~lA~~~~~---S~~~l~r~Fk~~~G~t~~~yi------~~~Rl~~A~~lL~ 248 (287)
T TIGR02297 193 FLIEENYKQHLRLPEYADRLGI---SESRLNDICRRFSALSPKRLI------IERVMQEARRLLL 248 (287)
T ss_pred HHHHHhhccCCCHHHHHHHHCC---CHHHHHHHHHHHhCCCHHHHH------HHHHHHHHHHHHH
Confidence 445432 368999999999999 999999999988776644432 2345555555554
No 363
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=57.26 E-value=20 Score=27.30 Aligned_cols=60 Identities=13% Similarity=0.105 Sum_probs=47.0
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
-.|.+|-.+.+ .-|...-|+++++ ....+.|-++.|.. .-+|.+. +..+.+|+.++.|..
T Consensus 25 ~~L~~f~avae---~gs~s~AA~~L~i---sQpavS~~I~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~~ 87 (314)
T PRK09508 25 NLLTVFDAVMQ---EQNITRAAHNLGM---SQPAVSNAVARLKVMFNDELFVRY-----GRGIQPTARARQLFG 87 (314)
T ss_pred HHHHHHHHHHh---cCCHHHHHHHhCC---CHHHHHHHHHHHHHhhCCCcEEEc-----CCCCcCcHHHHHHHH
Confidence 35667777774 5678999999999 88889888888853 5588887 467999999886653
No 364
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=57.07 E-value=8.5 Score=22.41 Aligned_cols=24 Identities=17% Similarity=0.367 Sum_probs=18.0
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
..+|..++|+++|+ ++..+.++.+
T Consensus 13 ~gls~~~lA~~~g~---s~s~v~~iE~ 36 (64)
T PF13560_consen 13 AGLSQAQLADRLGV---SQSTVSRIER 36 (64)
T ss_dssp HTS-HHHHHHHHTS----HHHHHHHHT
T ss_pred cCCCHHHHHHHHCc---CHHHHHHHHC
Confidence 46999999999999 7777777654
No 365
>PRK09801 transcriptional activator TtdR; Provisional
Probab=56.95 E-value=19 Score=27.55 Aligned_cols=62 Identities=15% Similarity=0.164 Sum_probs=49.9
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
..-+|.+|-.+.+ .-|...-|+++++ ..+.+.|-++.|.. .-+|.+. +..+.+|+.++.|..
T Consensus 7 ~~~~L~~F~~v~~---~gs~t~AA~~L~i---SQpavS~~I~~LE~~LG~~Lf~R~-----~r~~~lT~~G~~l~~ 71 (310)
T PRK09801 7 LAKDLQVLVEIVH---SGSFSAAAATLGQ---TPAFVTKRIQILENTLATTLLNRS-----ARGVALTESGQRCYE 71 (310)
T ss_pred HHHHHHHHHHHHH---cCCHHHHHHHhCc---CHHHHHHHHHHHHHHhCCEeeeec-----CCCCcccHhHHHHHH
Confidence 4567788888884 5678999999999 88899988888854 4478876 578999999987764
No 366
>PRK15044 transcriptional regulator SirC; Provisional
Probab=56.68 E-value=28 Score=27.33 Aligned_cols=37 Identities=22% Similarity=0.227 Sum_probs=30.1
Q ss_pred HhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 37 ELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 37 ~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
.-++.+.|... ..+.|+++||+++|+ ++..+.|.++.
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgm---S~~tL~R~Fk~ 231 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFM---SVSSLKRKLAA 231 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCC---CHHHHHHHHHH
Confidence 34566777543 378999999999999 99999999886
No 367
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=56.61 E-value=18 Score=27.87 Aligned_cols=42 Identities=7% Similarity=0.245 Sum_probs=31.5
Q ss_pred hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+.+.|.++ ..++|+++||+.+|+ ++..+.|+.+.-+...+.+
T Consensus 196 ~~~~i~~~~~~~~tl~~lA~~~~~---S~~~l~r~Fk~~~G~t~~~ 238 (302)
T PRK10371 196 MLGFIAENYDQALTINDVAEHVKL---NANYAMGIFQRVMQLTMKQ 238 (302)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCc---CHHHHHHHHHHHhCCCHHH
Confidence 44555432 368999999999999 9999999998765544444
No 368
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=56.46 E-value=7.8 Score=31.44 Aligned_cols=44 Identities=9% Similarity=0.169 Sum_probs=34.2
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
..+++.|.=++|..|+-|||+++|+ +...+.-.++.|...|+++
T Consensus 343 ~~~l~~L~~~DG~~slldIA~~~~~---~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 343 MAMLWVLNYSDGKNSLLDIAERIGL---PFDELADAARKLLEAGLLK 386 (386)
T ss_dssp HHHHHHHHH-EEEEEHHHHHHHHT-----HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHhccCCCcHHHHHHHHCc---CHHHHHHHHHHHHHcCCCC
Confidence 3466777655789999999999999 9999999999999999874
No 369
>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=56.27 E-value=10 Score=17.99 Aligned_cols=21 Identities=19% Similarity=0.464 Sum_probs=17.4
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHH
Q 040869 50 AITLSELVSALDIQPTKTTGLFRL 73 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~Rl 73 (131)
+.|..++|+.+|+ ....+++.
T Consensus 21 ~~s~~~ia~~~~i---s~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGV---SRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCC---CHHHHHHh
Confidence 4699999999999 77777765
No 370
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=55.77 E-value=13 Score=24.01 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=21.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
..+|.++||+.+|+ ++..+.++|..
T Consensus 22 ~~ls~~~ia~dL~~---s~~~le~vL~l 46 (89)
T PF10078_consen 22 SGLSLEQIAADLGT---SPEHLEQVLNL 46 (89)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHHcC
Confidence 46999999999999 88888888763
No 371
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=55.70 E-value=21 Score=27.40 Aligned_cols=61 Identities=15% Similarity=0.110 Sum_probs=47.4
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhcccccc
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.-.|.+|..+.+ .-|.+.-|+++++ .++.+.|-++.|.. .-+|.+. +....+|+.++.|..
T Consensus 31 l~~L~~f~av~e---~gs~s~AA~~L~i---sQpavS~~I~~LE~~lG~~LF~R~-----~r~v~lT~~G~~l~~ 94 (317)
T PRK11482 31 LNLLTIFEAVYV---HKGIVNAAKILNL---TPSAISQSIQKLRVIFPDPLFIRK-----GQGVTPTAYATHLHE 94 (317)
T ss_pred hhHHHHHHHHHH---cCCHHHHHHHhCC---ChHHHHHHHHHHHHHhCCcceEec-----CCCccCCHHHHHHHH
Confidence 345677877874 4589999999999 88888888888754 5588887 477999999986654
No 372
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=55.45 E-value=15 Score=25.42 Aligned_cols=26 Identities=12% Similarity=0.220 Sum_probs=19.2
Q ss_pred HHHhCC-CCCCHHHHHhhcCCCCCCcchHH
Q 040869 43 IIHSHG-RAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 43 ~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
++.+.| ...|..+||++.|+ +...++
T Consensus 20 lf~~~G~~~~s~~~IA~~agv---sk~~ly 46 (189)
T TIGR03384 20 SIGERGSLDVTIAQIARRAGV---SSGIIS 46 (189)
T ss_pred HHHhcCcccCCHHHHHHHhCC---CHHHHH
Confidence 344444 67999999999999 555555
No 373
>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=55.42 E-value=20 Score=24.89 Aligned_cols=32 Identities=6% Similarity=0.266 Sum_probs=23.3
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
+..|+.... .++|.+|||+.+|+ +...+.++.
T Consensus 11 qr~VL~Lr~---~GlTq~EIAe~Lgi---S~stV~~~e 42 (137)
T TIGR00721 11 QIKVLELRE---KGLSQKEIAKELKT---TRANVSAIE 42 (137)
T ss_pred HHHHHHHHH---cCCCHHHHHHHHCc---CHHHHHHHH
Confidence 344555543 57999999999999 777766444
No 374
>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=55.30 E-value=23 Score=25.69 Aligned_cols=39 Identities=15% Similarity=0.154 Sum_probs=31.7
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
++..|.+||.+++.-. -++..+..+++.|...|++.+..
T Consensus 40 dG~rt~~eI~~~l~~~-~p~~~v~~~L~~L~~~G~l~~~~ 78 (193)
T TIGR03882 40 DGRRTLDEIIAALAGR-FPAEEVLYALDRLERRGYLVEDA 78 (193)
T ss_pred cCCCCHHHHHHHhhcc-CCHHHHHHHHHHHHHCCCEeccC
Confidence 5789999998887641 14667999999999999999754
No 375
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=55.13 E-value=18 Score=28.02 Aligned_cols=34 Identities=26% Similarity=0.364 Sum_probs=27.3
Q ss_pred hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
|.+.|..+ ..+.|+++||+.+|. +++.+.|.++.
T Consensus 186 i~~~I~~~~~~~~sl~~lA~~~gm---S~stl~R~Fk~ 220 (291)
T PRK15186 186 IYNIIISDISRKWALKDISDSLYM---SCSTLKRKLKQ 220 (291)
T ss_pred HHHHHHhCccCCCCHHHHHHHHCc---CHHHHHHHHHH
Confidence 44555433 378999999999999 99999999886
No 376
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=54.97 E-value=22 Score=27.12 Aligned_cols=61 Identities=18% Similarity=0.253 Sum_probs=46.3
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.|.+|..+.+ ...|...-|+++++ ..+.+.|-++.|. ..-+|.+.+ .+.+.+|+.++.|.+
T Consensus 5 ~L~~f~~v~~--~g~S~s~AA~~L~i---sQpavS~~ik~LE~~lg~~Lf~R~~----r~~~~lT~~G~~l~~ 68 (313)
T PRK12684 5 QLRFVREAVR--QNFNLTEAAKALYT---SQPGVSKAIIELEDELGVEIFTRHG----KRLRGLTEPGRIILA 68 (313)
T ss_pred HHHHHHHHHH--cCCCHHHHHHHhcC---CChHHHHHHHHHHHHhCCeeEEEcC----CcccccChhHHHHHH
Confidence 5678888874 23489999999999 8888888888875 456888874 333589999987764
No 377
>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=54.91 E-value=18 Score=28.18 Aligned_cols=39 Identities=13% Similarity=0.216 Sum_probs=26.3
Q ss_pred CCCCHHHHHhhcCCCCCCcc---hHH---HHH-HHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTT---GLF---RLM-RLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~---~l~---RlL-r~L~~~gl~~~~~ 87 (131)
-.+|+++||..||+++.+.. .+. |++ ..|..+|+++...
T Consensus 94 V~~sie~LA~ecGLst~s~~Gn~sitRasR~i~e~le~~Gli~~~~ 139 (281)
T PF02387_consen 94 VQASIEQLADECGLSTKSAAGNKSITRASRLISEFLEPLGLITCEK 139 (281)
T ss_pred eeecHHHHHHHhCCcccCCCCCeeHHHHHHHHHHHHHhcCCeeeee
Confidence 57999999999998433222 244 445 3456799997643
No 378
>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=54.90 E-value=13 Score=25.40 Aligned_cols=36 Identities=11% Similarity=0.078 Sum_probs=25.5
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
+..+|.+|+++..+- ++..+..+...|...|+=...
T Consensus 45 gk~Lt~~e~~~~~~p---~~~~v~~V~~wL~~~G~~~~~ 80 (143)
T PF09286_consen 45 GKYLTPEEFAALFAP---SPEDVAAVKSWLKSHGLTVVE 80 (143)
T ss_dssp T----HHHHHHHHS-----HHHHHHHHHHHHHCT-EEEE
T ss_pred ccCCCHHHHHHHHCC---CHHHHHHHHHHHHHcCCceeE
Confidence 356999999999999 889999999999999974443
No 379
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=54.86 E-value=22 Score=27.52 Aligned_cols=42 Identities=12% Similarity=0.196 Sum_probs=31.7
Q ss_pred hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+.+.|..+ ..++|+++||+.+|+ +++.+.|+.+......+-+
T Consensus 223 ~~~~i~~~~~~~~sl~~lA~~~~~---S~~~l~r~fk~~~g~s~~~ 265 (322)
T PRK09393 223 LIDWMRAHLAEPHTVASLAARAAM---SPRTFLRRFEAATGMTPAE 265 (322)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHH
Confidence 34444432 368999999999999 9999999998876655433
No 380
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=54.57 E-value=25 Score=26.09 Aligned_cols=53 Identities=19% Similarity=0.199 Sum_probs=40.8
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
-.+|.+++|++++. ++....|.|-.|...|++.+..... +.....|..+..+.
