YIAD - ECOLI - GREMLIN Contacts

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YIAD - Probable lipoprotein YiaD

UniProt:	P37665	Sequences: MKKRVYLIAAVVSGALAVSGCTTNPYTGEREAGKSAIGAGLGSLVGAGIGALSSSKKDRGKGALIGAAAGAALGGGVGYYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALITQGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12271
Length:	219 (210)
Sequences:	5871 (4889)
Seq/√Len:	337.3

ECOLI - YIAD MOTB PAL YFIB MBHA OMPA
BACSU - MOTB YTXE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
117_D	124_K	5.263	1.00
119_S	160_L	3.800	1.00
155_T	206_K	3.615	1.00
191_L	195_N	3.439	1.00
151_Y	195_N	3.394	1.00
132_T	175_A	3.349	1.00
199_S	205_G	3.325	1.00
149_I	191_L	3.268	1.00
198_A	205_G	3.226	1.00
165_S	190_G	3.046	1.00
118_S	155_T	2.906	1.00
200_N	205_G	2.872	1.00
162_M	166_Q	2.839	1.00
166_Q	170_D	2.797	1.00
131_L	175_A	2.706	1.00
163_R	167_Q	2.606	1.00
132_T	179_Q	2.566	1.00
173_A	188_T	2.560	1.00
121_A	167_Q	2.488	1.00
148_V	173_A	2.216	1.00
202_T	205_G	2.114	1.00
198_A	208_Q	2.022	1.00
123_L	175_A	1.996	1.00
154_S	206_K	1.958	1.00
109_N	213_E	1.956	1.00
85_E	89_R	1.933	1.00
200_N	206_K	1.927	1.00
160_L	163_R	1.906	1.00
25_P	28_G	1.878	1.00
201_S	205_G	1.684	1.00
149_I	215_T	1.661	1.00
177_I	186_I	1.634	1.00
153_D	161_N	1.569	1.00
135_A	176_L	1.567	1.00
77_V	81_M	1.558	1.00
123_L	127_G	1.550	1.00
128_A	175_A	1.544	1.00
175_A	179_Q	1.539	1.00
163_R	174_S	1.520	1.00
117_D	120_S	1.499	1.00
170_D	174_S	1.491	1.00
125_P	128_A	1.467	1.00
170_D	173_A	1.404	1.00
147_N	189_Q	1.397	1.00
154_S	200_N	1.384	1.00
77_V	80_Y	1.382	1.00
173_A	186_I	1.352	1.00
49_I	53_S	1.328	1.00
199_S	202_T	1.326	1.00
158_H	193_P	1.324	1.00
177_I	183_A	1.323	1.00
32_A	36_A	1.314	1.00
162_M	194_A	1.290	1.00
204_E	208_Q	1.271	1.00
157_G	160_L	1.265	1.00
71_A	75_G	1.237	1.00
79_Y	83_V	1.229	1.00
158_H	194_A	1.228	1.00
172_V	212_V	1.222	1.00
147_N	187_R	1.214	1.00
182_D	185_R	1.209	1.00
107_I	213_E	1.206	1.00
149_I	189_Q	1.169	1.00
72_A	76_G	1.168	1.00
155_T	203_A	1.167	1.00
78_G	82_D	1.162	1.00
25_P	29_E	1.158	1.00
166_Q	190_G	1.158	1.00
115_T	127_G	1.149	1.00
14_G	17_A	1.145	1.00
181_V	186_I	1.142	1.00
130_T	133_G	1.140	1.00
169_A	190_G	1.138	1.00
156_G	160_L	1.125	1.00
107_I	215_T	1.125	1.00
68_A	72_A	1.119	1.00
26_Y	30_R	1.098	1.00
81_M	85_E	1.097	1.00
87_K	90_D	1.091	1.00
160_L	193_P	1.073	1.00
181_V	185_R	1.071	1.00
136_M	139_K	1.067	1.00
149_I	195_N	1.061	1.00
83_V	87_K	1.061	1.00
12_V	16_L	1.059	1.00
66_G	70_G	1.059	1.00
69_A	72_A	1.054	1.00
87_K	140_E	1.054	1.00
173_A	177_I	1.048	1.00
70_G	74_G	1.046	1.00
72_A	75_G	1.033	1.00
100_T	109_N	0.999	1.00
202_T	206_K	0.992	1.00
167_Q	170_D	0.992	1.00
76_G	79_Y	0.991	1.00
