YDGG - BACSU - GREMLIN Contacts

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YDGG - Uncharacterized HTH-type transcriptional regulator YdgG

UniProt:	P96705	Sequences: MNEQKLCQAINLFVEVLLEGTEFVHREINQDVFKHISREQADLLKILKVKGPTSPGSLAMYQNVHKSAISNRLKKLLEKGLVQWDDCPEKSDRRSKLINITPSGEHILEELDSAIFNALKPLIDDIDEEHLHSIIEIFTILKSKFKGGDSAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	152 (131)
Sequences:	24328 (17931)
Seq/√Len:	1566.7

ECOLI - SLYA MPRA MARR
BACSU - YDGG YSMB YFIV YUSO YPOP YWAE YWHA YYBA YCGE MHQR OHRR YDGJ YETL YXAD YKOM YHJH YVMB YWOH YDCH YVNA YBFA
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_D	99_N	3.012	1.00
87_C	91_S	2.780	1.00
130_H	140_I	2.776	1.00
52_P	99_N	2.702	1.00
87_C	97_L	2.571	1.00
54_S	95_S	2.564	1.00
83_Q	99_N	2.547	1.00
127_D	130_H	2.340	1.00
133_S	136_E	2.171	1.00
133_S	137_I	2.137	1.00
48_K	108_L	2.011	1.00
86_D	96_K	2.003	1.00
54_S	57_S	1.967	1.00
40_Q	79_K	1.901	1.00
48_K	100_I	1.889	1.00
87_C	95_S	1.857	1.00
125_D	144_K	1.857	1.00
126_I	137_I	1.846	1.00
130_H	133_S	1.669	1.00
77_L	84_W	1.657	1.00
80_G	103_S	1.617	1.00
134_I	137_I	1.564	1.00
103_S	107_I	1.560	1.00
87_C	90_K	1.534	1.00
55_P	73_L	1.527	1.00
16_V	139_T	1.505	1.00
50_K	61_Y	1.474	1.00
43_L	72_R	1.466	1.00
40_Q	75_K	1.455	1.00
130_H	136_E	1.418	1.00
103_S	106_H	1.418	1.00
73_L	98_I	1.413	1.00
74_K	78_E	1.404	1.00
48_K	105_E	1.399	1.00
37_S	40_Q	1.379	1.00
52_P	97_L	1.368	1.00
107_I	110_E	1.367	1.00
16_V	142_K	1.334	1.00
84_W	96_K	1.321	1.00
46_I	61_Y	1.315	1.00
137_I	140_I	1.255	1.00
34_K	114_A	1.247	1.00
16_V	135_I	1.237	1.00
74_K	93_R	1.217	1.00
136_E	140_I	1.166	1.00
57_S	60_M	1.157	1.00
43_L	69_I	1.150	1.00
31_D	114_A	1.143	1.00
56_G	66_K	1.131	1.00
50_K	53_T	1.128	1.00
65_H	68_A	1.124	1.00
34_K	110_E	1.105	1.00
130_H	137_I	1.087	1.00
56_G	60_M	1.087	1.00
19_E	142_K	1.082	1.00
135_I	139_T	1.073	1.00
106_H	110_E	1.066	1.00
55_P	96_K	1.058	1.00
131_L	135_I	1.049	1.00
67_S	70_S	1.043	1.00
52_P	85_D	1.036	1.00
18_L	21_T	1.029	1.00
20_G	142_K	1.026	1.00
64_V	68_A	1.021	1.00
55_P	66_K	1.015	1.00
129_E	133_S	1.010	1.00
53_T	57_S	0.997	1.00
34_K	111_L	0.989	1.00
55_P	69_I	0.981	1.00
29_N	33_F	0.977	1.00
81_L	107_I	0.974	1.00
51_G	105_E	0.968	1.00
39_E	72_R	0.960	1.00
55_P	98_I	0.954	1.00
70_S	74_K	0.951	1.00
57_S	61_Y	0.941	1.00
64_V	69_I	0.939	1.00
68_A	71_N	0.935	1.00
102_P	105_E	0.933	1.00
53_T	61_Y	0.923	1.00
85_D	97_L	0.922	1.00
47_L	82_V	0.915	1.00
83_Q	101_T	0.910	1.00
133_S	140_I	0.905	1.00
65_H	71_N	0.905	1.00
100_I	104_G	0.899	1.00
23_F	142_K	0.896	1.00
102_P	106_H	0.891	1.00
27_E	118_A	0.891	1.00
114_A	117_N	0.882	1.00
74_K	77_L	0.881	1.00
79_K	103_S	0.873	1.00
21_T	25_H	0.870	1.00
35_H	79_K	0.868	1.00
119_L	122_L	0.867	1.00
105_E	109_E	0.867	1.00