T Consensus 18 ~~~t~~ela~~l~~---S~qta~R~l~~le~~~~I~R~~~~~-Gq~i~iTekG~~~L 70 (214)
T COG1339 18 VKVTSSELAKRLGV---SSQTAARKLKELEDEGYITRTISKR-GQLITITEKGIDLL 70 (214)
T ss_pred ccccHHHHHHHhCc---CcHHHHHHHHhhccCCcEEEEecCC-CcEEEehHhHHHHH
Confidence 45999999999999 9999999999999999999754210 33456666665444
No 381
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=54.49 E-value=20 Score=26.82 Aligned_cols=43 Identities=7% Similarity=-0.001 Sum_probs=31.3
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH-HhhcCCc
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR-LLVHSSC 82 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr-~L~~~gl 82 (131)
+.-+..|+..++ .++|..|||+++++ .+.++...+. .+...|+
T Consensus 145 S~RE~eVL~Lia---~G~SnkEIA~~L~I---S~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 145 TKYQNDVFILYS---FGFSHEYIAQLLNI---TVGSSKNKISEILKFFGI 188 (217)
T ss_pred CHHHHHHHHHHH---CCCCHHHHHHHhCC---CHHHHHHHHHHHHHHhCC
Confidence 556778999888 46999999999999 7777654443 2334454
No 382
>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=54.36 E-value=37 Score=20.19 Aligned_cols=41 Identities=20% Similarity=0.373 Sum_probs=31.6
Q ss_pred hHHHHHhCCCCCCHHHHHhhc----CCCCCCcchHHHHHHHhhcCCcee
Q 040869 40 IADIIHSHGRAITLSELVSAL----DIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~----~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+...+.+. ++.|+.++.+++ +. ++...-.++|+|.+.+.+.
T Consensus 32 i~~~l~~~-~~~tl~~l~~~~d~~~~l---~~g~~L~~l~~LiA~k~i~ 76 (79)
T PF08721_consen 32 ILARLRKN-PTMTLRDLCKELDKDYEL---EPGTALPLLRHLIATKRIK 76 (79)
T ss_dssp HHHHHHHT-TTSBHHHHHHHHHHHCT-----TTHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHc-CCCCHHHHHHHHHHhcCC---CcCChHHHHHHHHhCChhc
Confidence 56677653 459999999887 77 8888889999999988765
No 383
>PRK13500 transcriptional activator RhaR; Provisional
Probab=54.30 E-value=23 Score=27.38 Aligned_cols=57 Identities=11% Similarity=0.043 Sum_probs=40.2
Q ss_pred hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
+.+.|.+. ..++|++++|+++++ ++..|.|+.+.-+...+.+.- ..+++....+.|.
T Consensus 211 i~~yI~~~~~e~isl~~lA~~~~i---S~~~L~r~FK~~tG~T~~~yi------~~~RL~~A~~LL~ 268 (312)
T PRK13500 211 LITRLAASLKSPFALDKFCDEASC---SERVLRQQFRQQTGMTINQYL------RQVRVCHAQYLLQ 268 (312)
T ss_pred HHHHHHHcccCCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHHHH------HHHHHHHHHHHHH
Confidence 55566543 368999999999999 999999999887766655443 2345555555554
No 384
>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=54.22 E-value=11 Score=27.57 Aligned_cols=41 Identities=17% Similarity=0.290 Sum_probs=24.7
Q ss_pred HHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 54 SELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 54 ~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
.+.++..++ ...-...+|.-|+..|-|.+.. .|.|+++|-+
T Consensus 156 ~~~~~~~~L---~~~eae~lL~~lv~~gWl~~s~----~G~y~L~~Ra 196 (200)
T PF07574_consen 156 TQLAQDKGL---SKSEAESLLDRLVEDGWLYRSR----EGFYSLGPRA 196 (200)
T ss_dssp --------------HHHHHHHHHHHHTTSE-EEE----TTEEEE-HHH
T ss_pred ccccccccc---hHHHHHHHHHHHHHCCCceeCC----CCEEEEChHH
Confidence 344444455 5677999999999999998776 7999999854
No 385
>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=54.15 E-value=4.5 Score=23.01 Aligned_cols=29 Identities=21% Similarity=0.387 Sum_probs=18.6
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhc-CCce
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVH-SSCF 83 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~-~gl~ 83 (131)
.++++.|||+.+|+ ++. .|++.|.. .|+.
T Consensus 2 ~~i~V~elAk~l~v---~~~---~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 2 EKIRVSELAKELGV---PSK---EIIKKLFKELGIM 31 (54)
T ss_dssp -EE-TTHHHHHHSS---SHH---HHHHHH-HHHTS-
T ss_pred CceEHHHHHHHHCc---CHH---HHHHHHHHhCCcC
Confidence 35789999999999 655 45555533 6766
No 386
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=53.90 E-value=3.3 Score=31.95 Aligned_cols=22 Identities=14% Similarity=0.357 Sum_probs=18.2
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+|..|||++.|+ +..++.|+|+
T Consensus 2 ~ti~dIA~~aGV---S~~TVSrvLn 23 (346)
T PRK10401 2 ITIRDVARQAGV---SVATVSRVLN 23 (346)
T ss_pred CCHHHHHHHhCC---CHHHHHHHHC
Confidence 578899999999 7788887775
No 387
>PF14493 HTH_40: Helix-turn-helix domain
Probab=53.90 E-value=20 Score=22.55 Aligned_cols=33 Identities=12% Similarity=0.367 Sum_probs=28.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc-ee
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC-FN 84 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl-~~ 84 (131)
.++|++|||+.-++ .+.++..-|-.++..|. +.
T Consensus 12 ~G~si~eIA~~R~L---~~sTI~~HL~~~~~~g~~~~ 45 (91)
T PF14493_consen 12 KGLSIEEIAKIRGL---KESTIYGHLAELIESGEPLD 45 (91)
T ss_pred cCCCHHHHHHHcCC---CHHHHHHHHHHHHHhCCCCC
Confidence 46999999999999 99999988888888887 44
No 388
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=53.67 E-value=23 Score=27.02 Aligned_cols=60 Identities=22% Similarity=0.300 Sum_probs=46.3
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcce-ecchhcccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAY-GLTAASTLLIK 106 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y-~~t~~s~~L~~ 106 (131)
+|.+|..+.+ ...|...-|+++++ ..+.+.|-++.|. ..-+|.+. ++++ .+|+.++.|..
T Consensus 5 ~L~~F~~v~~--~~~S~s~AA~~L~i---sQpavS~~I~~LE~~lg~~Lf~R~-----~r~~~~lT~~G~~l~~ 68 (309)
T PRK12683 5 QLRIIREAVR--QNFNLTEVANALYT---SQSGVSKQIKDLEDELGVEIFIRR-----GKRLTGLTEPGKELLQ 68 (309)
T ss_pred HHHHHHHHHH--ccCCHHHHHHHhcC---CcHHHHHHHHHHHHHhCCeeEeeC-----CCCcCCcCHHHHHHHH
Confidence 5778888874 34589999999999 8888888888875 35588876 3555 79999987764
No 389
>PRK04158 transcriptional repressor CodY; Validated
Probab=53.54 E-value=26 Score=26.91 Aligned_cols=45 Identities=11% Similarity=0.198 Sum_probs=38.7
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
-||+.|...+|-+.++.||.+.|+ -.+-+---||-+.+.|+++-.
T Consensus 190 hIf~eL~g~EG~lvASkiADrvgI---TRSVIVNALRK~ESAGvIESr 234 (256)
T PRK04158 190 HIFEELDGNEGLLVASKIADRVGI---TRSVIVNALRKLESAGVIESR 234 (256)
T ss_pred HHHHhcCCCcceEEeeecccccCC---chhhhhhhhhhhhcccceeec
Confidence 378888765688999999999999 777888889999999999865
No 390
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=53.09 E-value=22 Score=27.55 Aligned_cols=62 Identities=15% Similarity=0.191 Sum_probs=47.9
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCccee-cchhccccccC
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYG-LTAASTLLIKD 107 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~-~t~~s~~L~~~ 107 (131)
-+|.+|-.+.+ ...|...-|+++++ .++.+.|-++.|.. .-+|.+. ++... +|+.++.|.+.
T Consensus 4 ~~L~~F~~vae--~~gS~s~AA~~L~i---sQpavS~~I~~LE~~lG~~LF~R~-----~r~v~~LT~~G~~l~~~ 69 (327)
T PRK12680 4 TQLRYLVAIAD--AELNITLAAARVHA---TQPGLSKQLKQLEDELGFLLFVRK-----GRSLESVTPAGVEVIER 69 (327)
T ss_pred HHHHHHHHHHH--ccCCHHHHHHHhcC---CchHHHHHHHHHHHHhCCeEEEEC-----CCcCCccCccHHHHHHH
Confidence 35788888884 13689999999999 88899988888863 5588877 46674 99999877643
No 391
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=52.94 E-value=22 Score=25.86 Aligned_cols=41 Identities=15% Similarity=0.210 Sum_probs=35.1
Q ss_pred CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 52 TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 52 s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
...+||..+|+ ++..+.-++++.-..|+++.. +|....++.
T Consensus 118 ~~~~La~~l~i---~~~~l~fml~VF~EL~FVti~-----~g~i~~~~~ 158 (195)
T PF10141_consen 118 QLQALAKYLGI---SPDTLKFMLKVFFELGFVTIE-----DGVISLNPN 158 (195)
T ss_pred HHHHHHHHHCc---CHHHHHHHHHHHHHcCcEEEe-----CCEEEeCCC
Confidence 36899999999 999999999999999999987 576666543
No 392
>PHA01976 helix-turn-helix protein
Probab=52.88 E-value=15 Score=21.36 Aligned_cols=24 Identities=17% Similarity=0.284 Sum_probs=19.4
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
..+|..|+|+++|+ ++..+.++.+
T Consensus 14 ~glt~~~lA~~~gv---s~~~v~~~e~ 37 (67)
T PHA01976 14 RAWSAPELSRRAGV---RHSLIYDFEA 37 (67)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHHc
Confidence 56999999999999 7777776653
No 393
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=52.63 E-value=15 Score=27.76 Aligned_cols=35 Identities=17% Similarity=0.309 Sum_probs=26.6
Q ss_pred ChHHHHHhC-CCC-CCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 39 GIADIIHSH-GRA-ITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 39 ~ifd~l~~~-~~~-~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
.+.+.|.++ ..| +|+++||+++|+ +++.|.|+.+-
T Consensus 201 ~~~~~I~~~l~~~~ls~~~lA~~~gi---S~r~L~r~Fk~ 237 (302)
T PRK09685 201 KVVALIDQSIQEEILRPEWIAGELGI---SVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHCC---CHHHHHHHHHH
Confidence 344555432 245 999999999999 99999998874
No 394
>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=52.62 E-value=21 Score=22.01 Aligned_cols=36 Identities=14% Similarity=0.200 Sum_probs=25.8
Q ss_pred CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 52 TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 52 s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+.+|++..|+.|-..+.+..+++-|...|++....
T Consensus 24 ~Y~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 24 VYEELCESLGVDPLSYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHHHHHTTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 356788898985555667888888899999998754
No 395
>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=52.55 E-value=18 Score=22.48 Aligned_cols=38 Identities=13% Similarity=0.016 Sum_probs=24.6
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
.|.+|..+|...++-...++..+..++..|...||=-.
