YDCN - ECOLI - GREMLIN Contacts

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YDCN - Uncharacterized HTH-type transcriptional regulator YdcN

UniProt:	P77626	Sequences: MENLARFLSTTLKQLRQQRGWSLSRLAEATGVSKAMLGQIERNESSPTVATLWKIATGLNVPFSTFISPPQSATPSVYDPQQQAMVITSLFPYDPQLCFEHFSIQMASGAISESTPHEKGVIEHVVVIDGQLDLCVDGEWQTLNCGEGVRFAADVTHIYRNGGEQTVHFHSLIHYPRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13757
Length:	178 (167)
Sequences:	5976 (4018)
Seq/√Len:	310.9

ECOLI - YDCN PUUR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
131_Q	144_N	4.038	1.00
129_D	168_H	3.840	1.00
133_D	140_W	3.122	1.00
133_D	160_R	3.020	1.00
132_L	167_V	2.925	1.00
133_D	142_T	2.915	1.00
133_D	162_G	2.864	1.00
103_S	168_H	2.856	1.00
131_Q	142_T	2.727	1.00
105_Q	166_T	2.628	1.00
107_A	166_T	2.319	1.00
105_Q	168_H	2.259	1.00
129_D	145_C	2.179	1.00
25_R	29_A	2.104	1.00
24_S	28_E	2.080	1.00
23_L	37_L	1.917	1.00
137_D	155_V	1.893	1.00
135_C	140_W	1.889	1.00
14_Q	18_Q	1.862	1.00
15_L	61_V	1.849	1.00
134_L	149_V	1.816	1.00
26_L	59_L	1.782	1.00
25_R	28_E	1.776	1.00
24_S	34_K	1.758	1.00
111_I	160_R	1.743	1.00
101_H	124_H	1.724	1.00
119_K	123_E	1.637	1.00
125_V	171_S	1.633	1.00
143_L	147_E	1.623	1.00
128_I	170_H	1.611	1.00
135_C	160_R	1.590	1.00
129_D	165_Q	1.578	1.00
123_E	157_H	1.550	1.00
125_V	149_V	1.546	1.00
132_L	169_F	1.544	1.00
135_C	158_I	1.526	1.00
36_M	40_I	1.521	1.00
33_S	36_M	1.483	1.00
101_H	172_L	1.481	1.00
131_Q	163_G	1.467	1.00
21_W	29_A	1.466	1.00
7_F	43_N	1.443	1.00
126_V	170_H	1.440	1.00
32_V	51_T	1.376	1.00
131_Q	162_G	1.375	1.00
142_T	162_G	1.353	1.00
129_D	166_T	1.346	1.00
127_V	167_V	1.345	1.00
40_I	47_P	1.341	1.00
15_L	19_R	1.303	1.00
88_T	105_Q	1.292	1.00
11_T	14_Q	1.277	1.00
119_K	157_H	1.275	1.00
19_R	60_N	1.258	1.00
62_P	65_T	1.249	1.00
75_P	78_Y	1.240	1.00
88_T	103_S	1.237	1.00
122_I	150_R	1.223	1.00
135_C	138_G	1.215	1.00
38_G	42_R	1.207	1.00
136_V	155_V	1.189	1.00
144_N	147_E	1.185	1.00
111_I	158_I	1.148	1.00
163_G	167_V	1.148	1.00
76_S	79_D	1.147	1.00
80_P	83_Q	1.134	1.00
86_V	107_A	1.125	1.00
124_H	148_G	1.116	1.00
21_W	26_L	1.111	1.00
30_T	58_G	1.100	1.00
13_K	17_Q	1.097	1.00
15_L	59_L	1.092	1.00
103_S	126_V	1.091	1.00
120_G	154_D	1.089	1.00
161_N	166_T	1.074	1.00
137_D	156_T	1.070	1.00
82_Q	85_M	1.070	1.00
56_A	61_V	1.052	1.00
32_V	36_M	1.050	1.00
36_M	45_S	1.048	1.00
106_M	169_F	1.032	1.00
26_L	58_G	1.030	1.00
136_V	151_F	1.024	1.00
103_S	128_I	1.011	1.00
56_A	66_F	1.005	1.00
36_M	39_Q	1.002	1.00
127_V	132_L	1.002	1.00
9_S	43_N	0.988	1.00
16_R	41_E	0.986	1.00
108_S	165_Q	0.977	1.00
99_F	150_R	0.976	1.00
21_W	25_R	0.975	1.00
103_S	170_H	0.968	1.00
128_I	168_H	0.960	1.00
10_T	14_Q	0.953	1.00
104_I	169_F	0.940	1.00
74_T	78_Y	0.926	1.00
127_V	169_F	0.920	1.00
36_M	51_T	0.903	1.00
35_A	38_G	0.900	1.00
27_A	34_K	0.898	1.00
108_S	166_T	0.889	1.00
126_V	148_G	0.886	1.00
15_L	18_Q	0.878	1.00
30_T	34_K	0.876	1.00
81_Q	85_M	0.874	1.00
99_F	172_L	0.869	1.00
108_S	161_N	0.869	1.00
97_L	150_R	0.863	1.00
97_L	122_I	0.861	1.00
23_L	38_G	0.860	1.00
8_L	52_L	0.857	1.00
80_P	85_M	0.855	1.00
117_H	157_H	0.848	1.00
32_V	37_L	0.847	1.00
79_D	147_E	0.845	1.00
39_Q	44_E	0.833	1.00
81_Q	84_A	0.818	1.00
80_P	84_A	0.815	1.00
52_L	63_F	0.804	1.00
30_T	37_L	0.800	1.00
117_H	159_Y	0.792	1.00
40_I	55_I	0.792	1.00
53_W	57_T	0.790	1.00
