ADHR - BACSU - GREMLIN Contacts

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ADHR - HTH-type transcriptional regulator AdhR

UniProt:	O06008	Sequences: MNIAQVAKQFGLTAATLRYYERVGLIPPVKRKDSGIRDYDEEDIKWIEFIKCMRNAGLSIEALIEYTTLFTEGDRTVEARKNILADERQRLIEKRKEIDETIKRLDTKIKDYDGKLRENEAKLKSRPKTESLHGSVEQRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	140 (113)
Sequences:	11907 (8321)
Seq/√Len:	782.7

ECOLI - CUER ZNTR SOXR
BACSU - ADHR YYAN YFMP CUER MTA YDFL BLTR BMRR

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_I	102_I	3.518	1.00
40_D	43_D	3.511	1.00
19_Y	23_V	2.692	1.00
15_A	22_R	2.572	1.00
95_R	99_D	2.551	1.00
88_R	106_D	2.341	1.00
85_A	109_I	2.270	1.00
32_K	38_D	2.080	1.00
14_A	18_R	1.919	1.00
2_N	38_D	1.853	1.00
87_E	90_R	1.833	1.00
88_R	92_I	1.823	1.00
81_K	85_A	1.822	1.00
4_A	8_K	1.785	1.00
54_R	60_I	1.779	1.00
6_V	44_I	1.704	1.00
23_V	64_I	1.685	1.00
59_S	62_A	1.677	1.00
6_V	47_I	1.591	1.00
90_R	94_K	1.579	1.00
46_W	67_T	1.556	1.00
51_K	54_R	1.525	1.00
102_I	106_D	1.497	1.00
94_K	97_E	1.489	1.00
46_W	71_T	1.483	1.00
93_E	97_E	1.483	1.00
2_N	5_Q	1.417	1.00
85_A	113_D	1.395	1.00
3_I	18_R	1.392	1.00
84_L	109_I	1.373	1.00
5_Q	8_K	1.348	1.00
25_L	50_I	1.334	1.00
96_K	99_D	1.300	1.00
99_D	102_I	1.275	1.00
92_I	106_D	1.273	1.00
91_L	95_R	1.244	1.00
88_R	102_I	1.235	1.00
79_A	82_N	1.202	1.00
9_Q	44_I	1.201	1.00
107_T	111_D	1.175	1.00
64_I	68_T	1.156	1.00
62_A	65_E	1.151	1.00
6_V	43_D	1.142	1.00
62_A	87_E	1.130	1.00
95_R	98_I	1.130	1.00
21_E	27_P	1.110	1.00
55_N	97_E	1.100	1.00
5_Q	9_Q	1.099	1.00
50_I	63_L	1.094	1.00
30_K	40_D	1.090	1.00
13_T	16_T	1.084	1.00
92_I	95_R	1.083	1.00
17_L	39_Y	1.078	1.00
10_F	47_I	1.078	1.00
7_A	14_A	1.078	1.00
81_K	113_D	1.051	1.00
95_R	102_I	1.008	1.00
92_I	96_K	1.008	1.00
23_V	61_E	1.004	1.00
96_K	100_E	1.001	1.00
30_K	38_D	0.995	1.00
51_K	55_N	0.987	1.00
88_R	109_I	0.986	1.00
4_A	14_A	0.974	1.00
20_Y	47_I	0.970	1.00
93_E	96_K	0.952	1.00
17_L	47_I	0.951	1.00
89_Q	92_I	0.945	1.00
19_Y	60_I	0.940	1.00
72_E	75_R	0.931	1.00
85_A	88_R	0.926	1.00
16_T	19_Y	0.925	1.00
89_Q	93_E	0.921	1.00
61_E	64_I	0.917	1.00
56_A	101_T	0.895	1.00
57_G	94_K	0.887	1.00
44_I	48_E	0.879	1.00
90_R	93_E	0.878	1.00
10_F	44_I	0.871	1.00
99_D	103_K	0.866	1.00
10_F	17_L	0.863	1.00
32_K	36_I	0.862	1.00
82_N	86_D	0.859	1.00
81_K	99_D	0.857	1.00
26_I	43_D	0.849	1.00