T Consensus 19 ~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI~Vv 56 (82)
T PF03979_consen 19 KGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGIEVV 56 (82)
T ss_dssp HSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT----B
T ss_pred cCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCCEEe
Confidence 37899999999998322288899999999999996443
No 396
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=52.39 E-value=29 Score=21.03 Aligned_cols=29 Identities=14% Similarity=0.294 Sum_probs=25.1
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVH 79 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~ 79 (131)
+.++|+.|.|+.+|+ ++..+.+.++....
T Consensus 11 s~~~s~~~Aa~~lG~---~~~~v~~wv~~fR~ 39 (65)
T PF05344_consen 11 SQQISVAQAADRLGT---DPGTVRRWVRMFRQ 39 (65)
T ss_pred cccccHHHHHHHHCc---CHHHHHHHHHHHHH
Confidence 479999999999999 99998888876554
No 397
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=52.26 E-value=15 Score=25.02 Aligned_cols=23 Identities=13% Similarity=0.163 Sum_probs=19.0
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
...|.+|||+.+|+ ++..+++.+
T Consensus 124 ~~~s~~EIA~~lgi---s~~tV~~~l 146 (163)
T PRK07037 124 HGETQKDIARELGV---SPTLVNFMI 146 (163)
T ss_pred cCCCHHHHHHHHCC---CHHHHHHHH
Confidence 46999999999999 887766554
No 398
>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=52.14 E-value=24 Score=20.37 Aligned_cols=36 Identities=19% Similarity=0.172 Sum_probs=30.1
Q ss_pred CCCCHHHHHhhc---CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSAL---DIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~---~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+++-+||-+++ ++ ++.....+|..|+..|.+..++
T Consensus 16 ~G~~keeLrsrl~~~~l---~~k~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 16 PGMPKEELRSRLFKPRL---PPKLFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp S-EEHHHHHHHCST-TS----HCCHHHHHHHHHHTTSEEEES
T ss_pred cCcCHHHHHHHHhhccC---CHHHHHHHHHHHHHCCCeeeEC
Confidence 568899999888 66 8899999999999999999763
No 399
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=52.00 E-value=41 Score=28.98 Aligned_cols=44 Identities=7% Similarity=0.067 Sum_probs=38.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
.|.+..||++.+++ ++.....+|+.|+..|.+.+-. ++.|-++.
T Consensus 505 ~p~~~~~~~~~l~~---~~~~~~~~l~~l~~~g~lv~l~----~~~~~~~~ 548 (614)
T PRK10512 505 EPWWVRDLAKETGT---DEQAMRLTLRQAAQQGIITAIV----KDRYYRND 548 (614)
T ss_pred CCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec----CCEEECHH
Confidence 68899999999999 9999999999999999888775 56666555
No 400
>PRK09480 slmA division inhibitor protein; Provisional
Probab=51.88 E-value=19 Score=25.05 Aligned_cols=21 Identities=24% Similarity=0.536 Sum_probs=16.9
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHH
Q 040869 48 GRAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
|...|+++||+++|+ ++..+|
T Consensus 28 G~~~ti~~Ia~~agv---s~gt~Y 48 (194)
T PRK09480 28 GERITTAKLAARVGV---SEAALY 48 (194)
T ss_pred CCccCHHHHHHHhCC---CHhHHH
Confidence 467999999999999 555554
No 401
>PRK09483 response regulator; Provisional
Probab=51.67 E-value=24 Score=24.64 Aligned_cols=36 Identities=17% Similarity=0.189 Sum_probs=25.8
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
.-+..|+..+. .+.|..|||+++++ .+.++....+.
T Consensus 151 ~rE~~vl~~~~---~G~~~~~Ia~~l~i---s~~TV~~~~~~ 186 (217)
T PRK09483 151 ERELQIMLMIT---KGQKVNEISEQLNL---SPKTVNSYRYR 186 (217)
T ss_pred HHHHHHHHHHH---CCCCHHHHHHHhCC---CHHHHHHHHHH
Confidence 44556676665 45899999999999 77776554443
No 402
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=51.23 E-value=23 Score=23.37 Aligned_cols=23 Identities=26% Similarity=0.414 Sum_probs=18.5
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
..+|..+||++.|+ ++..+++-.
T Consensus 31 ~~~t~~~Ia~~agv---s~~~~Y~~f 53 (201)
T COG1309 31 AATTVDEIAKAAGV---SKGTLYRHF 53 (201)
T ss_pred CCCCHHHHHHHhCC---CcchhHHHc
Confidence 57999999999999 777766443
No 403
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=51.09 E-value=32 Score=18.36 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=21.6
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
|-+.|... .-+..+.|+.+|+ +...|+|-|+
T Consensus 10 i~~aL~~~--~gn~~~aA~~Lgi---sr~tL~~klk 40 (42)
T PF02954_consen 10 IRQALERC--GGNVSKAARLLGI---SRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHT--TT-HHHHHHHHTS----HHHHHHHHH
T ss_pred HHHHHHHh--CCCHHHHHHHHCC---CHHHHHHHHH
Confidence 34455543 3467899999999 9999998876
No 404
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=51.07 E-value=16 Score=31.31 Aligned_cols=43 Identities=19% Similarity=0.248 Sum_probs=33.8
Q ss_pred HhChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 37 ELGIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 37 ~L~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
+-.|.+.|-++. .-+|+.|||+++++ ++..+.|+.|.|--.|+
T Consensus 358 E~~IA~yIl~n~~~v~~~si~eLA~~~~v---S~aTV~Rf~kkLGf~Gf 403 (638)
T PRK14101 358 ERRVADLALNHPRSIINDPIVDIARKADV---SQPTVIRFCRSLGCQGL 403 (638)
T ss_pred HHHHHHHHHhCHHHHHhccHHHHHHHhCC---CHHHHHHHHHHhCCCCH
Confidence 345666664332 35899999999999 99999999999887776
No 405
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=51.05 E-value=32 Score=23.89 Aligned_cols=56 Identities=20% Similarity=0.145 Sum_probs=33.2
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCC--CCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 40 IADIIHSHGRAITLSELVSALDIQ--PTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~--~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
++..|-+.....|.+||.+++.-. .-...+++| .|...|+++.... +|.-+|...+
T Consensus 6 ~i~~Li~~~~i~tqeeL~~~L~~~G~~vsqaTIsR---dL~elglvk~~~~-~g~~~Y~~~~ 63 (146)
T TIGR01529 6 RIKEIITEEKISTQEELVALLKAEGIEVTQATVSR---DLRELGAVKVRDE-DGSYVYSLPA 63 (146)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHH---HHHHcCCEEEECC-CCcEEEeecc
Confidence 444454446789999999987520 015567888 4556788765431 1223576543
No 406
>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=50.80 E-value=9.7 Score=20.27 Aligned_cols=26 Identities=15% Similarity=0.289 Sum_probs=19.4
Q ss_pred CHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 52 TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 52 s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
|..|+|+.+|+ +++ -||.....|++.
T Consensus 1 ti~e~A~~~gv---s~~----tlR~ye~~Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGV---SPR----TLRYYEREGLLP 26 (38)
T ss_dssp EHHHHHHHHTS----HH----HHHHHHHTTSS-
T ss_pred CHHHHHHHHCC---CHH----HHHHHHHCCCCC
Confidence 46899999999 555 567777889884
No 407
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=50.73 E-value=24 Score=27.31 Aligned_cols=35 Identities=20% Similarity=0.299 Sum_probs=28.0
Q ss_pred ChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 39 GIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 39 ~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
.+.+.|... ..++|+++||+.+|+ ++..+.|+.+.
T Consensus 146 ~v~~yI~~~~~~~lsl~~lA~~~g~---S~~~L~R~Fk~ 181 (274)
T PRK09978 146 RVCTVINNNIAHEWTLARIASELLM---SPSLLKKKLRE 181 (274)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCc---CHHHHHHHHHh
Confidence 455666543 368999999999999 99999999874
No 408
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=50.63 E-value=19 Score=24.08 Aligned_cols=25 Identities=12% Similarity=0.118 Sum_probs=20.0
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
...|..|||+.+|+ ++..++..+..
T Consensus 128 ~~~~~~eIA~~lgi---s~~tv~~~~~r 152 (161)
T TIGR02985 128 EGKSYKEIAEELGI---SVKTVEYHISK 152 (161)
T ss_pred cCCCHHHHHHHHCC---CHHHHHHHHHH
Confidence 46899999999999 88876655543
No 409
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=50.55 E-value=24 Score=27.73 Aligned_cols=50 Identities=10% Similarity=0.065 Sum_probs=39.9
Q ss_pred hChHHHHHhCCCCCCHHHHHhhcCCC--CCCcchHHHHHHHhhcCCceeecc
Q 040869 38 LGIADIIHSHGRAITLSELVSALDIQ--PTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 38 L~ifd~l~~~~~~~s~~eLA~~~~~~--~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..|.++|++++.|+.+..||..+.=. ...++.++=-||-|-..|+.++..
T Consensus 9 ieIl~il~esd~plgak~Ia~el~kRGy~igeRavRYhlk~lderglt~kvg 60 (325)
T COG1693 9 IEILRILAESDEPLGAKIIALELRKRGYNIGERAVRYHLKKLDERGLTRKVG 60 (325)
T ss_pred HHHHHHHHhcCCccchHHHHHHHHhcccchhHHHHHHHHHHHhhccchhhcc
Confidence 35788899888999999999987410 016678888999999999998875
No 410
>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=50.42 E-value=24 Score=22.16 Aligned_cols=44 Identities=11% Similarity=0.197 Sum_probs=28.5
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
.|..|+|+.+|+ ++.. +|+....|++.......|...|....+-
T Consensus 2 ~~i~e~A~~~gv---s~~t----Lr~ye~~Gli~p~r~~~g~R~y~~~dv~ 45 (91)
T cd04766 2 YVISVAAELSGM---HPQT----LRLYERLGLLSPSRTDGGTRRYSERDIE 45 (91)
T ss_pred cCHHHHHHHHCc---CHHH----HHHHHHCCCcCCCcCCCCCeeECHHHHH
Confidence 588999999999 6665 5555668999853211223456555543
No 411
>PRK15185 transcriptional regulator HilD; Provisional
Probab=50.40 E-value=25 Score=27.79 Aligned_cols=35 Identities=23% Similarity=0.301 Sum_probs=28.2
Q ss_pred ChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 39 GIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 39 ~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
.+.+.|..+ ..+.|++++|+.+++ ++..|.|.++.
T Consensus 210 rV~~~I~~n~~~~~SledLA~~lgm---S~~tL~R~FK~ 245 (309)
T PRK15185 210 RVYNIISSSPSRQWKLTDVADHIFM---STSTLKRKLAE 245 (309)
T ss_pred HHHHHHHhCccCCCCHHHHHHHHCc---CHHHHHHHHHH
Confidence 366666543 378999999999999 99999999874
No 412
>PRK00767 transcriptional regulator BetI; Validated
Probab=50.33 E-value=21 Score=24.99 Aligned_cols=25 Identities=16% Similarity=0.179 Sum_probs=18.6
Q ss_pred HHhCC-CCCCHHHHHhhcCCCCCCcchHH
Q 040869 44 IHSHG-RAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 44 l~~~~-~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
+.+.| ...|..+||+++|+ +...++
T Consensus 22 f~~~G~~~~s~~~Ia~~aGv---s~gslY 47 (197)
T PRK00767 22 IGEVGLLDATIAQIARRAGV---STGIIS 47 (197)
T ss_pred HHHcCcccCCHHHHHHHhCC---CHHHHH
Confidence 55445 57999999999999 555554
No 413
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=50.26 E-value=26 Score=25.02 Aligned_cols=32 Identities=9% Similarity=0.169 Sum_probs=24.3
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHH
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
+..+..|+..+. .+.|..|||+++++ .+.++.
