CUER - ECOLI - GREMLIN Contacts

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CUER - HTH-type transcriptional regulator CueR

UniProt:	P0A9G4	Sequences: MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADVKRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCCHHRAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13256
Length:	135 (114)
Sequences:	12741 (8869)
Seq/√Len:	830.7

ECOLI - CUER ZNTR SOXR
BACSU - ADHR CUER YYAN YFMP MTA BLTR YDFL 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_E	102_R	3.728	1.00
40_T	43_H	3.371	1.00
88_V	106_L	2.952	1.00
95_I	99_Q	2.797	1.00
19_F	23_K	2.749	1.00
85_L	109_A	2.656	1.00
15_K	22_E	2.463	1.00
87_K	90_E	1.944	1.00
32_S	38_T	1.914	1.00
14_S	18_R	1.828	1.00
6_V	44_L	1.822	1.00
4_S	8_K	1.777	1.00
2_N	38_T	1.754	1.00
23_K	64_G	1.713	1.00
88_V	92_E	1.690	1.00
81_K	85_L	1.687	1.00
54_R	60_L	1.686	1.00
102_R	106_L	1.676	1.00
59_N	62_E	1.618	1.00
6_V	47_L	1.604	1.00
88_V	102_R	1.603	1.00
51_R	54_R	1.580	1.00
46_E	71_N	1.576	1.00
94_H	97_E	1.561	1.00
92_E	106_L	1.551	1.00
93_R	97_E	1.527	1.00
99_Q	102_R	1.507	1.00
46_E	67_V	1.453	1.00
81_K	113_P	1.450	1.00
90_E	94_H	1.448	1.00
85_L	113_P	1.436	1.00
95_I	98_L	1.401	1.00
84_T	109_A	1.387	1.00
25_L	50_L	1.336	1.00
2_N	5_D	1.296	1.00
88_V	109_A	1.270	1.00
5_D	8_K	1.270	1.00
92_E	95_I	1.269	1.00
9_I	44_L	1.250	1.00
3_I	18_R	1.246	1.00
62_E	87_K	1.219	1.00
30_M	40_T	1.211	1.00
96_E	99_Q	1.197	1.00
79_D	82_R	1.173	1.00
91_I	95_I	1.160	1.00
13_T	16_A	1.154	1.00
96_E	100_S	1.145	1.00
10_T	47_L	1.137	1.00
6_V	43_H	1.123	1.00
94_H	98_L	1.112	1.00
20_Y	47_L	1.111	1.00
51_R	55_Q	1.091	1.00
95_I	102_R	1.078	1.00
64_G	68_N	1.047	1.00
98_L	102_R	1.041	1.00
50_L	63_S	1.029	1.00
5_D	9_I	1.021	1.00
107_A	111_A	1.017	1.00
7_A	14_S	1.008	1.00
92_E	96_E	0.995	1.00
62_E	65_E	0.977	1.00
21_E	27_T	0.973	1.00
21_E	39_Y	0.965	1.00
57_G	94_H	0.942	1.00
41_Q	45_N	0.935	1.00
4_S	14_S	0.930	1.00
55_Q	97_E	0.927	1.00
17_I	47_L	0.926	1.00
23_K	61_E	0.925	1.00
89_A	93_R	0.914	1.00
93_R	96_E	0.903	1.00
85_L	89_A	0.901	1.00
2_N	36_Y	0.900	1.00
17_I	39_Y	0.900	1.00
61_E	64_G	0.892	1.00
19_F	60_L	0.874	1.00
82_R	86_E	0.868	1.00
89_A	92_E	0.844	1.00
10_T	44_L	0.843	1.00
29_P	39_Y	0.842	1.00
12_L	51_R	0.830	1.00
26_V	43_H	0.819	1.00
87_K	94_H	0.818	1.00
44_L	48_T	0.818	1.00
30_M	38_T	0.817	1.00
26_V	50_L	0.816	1.00