156_G	161_N	0.985	1.00
170_D	188_T	0.980	1.00
36_A	40_G	0.965	1.00
175_A	178_T	0.962	1.00
24_N	29_E	0.956	1.00
27_T	30_R	0.955	1.00
118_S	153_D	0.951	1.00
160_L	167_Q	0.949	1.00
11_V	15_A	0.942	1.00
118_S	160_L	0.936	1.00
50_G	53_S	0.935	1.00
45_V	49_I	0.931	1.00
135_A	179_Q	0.929	1.00
151_Y	196_P	0.928	1.00
61_K	64_L	0.922	1.00
134_V	138_L	0.922	1.00
86_A	89_R	0.921	1.00
13_S	17_A	0.921	1.00
14_G	18_V	0.917	1.00
8_I	14_G	0.915	1.00
83_V	86_A	0.912	1.00
174_S	178_T	0.911	1.00
102_S	105_N	0.909	1.00
87_K	91_K	0.909	1.00
154_S	205_G	0.908	1.00
123_L	128_A	0.897	1.00
43_S	46_G	0.892	1.00
131_L	176_L	0.891	1.00
73_L	76_G	0.889	1.00
155_T	193_P	0.859	1.00
82_D	86_A	0.849	1.00
166_Q	188_T	0.848	1.00
36_A	39_A	0.848	1.00
183_A	194_A	0.846	1.00
129_N	133_G	0.841	1.00
71_A	74_G	0.841	1.00
62_G	65_I	0.840	1.00
136_M	140_E	0.840	1.00
59_R	63_A	0.833	1.00
131_L	172_V	0.831	1.00
153_D	210_R	0.830	1.00
150_G	212_V	0.825	1.00
34_K	38_G	0.822	1.00
26_Y	29_E	0.821	1.00
48_G	51_A	0.820	1.00
139_K	181_V	0.810	1.00
59_R	62_G	0.809	1.00
19_S	22_T	0.809	1.00
66_G	69_A	0.797	1.00
34_K	41_L	0.791	1.00
36_A	41_L	0.790	1.00
151_Y	194_A	0.788	1.00
65_I	68_A	0.787	1.00
121_A	164_L	0.782	1.00
203_A	206_K	0.780	1.00
104_D	107_I	0.779	1.00
116_F	212_V	0.779	1.00
69_A	73_L	0.778	1.00
44_L	48_G	0.777	1.00
63_A	67_A	0.764	1.00
67_A	71_A	0.761	1.00
15_A	21_C	0.760	1.00
156_G	159_D	0.759	1.00
96_G	99_V	0.759	1.00
78_G	81_M	0.758	1.00
8_I	12_V	0.756	1.00
24_N	28_G	0.756	1.00
116_F	172_V	0.755	1.00
9_A	18_V	0.755	1.00
43_S	47_A	0.754	1.00
22_T	27_T	0.754	1.00
139_K	182_D	0.752	1.00
196_P	209_N	0.752	1.00
197_I	208_Q	0.751	1.00
87_K	92_M	0.750	1.00
147_N	215_T	0.746	0.99
42_G	45_V	0.744	0.99
133_G	136_M	0.739	0.99
160_L	174_S	0.738	0.99
135_A	181_V	0.736	0.99
19_S	24_N	0.734	0.99
35_S	39_A	0.731	0.99
44_L	47_A	0.731	0.99
9_A	12_V	0.726	0.99
68_A	71_A	0.720	0.99
77_V	87_K	0.720	0.99
154_S	193_P	0.716	0.99
13_S	19_S	0.715	0.99
154_S	202_T	0.715	0.99
42_G	46_G	0.714	0.99
126_A	129_N	0.712	0.99
81_M	87_K	0.711	0.99
61_K	65_I	0.710	0.99
205_G	208_Q	0.705	0.99
124_K	127_G	0.705	0.99
70_G	73_L	0.703	0.99
148_V	186_I	0.703	0.99
15_A	19_S	0.702	0.99
148_V	188_T	0.701	0.99
58_D	61_K	0.699	0.99
86_A	90_D	0.698	0.99
33_G	37_I	0.697	0.99
104_D	149_I	0.697	0.99
118_S	156_G	0.690	0.99
13_S	16_L	0.689	0.99
118_S	161_N	0.686	0.99
138_L	146_V	0.682	0.99
141_Y	144_T	0.681	0.99
145_A	187_R	0.679	0.99
46_G	50_G	0.677	0.99
121_A	163_R	0.673	0.99
196_P	206_K	0.670	0.99
21_C	25_P	0.669	0.99
52_L	55_S	0.665	0.99
33_G	36_A	0.664	0.99
64_L	67_A	0.664	0.99
52_L	56_K	0.663	0.99
129_N	132_T	0.662	0.99
27_T	31_E	0.661	0.99
40_G	43_S	0.660	0.99
80_Y	92_M	0.658	0.99
82_D	85_E	0.655	0.99