T Consensus 152 t~rE~evl~~~~---~G~s~~eIA~~l~i---S~~TV~ 183 (216)
T PRK10840 152 SPKESEVLRLFA---EGFLVTEIAKKLNR---SIKTIS 183 (216)
T ss_pred CHHHHHHHHHHH---CCCCHHHHHHHHCC---CHHHHH
Confidence 344566777776 46999999999999 776654
No 414
>PRK13501 transcriptional activator RhaR; Provisional
Probab=50.08 E-value=21 Score=26.98 Aligned_cols=43 Identities=14% Similarity=0.179 Sum_probs=32.6
Q ss_pred hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
+.+.|.+. ..++|++++|+++++ ++..+.|+.+..+..-+.+-
T Consensus 181 i~~~I~~~~~e~~sl~~lA~~~~l---S~~~l~r~Fk~~~G~T~~qy 224 (290)
T PRK13501 181 IMSALQQSLGAYFDMADFCHKNQL---VERSLKQLFRQQTGMSISHY 224 (290)
T ss_pred HHHHHHHhhccCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHHH
Confidence 45555432 368999999999999 99999999987766655443
No 415
>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=50.05 E-value=17 Score=21.72 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=20.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
..+|..++|+++|+ +...+.++++
T Consensus 17 ~~~t~~~lA~~~gi---s~~tis~~~~ 40 (78)
T TIGR02607 17 LGLSIRALAKALGV---SRSTLSRIVN 40 (78)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHHc
Confidence 57999999999999 8888888765
No 416
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=49.79 E-value=43 Score=27.86 Aligned_cols=49 Identities=18% Similarity=0.148 Sum_probs=36.5
Q ss_pred HhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 24 FSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 24 ~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+||....+.... +..+.+|+.+|++.+++ .+ .-++..|..+|++....
T Consensus 357 ~~YW~~~i~~~L~---------~~~~~~si~~is~~T~i---~~---~Dii~tL~~l~~l~~~k 405 (450)
T PLN00104 357 RGYWTRVLLEILK---------KHKGNISIKELSDMTAI---KA---EDIVSTLQSLNLIQYRK 405 (450)
T ss_pred HHHHHHHHHHHHH---------hcCCCccHHHHHHHhCC---CH---HHHHHHHHHCCCEEecC
Confidence 3677776666542 33468999999999999 33 45788999999998764
No 417
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=49.74 E-value=46 Score=25.95 Aligned_cols=34 Identities=32% Similarity=0.401 Sum_probs=27.6
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN 84 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~ 84 (131)
+.|.|..|||..+++ ++..+.|..|.++...-+.
T Consensus 155 ~~prtl~eIa~a~~V---~~kei~rtyr~~~~~L~l~ 188 (285)
T COG1405 155 GVPRTLDEIAKALGV---SKKEIGRTYRLLVRELKLK 188 (285)
T ss_pred CCCccHHHHHHHHCC---CHHHHHHHHHHHHHhcCCC
Confidence 689999999999999 8888888888766554444
No 418
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=49.61 E-value=29 Score=24.99 Aligned_cols=39 Identities=15% Similarity=0.169 Sum_probs=29.8
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
-++-.|++.+.. .+.|+.+||.+.|+ +...+.-|+|.-.
T Consensus 20 ~~r~~Iy~~~~~--~~~sv~~vS~~ygi---~~~RV~AIvrLke 58 (172)
T PF12298_consen 20 ELREQIYEDVMQ--DGKSVREVSQKYGI---KIQRVEAIVRLKE 58 (172)
T ss_pred HHHHHHHHHHHh--CCCCHHHHHHHhCC---CHHHHHHHHHHHH
Confidence 345567777764 56799999999999 8888888877643
No 419
>PRK13502 transcriptional activator RhaR; Provisional
Probab=49.57 E-value=30 Score=25.91 Aligned_cols=58 Identities=10% Similarity=0.026 Sum_probs=39.2
Q ss_pred ChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 39 GIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 39 ~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
.+.+.|.+. ..+++++++|+.+|+ ++..|.|+.+.-+...+-+.- ..+++....+.|.
T Consensus 180 ~~~~~I~~~~~~~~~~~~lA~~~~i---S~~~L~r~fk~~~G~t~~~yi------~~~Rl~~A~~lL~ 238 (282)
T PRK13502 180 KLITALANSLECPFALDAFCQQEQC---SERVLRQQFRAQTGMTINQYL------RQVRICHAQYLLQ 238 (282)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHHHH------HHHHHHHHHHHHH
Confidence 455555432 367999999999999 999999999876665544432 2344454444444
No 420
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=49.51 E-value=46 Score=23.53 Aligned_cols=66 Identities=11% Similarity=0.135 Sum_probs=52.5
Q ss_pred HHHhChHHHHHh-CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccCc
Q 040869 35 AIELGIADIIHS-HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDK 108 (131)
Q Consensus 35 a~~L~ifd~l~~-~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~~ 108 (131)
+-=.|+.+.+.+ -+|...+--|++.+++ +-+-|.-+.-++...|+++-. +|-...|+.++.+++.+
T Consensus 12 ~~l~GLL~~l~n~fnGraDl~~L~~e~~v---didDL~piv~ta~~Lglv~~e-----~GDiilT~~Gk~~v~~~ 78 (157)
T COG4754 12 AQLVGLLYVLNNIFNGRADLPYLEKEMEV---DIDDLMPIVETASLLGLVTAE-----SGDIILTDEGKEYVESP 78 (157)
T ss_pred HHHHHHHHHHHHHhCCcccchhHHHHhCC---ChhhHHHHHHHHHhcCceecc-----CCCEEEehhhHHHHhCC
Confidence 334566777764 3577889999999999 999999999999999999976 46688899988666543
No 421
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=49.41 E-value=21 Score=23.22 Aligned_cols=25 Identities=16% Similarity=0.288 Sum_probs=20.9
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
.+.|..|||+.+|+ ++..+++.+.-
T Consensus 125 ~g~s~~eIA~~l~~---s~~~v~~~~~~ 149 (158)
T TIGR02937 125 EGLSYKEIAEILGI---SVGTVKRRLKR 149 (158)
T ss_pred cCCCHHHHHHHHCC---CHHHHHHHHHH
Confidence 46899999999999 88887776654
No 422
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=49.37 E-value=25 Score=19.32 Aligned_cols=25 Identities=12% Similarity=0.177 Sum_probs=18.9
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
.+|..+.|++.|+ +...|.|-++--
T Consensus 16 ~~S~r~AA~~ygV---p~sTL~~r~~g~ 40 (45)
T PF05225_consen 16 KMSIRKAAKKYGV---PRSTLRRRLRGK 40 (45)
T ss_dssp SS-HHHHHHHHT-----HHHHHHHHHHT
T ss_pred CCCHHHHHHHHCc---CHHHHHHHHcCC
Confidence 3999999999999 999999877643
No 423
>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=49.36 E-value=20 Score=26.97 Aligned_cols=24 Identities=13% Similarity=0.386 Sum_probs=21.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
...|+..||+..++ .|+.++|||+
T Consensus 28 ~~~t~~~Lae~F~v---spe~irrILk 51 (225)
T PF06413_consen 28 EEWTVERLAESFKV---SPEAIRRILK 51 (225)
T ss_pred cccCHHHHHhhCCC---CHHHHHHHHh
Confidence 45799999999999 9999999995
No 424
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=49.20 E-value=31 Score=26.35 Aligned_cols=58 Identities=9% Similarity=0.083 Sum_probs=45.1
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccc
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
+|.+|..+.+ --|...-|+++++ .++.+.|-++.|.. .-+|.+. ++...+|+.++.|.
T Consensus 12 ~L~~f~av~e---~gs~t~AA~~L~i---SQpavS~~I~~LE~~lg~~LF~R~-----~r~~~lT~~G~~l~ 72 (319)
T PRK10216 12 LLLCLQLLMQ---ERSVTKAAKRMNV---TPSAVSKSLAKLRAWFDDPLFVNT-----PLGLSPTPLMVSME 72 (319)
T ss_pred HHHHHHHHHH---hCCHHHHHHHhCC---CHHHHHHHHHHHHHHhCCceEEec-----CCCcccCHHHHHHH
Confidence 4667888874 3588899999999 88888888888754 4588887 46688999887664
No 425
>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=49.15 E-value=14 Score=22.79 Aligned_cols=28 Identities=7% Similarity=0.083 Sum_probs=18.7
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
|.-.|+.+||+.+|.. ..++.+.+.|+.
T Consensus 15 G~v~TYg~iA~~~g~p-~~~R~Vg~al~~ 42 (79)
T cd06445 15 GEVTTYGQIAKLAGTP-KAARAVGSALAR 42 (79)
T ss_pred CCcCcHHHHHHHHCCC-CcHHHHHHHHHh
Confidence 6789999999999981 123344444443
No 426
>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=49.01 E-value=20 Score=22.97 Aligned_cols=44 Identities=9% Similarity=0.197 Sum_probs=28.9
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CCCcceecchhc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQEEAYGLTAAS 101 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~~~~y~~t~~s 101 (131)
++..|+|+.+|+ .++ .+|+-...|++...... .+...|....+-
T Consensus 1 m~I~eva~~~gv---s~~----tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~ 45 (95)
T cd04780 1 MRMSELSKRSGV---SVA----TIKYYLREGLLPEGRRLAPNQAEYSEAHVE 45 (95)
T ss_pred CCHHHHHHHHCc---CHH----HHHHHHHCCCCCCCcCCCCCCeecCHHHHH
Confidence 478999999999 554 56777789999864321 122345554443
No 427
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=48.90 E-value=13 Score=30.60 Aligned_cols=24 Identities=21% Similarity=0.444 Sum_probs=22.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
.|+|..+||..+|+ +++++.|..+
T Consensus 317 kPLtlkdiA~~lgl---heSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGL---HESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCC---Cccchhhhhc
Confidence 79999999999999 9999999864
No 428
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=48.85 E-value=22 Score=28.63 Aligned_cols=50 Identities=2% Similarity=0.009 Sum_probs=40.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.++....+.++.|. +.......+..|...|++..+ ++++.+|+.+..+.+
T Consensus 337 ~Gld~~~f~~~~g~---~~~~~~~~l~~l~~~gll~~~-----~~~~~LT~~G~~~~d 386 (394)
T PRK08898 337 DGVPAHLFQERTGL---PLAAIEPQLAAAEQRGLLERD-----HTRIRPTPLGQRFLN 386 (394)
T ss_pred CCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEE-----CCEEEEChhHhHHHH
Confidence 46888888888888 666667788899999999976 578999999887754
No 429
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=48.83 E-value=16 Score=21.30 Aligned_cols=43 Identities=12% Similarity=0.125 Sum_probs=25.7
Q ss_pred CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 52 TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 52 s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
|..|+|+.+|+ ++..|+.. ...|++.......|...|....+-
T Consensus 2 ti~eva~~~gv---s~~tlr~y----~~~gll~~~~~~~g~r~y~~~dv~ 44 (69)
T PF13411_consen 2 TIKEVAKLLGV---SPSTLRYY----EREGLLPPPRDENGYRYYSEEDVE 44 (69)
T ss_dssp EHHHHHHHTTT---THHHHHHH----HHTTSSTTBESTTSSEEE-HHHHH
T ss_pred cHHHHHHHHCc---CHHHHHHH----HHhcCcccccccCceeeccHHHHH
Confidence 68899999999 77765554 556766654311122446555443
No 430
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=48.82 E-value=31 Score=27.57 Aligned_cols=27 Identities=22% Similarity=0.353 Sum_probs=22.4
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
+.++|+++||+.+|+ ++..+.|+.+..
T Consensus 97 ~~~lsl~eLA~~lG~---S~~~L~R~Fkk~ 123 (353)
T PRK15435 97 ETPVTLEALADQVAM---SPFHLHRLFKAT 123 (353)
T ss_pred CCCCCHHHHHHHHCC---CHHHHHHHHHHH
Confidence 468999999999999 888888777554
No 431
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=48.80 E-value=23 Score=25.29 Aligned_cols=25 Identities=16% Similarity=0.458 Sum_probs=18.8
Q ss_pred HHhCC-CCCCHHHHHhhcCCCCCCcchHH
Q 040869 44 IHSHG-RAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 44 l~~~~-~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
+.+.| ...|.++||++.|+ .+..+|
T Consensus 24 f~e~G~~~~t~~~Ia~~agv---s~~tlY 49 (215)
T PRK10668 24 FSQQGVSATSLADIAKAAGV---TRGAIY 49 (215)
T ss_pred HHHcCcccCCHHHHHHHhCC---ChHHHH
Confidence 44445 56999999999999 666655
No 432
>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=48.76 E-value=19 Score=25.79 Aligned_cols=27 Identities=22% Similarity=0.330 Sum_probs=24.4
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
...|..+||+++|. +...+.|.|+.+.