20_G	138_F	0.862	1.00
128_E	132_H	0.859	1.00
115_I	119_L	0.855	1.00
48_K	112_D	0.829	1.00
86_D	93_R	0.825	1.00
51_G	99_N	0.819	1.00
43_L	58_L	0.809	1.00
81_L	103_S	0.802	1.00
87_C	92_D	0.798	1.00
13_F	135_I	0.796	1.00
117_N	120_K	0.794	1.00
100_I	105_E	0.792	1.00
79_K	107_I	0.792	1.00
113_S	117_N	0.789	1.00
44_L	108_L	0.788	1.00
42_D	62_Q	0.782	1.00
90_K	97_L	0.776	1.00
31_D	117_N	0.774	1.00
73_L	82_V	0.772	1.00
46_I	62_Q	0.770	1.00
71_N	74_K	0.760	1.00
92_D	95_S	0.757	1.00
126_I	141_L	0.757	1.00
50_K	57_S	0.752	1.00
127_D	131_L	0.751	1.00
75_K	78_E	0.744	1.00
31_D	121_P	0.736	1.00
59_A	69_I	0.729	1.00
48_K	109_E	0.728	1.00
77_L	83_Q	0.728	1.00
46_I	50_K	0.722	1.00
39_E	68_A	0.720	1.00
41_A	111_L	0.717	1.00
123_I	131_L	0.713	1.00
121_P	124_D	0.712	1.00
75_K	79_K	0.712	1.00
55_P	70_S	0.712	1.00
74_K	84_W	0.708	1.00
18_L	22_E	0.706	1.00
132_H	135_I	0.702	1.00
139_T	143_S	0.701	1.00
86_D	90_K	0.694	1.00
71_N	75_K	0.694	1.00
77_L	82_V	0.692	1.00
113_S	116_F	0.690	1.00
106_H	109_E	0.677	1.00
73_L	77_L	0.676	1.00
132_H	136_E	0.676	1.00
25_H	29_N	0.667	1.00
59_A	66_K	0.663	1.00
69_I	73_L	0.658	1.00
46_I	58_L	0.658	1.00
22_E	26_R	0.653	1.00
46_I	53_T	0.653	1.00
110_E	114_A	0.651	1.00
126_I	131_L	0.651	1.00
129_E	132_H	0.650	1.00
31_D	118_A	0.647	1.00
17_L	21_T	0.646	1.00
84_W	98_I	0.644	1.00
117_N	121_P	0.638	1.00
27_E	30_Q	0.629	1.00
29_N	38_R	0.628	1.00
17_L	20_G	0.626	1.00
43_L	62_Q	0.624	1.00
28_I	31_D	0.622	1.00
20_G	141_L	0.622	1.00
140_I	144_K	0.613	1.00
45_K	49_V	0.609	1.00
137_I	144_K	0.605	1.00
47_L	100_I	0.600	1.00
118_A	121_P	0.588	1.00
112_D	116_F	0.583	1.00
116_F	120_K	0.581	1.00
16_V	19_E	0.580	1.00
12_L	135_I	0.578	1.00
47_L	53_T	0.576	1.00
27_E	121_P	0.574	1.00
41_A	115_I	0.563	1.00
56_G	59_A	0.554	1.00
108_L	112_D	0.553	1.00
76_L	81_L	0.553	1.00
42_D	46_I	0.549	1.00
80_G	83_Q	0.544	1.00
110_E	113_S	0.542	1.00
45_K	112_D	0.539	1.00
24_V	27_E	0.539	1.00
25_H	28_I	0.536	1.00
41_A	108_L	0.527	1.00
139_T	142_K	0.524	1.00
17_L	138_F	0.522	1.00
123_I	127_D	0.518	1.00
127_D	140_I	0.517	1.00
58_L	98_I	0.513	1.00
39_E	64_V	0.512	1.00
28_I	115_I	0.512	1.00
86_D	92_D	0.509	1.00
115_I	118_A	0.502	1.00
26_R	30_Q	0.501	1.00
27_E	31_D	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
3cdhA	4	0.8816	99.9	0.29	Contact Map
3bj6A	2	0.9737	99.9	0.292	Contact Map
2rdpA	2	0.9145	99.9	0.292	Contact Map
2nnnA	2	0.8816	99.9	0.293	Contact Map
3boqA	2	0.8618	99.9	0.294	Contact Map
3cjnA	2	0.9211	99.9	0.297	Contact Map
3e6mA	2	0.9474	99.9	0.299	Contact Map
4yifA	2	0.9276	99.9	0.3	Contact Map
1s3jA	2	0.9408	99.9	0.3	Contact Map
3deuA	2	0.8553	99.9	0.3	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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