123_L	172_V	0.654	0.99
60_G	63_A	0.653	0.99
18_V	21_C	0.653	0.99
80_Y	84_Q	0.653	0.99
147_N	217_S	0.652	0.99
37_I	41_L	0.651	0.99
60_G	64_L	0.647	0.99
85_E	101_R	0.647	0.99
63_A	66_G	0.645	0.99
91_K	136_M	0.644	0.99
132_T	136_M	0.644	0.99
162_M	188_T	0.643	0.99
17_A	20_G	0.641	0.98
48_G	52_L	0.640	0.98
162_M	192_G	0.639	0.98
62_G	69_A	0.636	0.98
119_S	157_G	0.632	0.98
49_I	52_L	0.631	0.98
80_Y	87_K	0.629	0.98
74_G	78_G	0.628	0.98
50_G	54_S	0.628	0.98
37_I	40_G	0.622	0.98
16_L	19_S	0.622	0.98
8_I	19_S	0.621	0.98
46_G	49_I	0.620	0.98
118_S	203_A	0.619	0.98
128_A	132_T	0.617	0.98
79_Y	82_D	0.615	0.98
18_V	23_T	0.614	0.98
163_R	166_Q	0.614	0.98
67_A	74_G	0.613	0.98
90_D	94_G	0.611	0.98
198_A	202_T	0.611	0.98
135_A	139_K	0.609	0.98
196_P	200_N	0.604	0.98
65_I	69_A	0.601	0.98
149_I	213_E	0.599	0.98
121_A	171_S	0.594	0.98
138_L	181_V	0.592	0.97
151_Y	192_G	0.589	0.97
23_T	30_R	0.587	0.97
157_G	193_P	0.587	0.97
110_M	115_T	0.586	0.97
14_G	20_G	0.584	0.97
34_K	37_I	0.576	0.97
8_I	11_V	0.575	0.97
66_G	74_G	0.574	0.97
10_A	15_A	0.573	0.97
87_K	93_R	0.573	0.97
134_V	137_V	0.569	0.97
24_N	27_T	0.568	0.97
54_S	57_K	0.565	0.97
137_V	141_Y	0.564	0.97
139_K	180_G	0.564	0.97
146_V	186_I	0.564	0.97
38_G	41_L	0.560	0.96
47_A	51_A	0.560	0.96
144_T	214_I	0.560	0.96
47_A	50_G	0.559	0.96
124_K	129_N	0.559	0.96
163_R	170_D	0.556	0.96
142_P	145_A	0.555	0.96
27_T	32_A	0.555	0.96
176_L	181_V	0.553	0.96
24_N	31_E	0.548	0.96
67_A	70_G	0.548	0.96
11_V	19_S	0.547	0.96
45_V	48_G	0.546	0.96
23_T	27_T	0.545	0.96
198_A	201_S	0.545	0.96
119_S	167_Q	0.543	0.96
154_S	203_A	0.542	0.96
171_S	174_S	0.541	0.96
151_Y	209_N	0.540	0.96
55_S	58_D	0.536	0.95
112_N	115_T	0.536	0.95
35_S	41_L	0.531	0.95
49_I	54_S	0.529	0.95
35_S	38_G	0.528	0.95
116_F	150_G	0.527	0.95
187_R	217_S	0.526	0.95
66_G	71_A	0.524	0.95
10_A	13_S	0.518	0.95
9_A	13_S	0.517	0.95
139_K	179_Q	0.515	0.94
69_A	74_G	0.514	0.94
40_G	44_L	0.512	0.94
78_G	85_E	0.512	0.94
38_G	46_G	0.511	0.94
196_P	202_T	0.511	0.94
163_R	193_P	0.510	0.94
43_S	48_G	0.508	0.94
44_L	50_G	0.507	0.94
22_T	29_E	0.506	0.94
41_L	44_L	0.506	0.94
46_G	51_A	0.503	0.94
22_T	28_G	0.502	0.94
84_Q	89_R	0.500	0.94

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
2k1sA	1	0.6438	100	0.344	Contact Map
3ldtA	2	0.6484	100	0.345	Contact Map
3wpwA	2	0.6575	100	0.345	Contact Map
3s0yA	4	0.7534	100	0.362	Contact Map
3khnA	2	0.6895	100	0.37	Contact Map
4b62A	1	0.6347	100	0.37	Contact Map
3s06A	3	0.6301	100	0.379	Contact Map
1r1mA	1	0.5434	100	0.382	Contact Map
2hqsH	1	0.4932	100	0.387	Contact Map
2zvyA	2	0.6986	100	0.39	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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