97_E	100_S	0.802	1.00
9_I	48_T	0.789	1.00
9_I	41_Q	0.785	1.00
16_A	19_F	0.785	1.00
10_T	17_I	0.779	1.00
91_I	98_L	0.777	1.00
90_E	93_R	0.770	1.00
86_E	89_A	0.753	1.00
32_S	36_Y	0.751	1.00
58_F	66_L	0.744	1.00
99_Q	103_D	0.742	1.00
12_L	47_L	0.740	1.00
7_A	17_I	0.736	1.00
111_A	114_G	0.731	1.00
31_R	37_R	0.727	1.00
72_D	75_R	0.725	1.00
30_M	43_H	0.725	1.00
34_N	38_T	0.723	1.00
85_L	88_V	0.721	1.00
100_S	103_D	0.716	1.00
29_P	43_H	0.711	1.00
83_R	86_E	0.707	1.00
56_V	101_M	0.703	1.00
49_L	53_A	0.701	1.00
21_E	26_V	0.697	1.00
42_Q	45_N	0.690	1.00
82_R	85_L	0.684	1.00
47_L	54_R	0.681	1.00
13_T	19_F	0.678	1.00
3_I	7_A	0.675	1.00
111_A	115_D	0.675	1.00
76_H	79_D	0.669	1.00
81_K	109_A	0.667	1.00
78_A	82_R	0.667	1.00
62_E	86_E	0.655	1.00
21_E	29_P	0.651	1.00
19_F	22_E	0.646	1.00
31_R	34_N	0.642	1.00
107_A	110_N	0.639	1.00
101_M	104_Q	0.634	1.00
48_T	51_R	0.626	1.00
12_L	16_A	0.624	1.00
94_H	101_M	0.617	1.00
10_T	20_Y	0.611	1.00
43_H	46_E	0.610	1.00
83_R	87_K	0.606	1.00
45_N	48_T	0.604	1.00
110_N	113_P	0.604	1.00
91_I	101_M	0.602	1.00
80_V	83_R	0.600	1.00
86_E	90_E	0.600	1.00
65_E	68_N	0.599	1.00
24_G	27_T	0.592	1.00
91_I	105_L	0.590	1.00
97_E	101_M	0.587	1.00
54_R	63_S	0.586	1.00
91_I	102_R	0.586	1.00
84_T	105_L	0.586	1.00
76_H	80_V	0.581	1.00
100_S	104_Q	0.580	1.00
4_S	36_Y	0.580	1.00
46_E	68_N	0.578	1.00
103_D	107_A	0.574	1.00
52_Q	97_E	0.572	1.00
10_T	51_R	0.572	1.00
32_S	35_G	0.568	1.00
53_A	58_F	0.562	1.00
33_E	38_T	0.560	1.00
10_T	14_S	0.559	1.00
109_A	113_P	0.559	1.00
17_I	21_E	0.549	1.00
70_F	73_P	0.542	1.00
2_N	14_S	0.538	1.00
48_T	52_Q	0.534	1.00
6_V	10_T	0.531	1.00
92_E	99_Q	0.528	1.00
6_V	26_V	0.526	1.00
78_A	81_K	0.515	1.00
88_V	91_I	0.512	1.00
69_L	73_P	0.510	1.00
60_L	63_S	0.510	1.00
21_E	31_R	0.509	1.00
42_Q	46_E	0.506	1.00
88_V	95_I	0.503	1.00
110_N	114_G	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
1q06A	2	0.9407	100	0.165	Contact Map
2dg6A	2	0.9333	100	0.214	Contact Map
3gp4A	4	0.9704	100	0.22	Contact Map
3gpvA	2	0.8519	100	0.223	Contact Map
3hh0A	4	0.9704	100	0.227	Contact Map
2zhgA	2	0.8815	100	0.236	Contact Map
4ua1A	2	0.9185	99.9	0.241	Contact Map
3qaoA	2	0.9556	99.9	0.27	Contact Map
1r8dA	2	0.7926	99.9	0.295	Contact Map
2vz4A	2	0.7333	99.9	0.298	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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