11_T	15_L	0.787	1.00
39_Q	45_S	0.784	1.00
117_H	123_E	0.784	1.00
12_L	55_I	0.775	0.99
101_H	150_R	0.775	0.99
161_N	164_E	0.770	0.99
12_L	59_L	0.769	0.99
86_V	105_Q	0.769	0.99
49_V	52_L	0.764	0.99
61_V	66_F	0.763	0.99
108_S	163_G	0.762	0.99
23_L	30_T	0.758	0.99
12_L	56_A	0.757	0.99
124_H	172_L	0.749	0.99
23_L	34_K	0.746	0.99
100_E	173_I	0.745	0.99
151_F	157_H	0.740	0.99
35_A	39_Q	0.739	0.99
123_E	153_A	0.736	0.99
136_V	141_Q	0.735	0.99
29_A	58_G	0.734	0.99
91_F	101_H	0.729	0.99
40_I	46_S	0.714	0.99
141_Q	149_V	0.713	0.99
11_T	69_P	0.708	0.99
151_F	159_Y	0.703	0.99
127_V	144_N	0.701	0.99
87_I	91_F	0.697	0.99
116_P	158_I	0.697	0.99
73_A	139_E	0.692	0.99
109_G	164_E	0.689	0.99
106_M	167_V	0.688	0.99
7_F	10_T	0.678	0.99
99_F	124_H	0.677	0.99
106_M	132_L	0.674	0.99
46_S	50_A	0.660	0.98
37_L	55_I	0.657	0.98
29_A	60_N	0.655	0.98
53_W	63_F	0.654	0.98
12_L	38_G	0.650	0.98
131_Q	145_C	0.650	0.98
30_T	59_L	0.649	0.98
122_I	152_A	0.648	0.98
63_F	67_I	0.645	0.98
22_S	34_K	0.644	0.98
106_M	110_A	0.642	0.98
34_K	51_T	0.642	0.98
45_S	49_V	0.641	0.98
108_S	164_E	0.640	0.98
64_S	100_E	0.639	0.98
38_G	67_I	0.639	0.98
159_Y	171_S	0.637	0.98
47_P	51_T	0.631	0.98
30_T	54_K	0.630	0.98
22_S	25_R	0.628	0.98
101_H	126_V	0.626	0.98
153_A	157_H	0.625	0.98
10_T	13_K	0.617	0.97
104_I	171_S	0.613	0.97
45_S	48_T	0.610	0.97
108_S	162_G	0.609	0.97
83_Q	86_V	0.608	0.97
124_H	150_R	0.605	0.97
60_N	65_T	0.605	0.97
11_T	66_F	0.604	0.97
55_I	59_L	0.604	0.97
109_G	161_N	0.604	0.97
64_S	124_H	0.603	0.97
143_L	149_V	0.592	0.97
42_R	45_S	0.591	0.97
121_V	153_A	0.589	0.97
98_C	122_I	0.588	0.97
23_L	33_S	0.587	0.97
124_H	151_F	0.587	0.97
99_F	122_I	0.584	0.96
142_T	164_E	0.584	0.96
33_S	51_T	0.582	0.96
140_W	162_G	0.580	0.96
36_M	48_T	0.579	0.96
65_T	68_S	0.575	0.96
37_L	125_V	0.574	0.96
23_L	27_A	0.572	0.96
87_I	102_F	0.570	0.96
117_H	154_D	0.566	0.96
91_F	150_R	0.565	0.96
139_E	155_V	0.565	0.96
27_A	37_L	0.564	0.96
114_S	117_H	0.560	0.96
117_H	120_G	0.558	0.95
33_S	45_S	0.557	0.95
14_Q	17_Q	0.555	0.95
46_S	51_T	0.553	0.95
119_K	154_D	0.549	0.95
51_T	54_K	0.548	0.95
50_A	100_E	0.546	0.95
49_V	63_F	0.544	0.95
115_T	156_T	0.540	0.95
23_L	42_R	0.540	0.95
134_L	169_F	0.538	0.94
21_W	59_L	0.537	0.94
52_L	66_F	0.535	0.94
32_V	54_K	0.534	0.94
132_L	159_Y	0.531	0.94
32_V	58_G	0.531	0.94
127_V	143_L	0.529	0.94
134_L	159_Y	0.527	0.94
32_V	47_P	0.527	0.94
94_D	150_R	0.527	0.94
97_L	100_E	0.527	0.94
10_T	144_N	0.526	0.94
19_R	59_L	0.525	0.94
81_Q	86_V	0.522	0.94
48_T	85_M	0.518	0.93
53_W	159_Y	0.517	0.93
9_S	16_R	0.517	0.93
33_S	39_Q	0.516	0.93
140_W	160_R	0.516	0.93
101_H	170_H	0.515	0.93
63_F	114_S	0.514	0.93
10_T	17_Q	0.513	0.93
90_L	170_H	0.511	0.93
117_H	153_A	0.510	0.93
40_I	45_S	0.507	0.93
125_V	132_L	0.505	0.92
93_Y	97_L	0.501	0.92
46_S	56_A	0.500	0.92

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
1y9qA	1	0.9775	100	0.315	Contact Map
2bnmA	3	0.9607	100	0.356	Contact Map
4yarA	2	0.9831	100	0.366	Contact Map
4b29A	1	0.9494	100	0.434	Contact Map
4qm9A	1	0.764	100	0.454	Contact Map
2p5tA	2	0.5337	99.9	0.481	Contact Map
4lukA	2	0.8146	99.9	0.512	Contact Map
1j58A	5	0.8202	99.9	0.52	Contact Map
4e2qA	6	0.7247	99.9	0.533	Contact Map
3bu7A	3	0.8483	99.8	0.613	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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