T Consensus 119 ~g~s~~~iA~~lg~---s~~~V~r~l~l~~ 145 (187)
T TIGR00180 119 FSMTQEDLAKKIGK---SRAHITNLLRLLK 145 (187)
T ss_pred hCCCHHHHHHHHCc---CHHHHHHHHHHHc
Confidence 46899999999999 9999999999865
No 433
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=48.43 E-value=25 Score=26.86 Aligned_cols=34 Identities=15% Similarity=0.296 Sum_probs=27.0
Q ss_pred hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
+.+.+... .+++|+++||+.+|+ ++..+.|+.+.
T Consensus 139 v~~~I~~~~~~~~tl~~LA~~~gm---S~s~l~R~FK~ 173 (253)
T PRK09940 139 VRNIVNMKLAHPWKLKDICDCLYI---SESLLKKKLKQ 173 (253)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCc---CHHHHHHHHHH
Confidence 44555432 378999999999999 99999999876
No 434
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=48.13 E-value=40 Score=27.09 Aligned_cols=37 Identities=8% Similarity=0.086 Sum_probs=34.0
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
..|+++++|+..+|+ ....+...|-.|.-.|.+....
T Consensus 307 ~~~~~~d~l~~~~~~---~~~~~~~~L~~lel~G~i~~~~ 343 (350)
T COG0758 307 DEPKEIDRLASCTGL---TIAQVLAWLLELELEGKVKRLG 343 (350)
T ss_pred CCCccHHHHHHHhCC---CHHHHHHHHHHHHhcCcEEeeC
Confidence 489999999999999 9999999999999999999875
No 435
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=48.10 E-value=21 Score=23.93 Aligned_cols=20 Identities=20% Similarity=0.317 Sum_probs=14.5
Q ss_pred HHHHHhCCCCCCHHHHHhhcCC
Q 040869 41 ADIIHSHGRAITLSELVSALDI 62 (131)
Q Consensus 41 fd~l~~~~~~~s~~eLA~~~~~ 62 (131)
...+.+ ..+|..|+|+++|+
T Consensus 11 ~~ll~~--~Glsq~eLA~~~Gi 30 (120)
T PRK13890 11 LRLLDE--RHMTKKELSERSGV 30 (120)
T ss_pred HHHHHH--cCCCHHHHHHHHCc
Confidence 344443 56899999999987
No 436
>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=47.78 E-value=24 Score=22.72 Aligned_cols=44 Identities=9% Similarity=0.138 Sum_probs=28.6
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
.+..|+|+.+|+ ++..| |+-...|++.......|-..|....+-
T Consensus 2 ~~i~eva~~~gv---s~~tL----R~ye~~Gll~~~r~~~g~R~Y~~~dl~ 45 (102)
T cd04775 2 YTIGQMSRKFGV---SRSTL----LYYESIGLIPSARSEANYRLYSEADLS 45 (102)
T ss_pred CCHHHHHHHHCc---CHHHH----HHHHHCCCCCCCCCCCCCeeeCHHHHH
Confidence 578999999999 76655 788888999432211122346555543
No 437
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=47.77 E-value=16 Score=22.53 Aligned_cols=38 Identities=13% Similarity=0.327 Sum_probs=27.0
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
.+.++..|-. .++.|..++|.++.+ +...+.|.++-+.
T Consensus 18 ~~~ll~~ll~-~~~~s~~~la~~~~i---S~sti~~~i~~l~ 55 (87)
T PF05043_consen 18 NYQLLKLLLN-NEYVSIEDLAEELFI---SRSTIYRDIKKLN 55 (87)
T ss_dssp HHHHHHHHHH--SEEEHHHHHHHHT-----HHHHHHHHHHHH
T ss_pred HHHHHHHHHc-CCCcCHHHHHHHHCC---CHHHHHHHHHHHH
Confidence 3445555543 478999999999999 9999998887654
No 438
>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=47.65 E-value=19 Score=22.99 Aligned_cols=42 Identities=17% Similarity=0.139 Sum_probs=27.8
Q ss_pred CcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869 66 KTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 66 ~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
+...+.|++|.|...|++.+......-....+|+.++.+.++
T Consensus 55 ~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~l~g 96 (106)
T PF09382_consen 55 SKDDWERLIRQLILEGYLSEDNGGFAYPYLKLTPKGKELLNG 96 (106)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE-GGGHHHHCT
T ss_pred CHHHHHHHHHHHHHcCCceecCCcccccEEEECHHHHHHHCC
Confidence 677899999999999999776410002356777777755443
No 439
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=47.56 E-value=49 Score=19.56 Aligned_cols=28 Identities=25% Similarity=0.367 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCC
Q 040869 27 LSSMSLKCAIELGIADIIHSHGRAITLSELVSALDI 62 (131)
Q Consensus 27 ~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~ 62 (131)
+...|++.|+++ .+.|.|..||++.+++
T Consensus 39 iaAA~iY~acr~--------~~~~~t~~eIa~~~~V 66 (71)
T PF00382_consen 39 IAAACIYLACRL--------NGVPRTLKEIAEAAGV 66 (71)
T ss_dssp HHHHHHHHHHHH--------TTSSSSHHHHHHHCTS
T ss_pred HHHHHHHHHHHH--------cCCCcCHHHHHHHhCC
Confidence 455566666653 2579999999999998
No 440
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=47.55 E-value=59 Score=22.99 Aligned_cols=54 Identities=17% Similarity=0.235 Sum_probs=40.5
Q ss_pred CCCCCHHHHHhhcCC------CCC-----CcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869 48 GRAITLSELVSALDI------QPT-----KTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~------~~~-----~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.+|+.+..|++..|. .|+ +...++.+|+.|...|+++.+. .|+ .+|+.++.+.+
T Consensus 65 ~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~----~GR-~lT~~G~~~LD 129 (150)
T PRK09333 65 DGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK----KGR-VITPKGRSLLD 129 (150)
T ss_pred cCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC----CCC-EeCHHHHHHHH
Confidence 369999999999886 122 2234999999999999999875 454 47888875543
No 441
>PF07120 DUF1376: Protein of unknown function (DUF1376); InterPro: IPR010781 This entry is represented by Bacteriophage PBC5 (Sinorhizobium phage PBC5), Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.
Probab=47.54 E-value=33 Score=21.58 Aligned_cols=45 Identities=7% Similarity=0.015 Sum_probs=33.4
Q ss_pred CCCCCC--HHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869 47 HGRAIT--LSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA 100 (131)
Q Consensus 47 ~~~~~s--~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~ 100 (131)
.++|+. .+.||..+|+ .+..-.+++..+...++ ... +|++.+...
T Consensus 35 ~~~plp~d~~~Lar~~~~---s~~~~~~a~~~ll~~f~-~~~-----dg~~~~~r~ 81 (88)
T PF07120_consen 35 TEGPLPDDDKRLARICGC---STKEWRKALDFLLREFF-RLE-----DGRWWNKRC 81 (88)
T ss_pred hCCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHhCC-CCC-----CCCEehHHH
Confidence 367777 5559999999 88888888888888877 333 577776554
No 442
>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=47.44 E-value=18 Score=23.78 Aligned_cols=36 Identities=17% Similarity=0.329 Sum_probs=22.5
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
+-.+++.-- ..-+|++|||+.+|+ +...++..++..
T Consensus 22 Q~~~l~lyy--~eDlSlsEIAe~~~i---SRqaV~d~ikr~ 57 (101)
T PF04297_consen 22 QREILELYY--EEDLSLSEIAEELGI---SRQAVYDSIKRA 57 (101)
T ss_dssp HHHHHHHHC--TS---HHHHHHHCTS----HHHHHHHHHHH
T ss_pred HHHHHHHHH--ccCCCHHHHHHHHCC---CHHHHHHHHHHH
Confidence 334555443 356999999999999 888877666653
No 443
>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=47.42 E-value=19 Score=24.54 Aligned_cols=22 Identities=23% Similarity=0.252 Sum_probs=19.2
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+|.+|||..+|. ....+.|-.|
T Consensus 1 MT~eELA~~tG~---srQTINrWvR 22 (122)
T PF07037_consen 1 MTPEELAELTGY---SRQTINRWVR 22 (122)
T ss_pred CCHHHHHHHhCc---cHHHHHHHHH
Confidence 588999999999 8888888877
No 444
>COG3703 ChaC Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]
Probab=47.06 E-value=25 Score=25.79 Aligned_cols=37 Identities=11% Similarity=0.152 Sum_probs=28.2
Q ss_pred CCCCHH----HHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 49 RAITLS----ELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 49 ~~~s~~----eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
++.+.+ .||.++|.++++.+.|.+++..|..+|+=.+
T Consensus 130 g~l~~~~~A~~ia~a~G~sG~n~eYL~~t~~hL~~~gi~d~ 170 (190)
T COG3703 130 GDLDAEQIAAIIAAAVGLSGPNAEYLFNTLQHLRKLGIRDH 170 (190)
T ss_pred CCCcHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHhcCCcch
Confidence 445554 4556667777788999999999999998654
No 445
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=47.02 E-value=53 Score=18.60 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=35.6
Q ss_pred HHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 42 DIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 42 d~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
+++.+ .+++|++++-..+|+ +....--+|-++=..|+....+
T Consensus 3 ~~~~~-~~~itv~~~rd~lg~---sRK~ai~lLE~lD~~g~T~R~g 44 (50)
T PF09107_consen 3 ELLQK-NGEITVAEFRDLLGL---SRKYAIPLLEYLDREGITRRVG 44 (50)
T ss_dssp HHHHT-TSSBEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHhc-CCcCcHHHHHHHHCc---cHHHHHHHHHHHhccCCEEEeC
Confidence 55654 689999999999999 8888999999999999988774
No 446
>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=47.02 E-value=21 Score=20.72 Aligned_cols=22 Identities=14% Similarity=0.134 Sum_probs=18.5
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
.|..|+|+.+|+ ++..|++.-+
T Consensus 1 ~s~~eva~~~gv---s~~tlr~w~~ 22 (68)
T cd01104 1 YTIGAVARLTGV---SPDTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHH
Confidence 378999999999 8888887654
No 447
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=46.98 E-value=21 Score=25.12 Aligned_cols=25 Identities=16% Similarity=0.294 Sum_probs=17.9
Q ss_pred HHhCC-CCCCHHHHHhhcCCCCCCcchHH
Q 040869 44 IHSHG-RAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 44 l~~~~-~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
+.+.| ...|.++||++.|+ ++..+|
T Consensus 21 f~e~G~~~tSi~~Ia~~aGv---sk~~lY 46 (192)
T PRK14996 21 ALAEGFAAMTVRRIASEAQV---AAGQVH 46 (192)
T ss_pred HHhcChhhccHHHHHHHhCC---CcHHHH
Confidence 44334 56899999999999 555544
No 448
>PRK09726 antitoxin HipB; Provisional
Probab=46.85 E-value=19 Score=22.56 Aligned_cols=24 Identities=25% Similarity=0.275 Sum_probs=18.8
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
..+|..++|+++|+ .+..+.++.+
T Consensus 24 ~gltq~elA~~~gv---s~~tis~~e~ 47 (88)
T PRK09726 24 NGWTQSELAKKIGI---KQATISNFEN 47 (88)
T ss_pred cCCCHHHHHHHHCc---CHHHHHHHHC
Confidence 56999999999998 6666666555
No 449
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=46.81 E-value=22 Score=33.87 Aligned_cols=65 Identities=8% Similarity=0.067 Sum_probs=48.8
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc---------CcccChHHhHHh
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK---------DKPYCMSPTVSA 118 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~---------~~~~sl~~~~~~ 118 (131)
-||.|+.++|+.+|+ ++..+...|+.|...|.+-+.. +..|+...+-+.+.+ -.|-+-..+..|
T Consensus 987 ~gp~~~~~~a~~~gl---~~~~~~~~l~~l~~~g~~~~~~----~~~wc~~~~l~r~~r~sl~~lR~~~~pv~~~~~~~f 1059 (1490)
T PRK09751 987 HALVTAEQLAHEFSL---GIAIVEEQLQQLREQGLVMNLQ----QDIWVSDEVFRRLRLRSLQAAREATRPVAATTYARL 1059 (1490)
T ss_pred cCCCcHHHHHHHhCC---CHHHHHHHHHHHHhCCCEEecC----CCcccchHHHHHHHHHHHHHHHhhcCCCCHHHHHHH
Confidence 489999999999999 9999999999999999888733 456888776543321 234455555555
Q ss_pred h
Q 040869 119 F 119 (131)
Q Consensus 119 ~ 119 (131)
.