26_I	50_I	0.843	1.00
58_L	66_Y	0.829	1.00
21_E	26_I	0.820	1.00
34_S	38_D	0.819	1.00
76_T	80_R	0.816	1.00
29_V	39_Y	0.809	1.00
29_V	43_D	0.808	1.00
2_N	36_I	0.806	1.00
12_L	51_K	0.803	1.00
85_A	89_Q	0.799	1.00
9_Q	41_E	0.798	1.00
94_K	98_I	0.798	1.00
9_Q	48_E	0.794	1.00
41_E	45_K	0.792	1.00
7_A	17_L	0.790	1.00
86_D	89_Q	0.785	1.00
98_I	102_I	0.785	1.00
108_K	111_D	0.784	1.00
80_R	83_I	0.764	1.00
47_I	54_R	0.754	1.00
76_T	79_A	0.748	1.00
6_V	10_F	0.743	1.00
12_L	47_I	0.742	1.00
104_R	108_K	0.736	1.00
110_K	113_D	0.736	1.00
3_I	7_A	0.731	1.00
21_E	39_Y	0.724	1.00
65_E	68_T	0.700	1.00
19_Y	22_R	0.697	1.00
46_W	68_T	0.696	1.00
17_L	21_E	0.694	1.00
103_K	107_T	0.692	1.00
30_K	43_D	0.683	1.00
77_V	80_R	0.673	1.00
78_E	82_N	0.673	1.00
49_F	53_M	0.661	1.00
83_I	87_E	0.646	1.00
54_R	87_E	0.646	1.00
86_D	90_R	0.643	1.00
31_R	37_R	0.640	1.00
45_K	48_E	0.639	1.00
12_L	16_T	0.638	1.00
111_D	114_G	0.631	1.00
82_N	85_A	0.630	1.00
88_R	91_L	0.620	1.00
4_A	36_I	0.619	1.00
48_E	52_C	0.614	1.00
87_E	94_K	0.612	1.00
80_R	84_L	0.612	1.00
24_G	27_P	0.611	1.00
57_G	87_E	0.611	1.00
83_I	86_D	0.606	1.00
107_T	110_K	0.603	1.00
53_M	58_L	0.601	1.00
4_A	7_A	0.589	1.00
73_G	80_R	0.586	1.00
97_E	100_E	0.586	1.00
100_E	103_K	0.583	1.00
91_L	105_L	0.580	1.00
58_L	76_T	0.580	1.00
48_E	51_K	0.579	1.00
23_V	60_I	0.576	1.00
91_L	98_I	0.571	1.00
6_V	26_I	0.571	1.00
52_C	97_E	0.568	1.00
3_I	14_A	0.563	1.00
54_R	59_S	0.562	1.00
13_T	19_Y	0.558	1.00
21_E	29_V	0.551	1.00
70_F	73_G	0.551	1.00
108_K	112_Y	0.550	1.00
32_K	35_G	0.548	1.00
10_F	51_K	0.547	1.00
31_R	34_S	0.545	1.00
21_E	28_P	0.541	1.00
100_E	104_R	0.532	1.00
88_R	95_R	0.530	1.00
42_E	45_K	0.529	1.00
78_E	81_K	0.528	1.00
79_A	83_I	0.527	1.00
2_N	14_A	0.527	1.00
62_A	86_D	0.526	1.00
74_D	77_V	0.513	1.00
66_Y	69_L	0.512	1.00
101_T	104_R	0.500	1.00

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3gpvA	2	0.8214	100	0.215	Contact Map
3gp4A	4	0.9214	100	0.22	Contact Map
1q06A	2	0.9071	99.9	0.244	Contact Map
3qaoA	2	0.8214	99.9	0.255	Contact Map
3hh0A	4	0.9429	99.9	0.262	Contact Map
2dg6A	2	0.9357	99.9	0.264	Contact Map
4ua1A	2	0.8929	99.9	0.281	Contact Map
1r8dA	2	0.7643	99.9	0.287	Contact Map
2vz4A	2	0.7071	99.9	0.293	Contact Map
2zhgA	2	0.8429	99.9	0.297	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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