T Consensus 1060 l 1060 (1490)
T PRK09751 1060 L 1060 (1490)
T ss_pred h
Confidence 4
No 450
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=46.77 E-value=20 Score=23.27 Aligned_cols=31 Identities=10% Similarity=0.172 Sum_probs=25.5
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+|..|+++.+|+ ++. ++.-|+..|++....
T Consensus 7 ~lt~~Elc~~~gi---~~~----~l~eLve~GlIep~~ 37 (101)
T PRK10265 7 TFTITEFCLHTGV---SEE----ELNEIVGLGVIEPRE 37 (101)
T ss_pred EeeHHHHHHHHCc---CHH----HHHHHHHCCCeecCC
Confidence 5899999999999 776 556678899999754
No 451
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=46.77 E-value=38 Score=22.50 Aligned_cols=31 Identities=16% Similarity=0.183 Sum_probs=27.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC 82 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl 82 (131)
...|+.+||+..|+ ++..+++-.+.....|.
T Consensus 28 ~g~sv~evA~e~gI---s~~tl~~W~r~y~~~~~ 58 (121)
T PRK09413 28 PGMTVSLVARQHGV---AASQLFLWRKQYQEGSL 58 (121)
T ss_pred CCCCHHHHHHHHCc---CHHHHHHHHHHHhhccc
Confidence 57899999999999 99999999998865543
No 452
>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=46.76 E-value=21 Score=23.87 Aligned_cols=28 Identities=18% Similarity=0.334 Sum_probs=23.6
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
++..|+|+.+|+ ++..| |+-...|++..
T Consensus 1 m~I~e~a~~~gv---s~~tl----R~Ye~~GLl~~ 28 (126)
T cd04783 1 LTIGELAKAAGV---NVETI----RYYQRRGLLPE 28 (126)
T ss_pred CCHHHHHHHHCc---CHHHH----HHHHHCCCCCC
Confidence 478999999999 76654 88899999983
No 453
>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=46.52 E-value=31 Score=21.81 Aligned_cols=44 Identities=11% Similarity=0.114 Sum_probs=27.3
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
++..|+|+.+|+ ++..++.. ...|++.......|...|....+.
T Consensus 1 ~~~~eva~~~gi---~~~tlr~~----~~~Gll~~~~~~~g~r~y~~~dv~ 44 (100)
T cd00592 1 YTIGEVAKLLGV---SVRTLRYY----EEKGLLPPERSENGYRLYSEEDLE 44 (100)
T ss_pred CCHHHHHHHHCc---CHHHHHHH----HHCCCcCCCcCCCCCcccCHHHHH
Confidence 478999999999 77766555 557887632211223446555443
No 454
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=46.49 E-value=30 Score=21.96 Aligned_cols=32 Identities=25% Similarity=0.284 Sum_probs=27.0
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF 83 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~ 83 (131)
.+.++.++|..+|+ ++..|.|..+......+.
T Consensus 35 ~~~~l~~la~~~g~---S~~~l~r~f~~~~g~s~~ 66 (127)
T COG2207 35 EPLTLEDLARRLGM---SRRTLSRLFKKETGTSPS 66 (127)
T ss_pred CCCCHHHHHHHHCC---CHHHHHHHHHHHHCCCHH
Confidence 56999999999999 999999999866665553
No 455
>PLN03239 histone acetyltransferase; Provisional
Probab=46.32 E-value=80 Score=25.44 Aligned_cols=52 Identities=6% Similarity=0.081 Sum_probs=37.1
Q ss_pred HhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 24 FSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 24 ~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+||....+....+. ...+..+|+.+|++.+|+ .+ .-++.+|..+|++....
T Consensus 264 ~~YW~~~il~~L~~~------~~~~~~~si~dis~~Tgi---~~---~DIi~tL~~l~~l~~~~ 315 (351)
T PLN03239 264 IPYWGSTIVDFLLNH------SGNDSSLSIMDIAKKTSI---MA---EDIVFALNQLGILKFIN 315 (351)
T ss_pred HHHHHHHHHHHHHhc------cCCCCCccHHHHHHHhCC---CH---HHHHHHHHHCCcEEEEC
Confidence 367777777765432 111257999999999999 33 35788899999998763
No 456
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=46.28 E-value=32 Score=25.14 Aligned_cols=34 Identities=12% Similarity=0.204 Sum_probs=26.4
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHH
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRL 73 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~Rl 73 (131)
+.-|..|+..+. .+.|..|||+++++ ++.++..-
T Consensus 136 T~RE~eVL~ll~---~G~snkeIA~~L~i---S~~TV~~h 169 (207)
T PRK11475 136 SPTEREILRFMS---RGYSMPQIAEQLER---NIKTIRAH 169 (207)
T ss_pred CHHHHHHHHHHH---CCCCHHHHHHHHCC---CHHHHHHH
Confidence 346677888887 46999999999999 77765533
No 457
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=46.04 E-value=26 Score=25.58 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=17.4
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFR 72 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~R 72 (131)
..+|..+||+++|+ .+..+|+
T Consensus 23 ~~lsmr~lA~~lgv---~~~slY~ 43 (205)
T PRK13756 23 EGLTTRKLAQKLGV---EQPTLYW 43 (205)
T ss_pred ccCCHHHHHHHhCC---CchHHHH
Confidence 57999999999999 6666664
No 458
>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=45.94 E-value=22 Score=20.71 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=17.3
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
.|..|+|+.+|+ ++..|+..-+
T Consensus 1 ~~i~evA~~~gv---s~~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIGV---KPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHH
Confidence 478999999999 8887765544
No 459
>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=45.94 E-value=35 Score=20.79 Aligned_cols=36 Identities=14% Similarity=0.209 Sum_probs=27.3
Q ss_pred CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 52 TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 52 s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
.+.++++..++.|.....+..++..|...|++....
T Consensus 31 ~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~~~~ 66 (87)
T cd08768 31 VYEELCEEIGVDPLTQRRISDLLSELEMLGLLETEV 66 (87)
T ss_pred HHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeEEEE
Confidence 356777777875556667888888899999998654
No 460
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=45.91 E-value=35 Score=24.88 Aligned_cols=29 Identities=24% Similarity=0.468 Sum_probs=24.3
Q ss_pred CCCC-CCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869 47 HGRA-ITLSELVSALDIQPTKTTGLFRLMRLLV 78 (131)
Q Consensus 47 ~~~~-~s~~eLA~~~~~~~~~~~~l~RlLr~L~ 78 (131)
++.| +|..+||+.+++ ++..+..++..|.
T Consensus 16 sg~pgls~~~La~~l~~---~~~~v~~~l~~L~ 45 (188)
T PRK00135 16 SGEEGLSLEQLAEILEL---EPTEVQQLLEELQ 45 (188)
T ss_pred cCCCCCCHHHHHHHHCC---CHHHHHHHHHHHH
Confidence 3666 999999999999 8777888888774
No 461
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=45.87 E-value=45 Score=23.27 Aligned_cols=47 Identities=15% Similarity=0.079 Sum_probs=31.4
Q ss_pred HHHHhChHHHHHhC-CCCCCHHHHHhhcCCCCC--Cc----chHHHHHHHhhcC
Q 040869 34 CAIELGIADIIHSH-GRAITLSELVSALDIQPT--KT----TGLFRLMRLLVHS 80 (131)
Q Consensus 34 ~a~~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~--~~----~~l~RlLr~L~~~ 80 (131)
+..+..|+..|.+. +..+|-++|++.+..+.. .+ ..+.||.+-|...
T Consensus 156 t~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~~ 209 (228)
T PRK11083 156 TRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAI 209 (228)
T ss_pred CHHHHHHHHHHHhCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhccC
Confidence 44566777888753 356999999999987211 12 2477888888543
No 462
>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=45.65 E-value=41 Score=19.51 Aligned_cols=39 Identities=21% Similarity=0.350 Sum_probs=21.9
Q ss_pred hHHHHHhCCCCCCHHHHHhhc----CCCCCCcc----hHHHHHHHhhcCCcee
Q 040869 40 IADIIHSHGRAITLSELVSAL----DIQPTKTT----GLFRLMRLLVHSSCFN 84 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~----~~~~~~~~----~l~RlLr~L~~~gl~~ 84 (131)
|++.+. ++.|+++|++++ ++ ++. .+..++..|...|+++
T Consensus 22 Iw~~~~---g~~t~~ei~~~l~~~y~~---~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 22 IWELLD---GPRTVEEIVDALAEEYDV---DPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHH-----SSS-HHHHHHHHHHHTT-----HHHHHHHHHHHHHHHHHTT---
T ss_pred HHHHcc---CCCCHHHHHHHHHHHcCC---CHHHHHHHHHHHHHHHHHCcCcC
Confidence 555553 678888877654 45 444 3677888888888763
No 463
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=45.47 E-value=35 Score=23.70 Aligned_cols=36 Identities=14% Similarity=0.206 Sum_probs=33.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
-++|-.+||..+|. ....+.|++.-|...|++....
T Consensus 170 ~~~~~~~ia~~~g~---~~~~vsr~l~~l~~~g~i~~~~ 205 (214)
T COG0664 170 LPLTHKDLAEYLGL---SRETVSRILKELRKDGLISVRG 205 (214)
T ss_pred ccCCHHHHHHHhCC---chhhHHHHHHHHHhCCcEeeCC
Confidence 37999999999999 9999999999999999999763
No 464
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=45.47 E-value=36 Score=26.24 Aligned_cols=61 Identities=16% Similarity=0.240 Sum_probs=46.7
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcce-ecchhcccccc
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAY-GLTAASTLLIK 106 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y-~~t~~s~~L~~ 106 (131)
-+|..|..+.+ ...|...-|+++++ ..+.+.|-++.|. ..-+|.+.+ +.+ .+|+.++.|..
T Consensus 4 ~~L~~f~avae--~g~S~s~AA~~L~i---SQpavS~~I~~LE~~lG~~LF~R~~-----r~~~~LT~~G~~l~~ 68 (324)
T PRK12681 4 QQLRYIVEVVN--HNLNVSATAEGLYT---SQPGISKQVRMLEDELGIQIFARSG-----KHLTQVTPAGEEIIR 68 (324)
T ss_pred HHHHHHHHHHH--ccCCHHHHHHHhcC---CcHHHHHHHHHHHHHhCCEeEEECC-----CCCCccCHHHHHHHH
Confidence 35778888874 23589999999999 8888888888875 455888873 555 69999987754
No 465
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.47 E-value=34 Score=23.74 Aligned_cols=39 Identities=13% Similarity=0.298 Sum_probs=33.5
Q ss_pred hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869 40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF 83 (131)
Q Consensus 40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~ 83 (131)
+|+.+. .+++|..|+|++.|+ ....+++.++..-..|..
T Consensus 13 ~~~~~~--~~G~S~re~Ak~~gv---s~sTvy~wv~r~~e~G~~ 51 (138)
T COG3415 13 VVDAVV--GEGLSCREAAKRFGV---SISTVYRWVRRYRETGLD 51 (138)
T ss_pred HHHHHH--HcCccHHHHHHHhCc---cHHHHHHHHHHhcccccc
Confidence 455554 368999999999999 999999999999988887
No 466
>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=45.42 E-value=50 Score=21.40 Aligned_cols=49 Identities=14% Similarity=0.164 Sum_probs=36.7
Q ss_pred HHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869 42 DIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA 99 (131)
Q Consensus 42 d~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~ 99 (131)
+.+-+.-.+.++.+|-+... ....+.|++..++..|++.+ + +++|.++-
T Consensus 20 ~Yl~k~~~~~lLR~iKk~f~----~qk~~D~fie~li~~GYI~r-e----~krY~L~~ 68 (93)
T PF08820_consen 20 NYLLKYMTDFLLRFIKKDFP----KQKRLDIFIEALIKLGYIER-E----EKRYYLNL 68 (93)
T ss_pred HHHHHcCCHhhHHHHHHhhc----cccchhHHHHHHHHcCCeEe-c----CCEEEEec
Confidence 44443325677888877654 35678999999999999999 4 78998873
No 467
>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=45.40 E-value=18 Score=21.85 Aligned_cols=32 Identities=19% Similarity=0.220 Sum_probs=25.3
Q ss_pred HHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869 53 LSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 53 ~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
++.++.+++.. +++.+.|+.|.|..+|+...-
T Consensus 18 ie~~~~~~~~~--~~e~~~rf~~~L~~~Gv~~~L 49 (69)
T PF09269_consen 18 IERLVAMTNFD--DEESLRRFQRKLKKMGVEKAL 49 (69)
T ss_dssp HHHHHTTEEE---TGGGHHHHHHHHHHTTHHHHH
T ss_pred HHHHHHhcCCC--CHHHHHHHHHHHHHCCHHHHH
Confidence 56677777763 778999999999999988763
No 468
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=45.30 E-value=40 Score=17.26 Aligned_cols=23 Identities=26% Similarity=0.419 Sum_probs=17.4
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
..+|..++|+.+|+ ++..+.++.
T Consensus 9 ~~~s~~~la~~~~i---~~~~i~~~~ 31 (56)
T smart00530 9 KGLTQEELAEKLGV---SRSTLSRIE 31 (56)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHH
Confidence 46889999999998 666666543
No 469
>PRK10130 transcriptional regulator EutR; Provisional
Probab=45.20 E-value=34 Score=27.22 Aligned_cols=49 Identities=16% Similarity=0.156 Sum_probs=34.7
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI 105 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~ 105 (131)
..++|+.+||+.+|+ +++.|.|..+..........- ..+++...-+.|.
T Consensus 254 ~~~ltv~~lA~~~gv---S~r~L~r~Fk~~~G~sp~~yl------r~~RL~~ar~lL~ 302 (350)
T PRK10130 254 SEPVTVLDLCNQLHV---SRRTLQNAFHAILGIGPNAWL------KRIRLNAVRRELI 302 (350)
T ss_pred cCCCCHHHHHHHHCC---CHHHHHHHHHHHHCcCHHHHH------HHHHHHHHHHHHh
Confidence 368999999999999 999999998876655544432 2344454444454
No 470
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=45.11 E-value=40 Score=24.72 Aligned_cols=60 Identities=17% Similarity=0.223 Sum_probs=44.9
Q ss_pred HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc---CCceeecccCCCCcceecchhccccccC
Q 040869 37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH---SSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~---~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
.|.+|..+.+ .-|...-|+++++ .+..+.+-++.|.. .-+|.+.. +.+.+|+.++.|...
T Consensus 5 ~L~~F~~v~~---~~s~t~AA~~L~i---sqsavS~~I~~LE~~lg~~Lf~R~~-----~~~~lT~~G~~l~~~ 67 (297)
T COG0583 5 QLRAFVAVAE---EGSFTRAAERLGL---SQSAVSRQIKRLEEELGVPLFERTT-----RRVRLTEAGERLLER 67 (297)
T ss_pred HHHHHHHHHH---cCcHHHHHHHhCC---CChHHHHHHHHHHHHhCchheeecC-----CceeeCHhHHHHHHH
Confidence 4677888874 5688899999999 77777777777753 45788764 449999999876543
No 471
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=44.87 E-value=16 Score=30.29 Aligned_cols=24 Identities=13% Similarity=0.361 Sum_probs=22.2
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
.|+|..+||+.+|+ +++++.|..+
T Consensus 342 kPLtlkdvAe~lgl---heSTVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGM---HESTISRATT 365 (455)
T ss_pred cCccHHHHHHHhCC---Cccchhhhhc
Confidence 69999999999999 9999999864
No 472
>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=44.84 E-value=21 Score=21.19 Aligned_cols=35 Identities=17% Similarity=0.229 Sum_probs=18.3
Q ss_pred CCCCCHHHHHhhc---CCCCCCcchHHHHHHHhhcCCceeec
Q 040869 48 GRAITLSELVSAL---DIQPTKTTGLFRLMRLLVHSSCFNKT 86 (131)
Q Consensus 48 ~~~~s~~eLA~~~---~~~~~~~~~l~RlLr~L~~~gl~~~~ 86 (131)
+..+|+.+|+..+ |.+- +...+.|.|+- .|+....
T Consensus 11 ~p~~s~~~i~~~l~~~~~~v-S~~TI~r~L~~---~g~~~~~ 48 (72)
T PF01498_consen 11 NPRISAREIAQELQEAGISV-SKSTIRRRLRE---AGLKKRK 48 (72)
T ss_dssp -----HHHHHHHT---T--S--HHHHHHHHHH---T-EEEET
T ss_pred CCCCCHHHHHHHHHHccCCc-CHHHHHHHHHH---cCccccc
Confidence 4569999999998 5311 66677777664 5665544
No 473
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=44.78 E-value=27 Score=25.13 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=19.0
Q ss_pred HHHhCC-CCCCHHHHHhhcCCCCCCcchHH
Q 040869 43 IIHSHG-RAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 43 ~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
.+.+.| ...|..+||+++|+ +...+|
T Consensus 30 lf~e~Gy~~~s~~dIA~~aGv---s~gtiY 56 (212)
T PRK15008 30 TFSQFGFHGTRLEQIAELAGV---SKTNLL 56 (212)
T ss_pred HHHHhCcccCCHHHHHHHhCc---CHHHHH
Confidence 344445 56999999999999 555554
No 474
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=44.75 E-value=52 Score=23.08 Aligned_cols=55 Identities=16% Similarity=0.213 Sum_probs=41.9
Q ss_pred CCCCCHHHHHhhcCC------CCC-----CcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869 48 GRAITLSELVSALDI------QPT-----KTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD 107 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~------~~~-----~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~ 107 (131)
.+|+.++-|.+.-|- .|+ .....+.+|..|...|++++.+ .|+ ..||.++.|+++
T Consensus 65 ~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~----~GR-~ltp~GrsllD~ 130 (147)
T COG2238 65 DGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP----KGR-VLTPKGRSLLDR 130 (147)
T ss_pred cCchhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC----CCc-eeCccchhHHHH
Confidence 478999999988773 121 4456889999999999999985 343 778888877654
No 475
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=44.75 E-value=22 Score=26.92 Aligned_cols=25 Identities=16% Similarity=0.295 Sum_probs=21.4
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMRL 76 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~ 76 (131)
.++|..|||+.+|+ ++..+.++.+.
T Consensus 235 ~~~t~~eIA~~lgv---S~~~V~q~~~~ 259 (270)
T TIGR02392 235 DKLTLQELAAEYGV---SAERIRQIEKN 259 (270)
T ss_pred CCcCHHHHHHHHCC---CHHHHHHHHHH
Confidence 58999999999999 88888876654
No 476
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=44.63 E-value=35 Score=25.09 Aligned_cols=36 Identities=14% Similarity=0.074 Sum_probs=27.1
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+--+..|+..+. .+.|..|||+++++ ++.++...+.
T Consensus 157 t~rE~~Vl~l~~---~G~s~~eIA~~L~i---S~~TVk~~~~ 192 (216)
T PRK10100 157 THREKEILNKLR---IGASNNEIARSLFI---SENTVKTHLY 192 (216)
T ss_pred CHHHHHHHHHHH---cCCCHHHHHHHhCC---CHHHHHHHHH
Confidence 445667888887 36999999999999 7777654443
No 477
>COG3177 Fic family protein [Function unknown]
Probab=44.60 E-value=35 Score=27.12 Aligned_cols=37 Identities=16% Similarity=0.214 Sum_probs=35.0
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK 87 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~ 87 (131)
++.+|+.+++...++ ......|-+..|...|++.+.+
T Consensus 302 ~~~~t~~~~~~~~~~---s~~Ta~r~l~~l~~~g~l~~~~ 338 (348)
T COG3177 302 EGYLTAAEIEAILGV---SKATATRDLKELLELGILEEVK 338 (348)
T ss_pred CCCccHHHHHHHhCc---cHHHHHHHHHHHHhCCCeeecC
Confidence 578999999999999 9999999999999999999985
No 478
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=44.42 E-value=24 Score=24.56 Aligned_cols=23 Identities=17% Similarity=0.238 Sum_probs=18.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
..+|..|||+.+|+ ++..++..+
T Consensus 149 ~g~s~~EIA~~lgi---s~~tVk~~l 171 (183)
T TIGR02999 149 AGLTVEEIAELLGV---SVRTVERDW 171 (183)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHH
Confidence 57999999999999 777766443
No 479
>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=44.41 E-value=13 Score=20.37 Aligned_cols=16 Identities=6% Similarity=-0.097 Sum_probs=8.4
Q ss_pred cchHHHHHHHhhcCCc
Q 040869 67 TTGLFRLMRLLVHSSC 82 (131)
Q Consensus 67 ~~~l~RlLr~L~~~gl 82 (131)
+....+++..+..+|+
T Consensus 26 ~~~~~~i~~~~~~l~~ 41 (52)
T cd01392 26 EETRERVLAAAEELGY 41 (52)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 3345555555555554
No 480
>PRK10651 transcriptional regulator NarL; Provisional
Probab=44.28 E-value=38 Score=23.34 Aligned_cols=37 Identities=16% Similarity=0.215 Sum_probs=27.0
Q ss_pred HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
.-+..|+..+. ...+..+||+++++ ++..+...++.+
T Consensus 158 ~rE~~vl~~l~---~g~~~~~ia~~l~i---s~~tV~~~~~~l 194 (216)
T PRK10651 158 PRERDILKLIA---QGLPNKMIARRLDI---TESTVKVHVKHM 194 (216)
T ss_pred HHHHHHHHHHH---cCCCHHHHHHHcCC---CHHHHHHHHHHH
Confidence 35667777776 45889999999999 777766555544
No 481
>PRK09526 lacI lac repressor; Reviewed
Probab=44.09 E-value=19 Score=27.54 Aligned_cols=24 Identities=13% Similarity=0.288 Sum_probs=19.7
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+..|..|||++.|+ +..++.|+|+
T Consensus 4 ~~~ti~dIA~~aGV---S~~TVSrvLn 27 (342)
T PRK09526 4 KPVTLYDVARYAGV---SYQTVSRVLN 27 (342)
T ss_pred CCCcHHHHHHHhCC---CHHHHHHHhc
Confidence 45799999999999 7777777775
No 482
>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=43.90 E-value=28 Score=22.47 Aligned_cols=44 Identities=16% Similarity=0.116 Sum_probs=28.7
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS 101 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s 101 (131)
++..|+|+.+|+ ++.. +|+-...|++.......|...|....+.
T Consensus 2 ~~i~eva~~~gv---s~~t----lR~ye~~Gll~~~r~~~g~R~Y~~~~l~ 45 (102)
T cd04789 2 YTISELAEKAGI---SRST----LLYYEKLGLITGTRNANGYRLYPDSDLQ 45 (102)
T ss_pred CCHHHHHHHHCc---CHHH----HHHHHHCCCCCCCcCCCCCeeCCHHHHH
Confidence 578999999999 6664 5577778999753211223446555443
No 483
>PRK10403 transcriptional regulator NarP; Provisional
Probab=43.69 E-value=39 Score=23.18 Aligned_cols=36 Identities=19% Similarity=0.271 Sum_probs=25.1
Q ss_pred HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869 36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL 77 (131)
Q Consensus 36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L 77 (131)
-+..|+..+. ...|..+||+++++ .+.+++..++.+
T Consensus 157 ~e~~vl~~~~---~g~s~~~ia~~l~~---s~~tv~~~~~~i 192 (215)
T PRK10403 157 RELDVLHELA---QGLSNKQIASVLNI---SEQTVKVHIRNL 192 (215)
T ss_pred HHHHHHHHHH---CCCCHHHHHHHcCC---CHHHHHHHHHHH
Confidence 4445666665 34999999999999 888765544443
No 484
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=43.56 E-value=36 Score=23.72 Aligned_cols=23 Identities=17% Similarity=0.281 Sum_probs=17.9
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
.++|..|||+.+|+ +...+.++.
T Consensus 20 ~GlTq~EIAe~LGi---S~~tVs~ie 42 (141)
T PRK03975 20 RGLTQQEIADILGT---SRANVSSIE 42 (141)
T ss_pred cCCCHHHHHHHHCC---CHHHHHHHH
Confidence 57999999999999 776554444
No 485
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=43.56 E-value=25 Score=23.94 Aligned_cols=20 Identities=10% Similarity=0.069 Sum_probs=17.1
Q ss_pred CCCCHHHHHhhcCCCCCCcchHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLF 71 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~ 71 (131)
..+|..|||+.+|+ ++..++
T Consensus 121 ~g~s~~EIA~~lgi---s~~tV~ 140 (160)
T PRK09642 121 EEKSYQEIALQEKI---EVKTVE 140 (160)
T ss_pred hCCCHHHHHHHHCC---CHHHHH
Confidence 56999999999999 777764
No 486
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=43.46 E-value=18 Score=27.43 Aligned_cols=22 Identities=14% Similarity=0.218 Sum_probs=14.6
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+|..|||++.|+ +..++.|+|+
T Consensus 1 ~ti~dIA~~aGV---S~~TVSrvLn 22 (328)
T PRK11303 1 MKLDEIARLAGV---SRTTASYVIN 22 (328)
T ss_pred CCHHHHHHHhCC---CHHHHHHHHc
Confidence 367788888887 5555555553
No 487
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=43.09 E-value=43 Score=24.13 Aligned_cols=36 Identities=19% Similarity=0.215 Sum_probs=28.9
Q ss_pred HhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCC
Q 040869 24 FSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDI 62 (131)
Q Consensus 24 ~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~ 62 (131)
+||-..+.--.|+++|..+.|+ +|..+++|-..+..
T Consensus 88 TGy~sIATAV~AvKlGA~~YLa---KPAdaDdi~aAl~~ 123 (182)
T COG4567 88 TGYASIATAVEAVKLGACDYLA---KPADADDILAALLR 123 (182)
T ss_pred ecchHHHHHHHHHHhhhhhhcC---CCCChHHHHHHHhh
Confidence 4666666677899999999998 58999998877653
No 488
>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=42.42 E-value=10 Score=31.64 Aligned_cols=35 Identities=23% Similarity=0.283 Sum_probs=29.5
Q ss_pred CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869 48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK 85 (131)
Q Consensus 48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~ 85 (131)
...+|++||++.+|+ ++..+.|.|..|+..|++..
T Consensus 532 ~~~~t~~ei~~~~~~---~~~~l~~~L~~l~~~~~l~~ 566 (588)
T PF00888_consen 532 NDSLTVEEISEKTGI---SEEELKRALKSLVKSKILIL 566 (588)
T ss_dssp SSEEEHHHHHHHC------HHHHHHHHHCCCTTTTCSE
T ss_pred CCCccHHHHHHHHCc---CHHHHHHHHHHHHhCCccee
Confidence 467999999999999 99999999999999999974
No 489
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=42.01 E-value=81 Score=22.96 Aligned_cols=55 Identities=16% Similarity=0.168 Sum_probs=39.4
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCC---Ccceecchh
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQ---EEAYGLTAA 100 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~---~~~y~~t~~ 100 (131)
....+|+= .+|+|-.||-+.-|+ + -..+++.|...|++.+.+..+. +-.|..|+.
T Consensus 91 EtLAIIAY-~QPITr~eIe~IRGv---~---s~~~l~~L~ergLI~~~Gr~~~~Grp~ly~TT~~ 148 (186)
T TIGR00281 91 EVLAIIAY-KQPITRARINEIRGV---K---SYQIVDDLVEKGLVVELGRKDTPGRSFIYETTPK 148 (186)
T ss_pred HHHHHHHH-cCCcCHHHHHHHcCC---C---HHHHHHHHHHCCCeEecCcCCCCCCCeeehhhHH
Confidence 34555552 479999999999999 5 3689999999999998732211 234777763
No 490
>PRK13749 transcriptional regulator MerD; Provisional
Probab=41.92 E-value=27 Score=23.65 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=33.1
Q ss_pred CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CCCcceecchhcc
Q 040869 50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQEEAYGLTAAST 102 (131)
Q Consensus 50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~~~~y~~t~~s~ 102 (131)
.+|+.|+|+++|+ +. +-+|+--..|++.....+ .|-..|....+.+
T Consensus 3 ~~tIgelA~~~gv---S~----~tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~r 49 (121)
T PRK13749 3 AYTVSRLALDAGV---SV----HIVRDYLLRGLLRPVACTTGGYGLFDDAALQR 49 (121)
T ss_pred CCcHHHHHHHHCC---CH----HHHHHHHHCCCCCCCCcCCCCCccCCHHHHHH
Confidence 3789999999999 54 468899999999865332 2345576666554
No 491
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=41.77 E-value=39 Score=24.68 Aligned_cols=38 Identities=16% Similarity=0.344 Sum_probs=28.0
Q ss_pred HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchH----HHHHHHh
Q 040869 34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL----FRLMRLL 77 (131)
Q Consensus 34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l----~RlLr~L 77 (131)
+--+..|...|+ .+.|-.|||.++++ .+.++ .++|+-|
T Consensus 150 T~RE~eVL~lla---~G~snkeIA~~L~i---S~~TVk~h~~~i~~KL 191 (211)
T COG2197 150 TPRELEVLRLLA---EGLSNKEIAEELNL---SEKTVKTHVSNILRKL 191 (211)
T ss_pred CHHHHHHHHHHH---CCCCHHHHHHHHCC---CHhHHHHHHHHHHHHc
Confidence 445666778787 57999999999999 66664 4555544
No 492
>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=41.75 E-value=37 Score=21.76 Aligned_cols=45 Identities=16% Similarity=0.153 Sum_probs=28.8
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST 102 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~ 102 (131)
.++.|+|+.+|+ +++.|+ +....|++.......|...|....+.+
T Consensus 2 ~~i~eva~~~gV---s~~tLR----~ye~~Gli~p~r~~~g~R~Ys~~dv~~ 46 (98)
T cd01279 2 YPISVAAELLGI---HPQTLR----VYDRLGLVSPARTNGGGRRYSNNDLEL 46 (98)
T ss_pred cCHHHHHHHHCc---CHHHHH----HHHHCCCCCCCcCCCCCeeECHHHHHH
Confidence 588999999999 766554 446688876422112244576666543
No 493
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=41.74 E-value=20 Score=27.45 Aligned_cols=22 Identities=14% Similarity=0.288 Sum_probs=18.4
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+|..|||+++|+ +..++.|+|+
T Consensus 2 ~Ti~dIA~~agV---S~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGV---STTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCC---CHHHHHHHHc
Confidence 488999999999 7788887775
No 494
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=41.64 E-value=44 Score=23.90 Aligned_cols=26 Identities=19% Similarity=0.388 Sum_probs=19.4
Q ss_pred HHhCC-CCCCHHHHHhhcCCCCCCcchHHH
Q 040869 44 IHSHG-RAITLSELVSALDIQPTKTTGLFR 72 (131)
Q Consensus 44 l~~~~-~~~s~~eLA~~~~~~~~~~~~l~R 72 (131)
+.+.| ..+|..+||++.|+ ++..+|+
T Consensus 25 ~~~~G~~~~si~~IA~~Agv---s~~t~Y~ 51 (203)
T PRK11202 25 SAERSFSSLSLREVAREAGI---APTSFYR 51 (203)
T ss_pred HhcCCcccCCHHHHHHHhCC---CcchHHH
Confidence 34334 57999999999999 6666664
No 495
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=41.64 E-value=29 Score=23.36 Aligned_cols=23 Identities=9% Similarity=0.079 Sum_probs=18.3
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLM 74 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlL 74 (131)
...|..|||+.+|+ ++..++..+
T Consensus 121 ~~~s~~EIA~~l~i---s~~tV~~~~ 143 (154)
T PRK06759 121 VGKTMGEIALETEM---TYYQVRWIY 143 (154)
T ss_pred cCCCHHHHHHHHCC---CHHHHHHHH
Confidence 46999999999999 777655443
No 496
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=41.47 E-value=53 Score=19.94 Aligned_cols=50 Identities=14% Similarity=0.197 Sum_probs=33.0
Q ss_pred CCCCHHHHHhhcCC-C--CCCc----chHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869 49 RAITLSELVSALDI-Q--PTKT----TGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT 98 (131)
Q Consensus 49 ~~~s~~eLA~~~~~-~--~~~~----~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t 98 (131)
.+.|...|...+.. . ..++ ..+.+-|+.++..|.|.+....+-.|+|.++
T Consensus 20 ~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G~sgsfkl~ 76 (77)
T PF00538_consen 20 KGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGKGASGSFKLS 76 (77)
T ss_dssp SSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCSTTSSEEEES
T ss_pred CCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecccCCccceecC
Confidence 56888888876532 1 1133 3588889999999999987421124777764
No 497
>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=41.14 E-value=21 Score=27.09 Aligned_cols=22 Identities=9% Similarity=0.294 Sum_probs=16.3
Q ss_pred CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 51 ITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 51 ~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
.|..|||++.|+ +..++.|+|+
T Consensus 2 ~ti~dIA~~agv---S~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAGV---SMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhCC---CHHHHHHHhC
Confidence 578888888888 6666666654
No 498
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=40.90 E-value=22 Score=27.16 Aligned_cols=24 Identities=13% Similarity=0.279 Sum_probs=20.0
Q ss_pred CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869 49 RAITLSELVSALDIQPTKTTGLFRLMR 75 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr 75 (131)
+..|..|||++.|+ +..++.|.|+
T Consensus 5 ~~~Ti~dIA~~agV---S~~TVSr~Ln 28 (342)
T PRK10014 5 KKITIHDVALAAGV---SVSTVSLVLS 28 (342)
T ss_pred CCCcHHHHHHHhCC---CHHHHHHHHC
Confidence 45799999999999 7788887775
No 499
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=40.88 E-value=46 Score=25.71 Aligned_cols=40 Identities=28% Similarity=0.396 Sum_probs=32.9
Q ss_pred ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869 39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSS 81 (131)
Q Consensus 39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g 81 (131)
.|-|.|..++|.+++.||+..+++ |...+.|..+.++...
T Consensus 59 EI~~el~~~gGRv~~~dL~~~LnV---d~~~ie~~~~~i~~~~ 98 (272)
T PF09743_consen 59 EIKDELYVHGGRVNLVDLAQALNV---DLDHIERRAQEIVKSD 98 (272)
T ss_pred HHHHHHHHcCCceEHHHHHHhcCc---CHHHHHHHHHHHHhCC
Confidence 455566556889999999999999 9999999999877644
No 500
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=40.84 E-value=38 Score=26.88 Aligned_cols=50 Identities=8% Similarity=0.112 Sum_probs=40.7
Q ss_pred CCCCHHHHHhhcCCCCCCcch-HHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869 49 RAITLSELVSALDIQPTKTTG-LFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK 106 (131)
Q Consensus 49 ~~~s~~eLA~~~~~~~~~~~~-l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~ 106 (131)
.++..+++.+..|. +... +...+..|...|++..+ ++++.+|+.++++.+
T Consensus 317 ~gl~~~~~~~~~~~---~~~~~~~~~~~~l~~~gl~~~~-----~~~~~lt~~G~~~~~ 367 (377)
T PRK08599 317 SGVSKARFEEKFGQ---SFEDVFGETIQELQEQGLLEED-----DDHVRLTKKGKFLGN 367 (377)
T ss_pred CCcCHHHHHHHHCc---CHHHHHHHHHHHHHHCCCEEEE-----CCEEEECccHhHHHH
Confidence 57888999999888 6543 66788889999999976 588999999887764
Done!