YCEI - ECOLI - GREMLIN Contacts

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YCEI - Protein YceI

UniProt:	P0A8X2	Sequences: MKKSLLGLTFASLMFSAGSAVAADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11820
Length:	191 (166)
Sequences:	4319 (3145)
Seq/√Len:	244.1

ECOLI - YCEI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_D	76_N	2.970	1.00
77_T	105_A	2.876	1.00
98_N	101_K	2.828	1.00
124_D	131_T	2.625	1.00
74_T	104_Q	2.537	1.00
72_N	108_T	2.476	1.00
107_F	123_G	2.294	1.00
120_D	137_E	2.277	1.00
98_N	128_N	2.212	1.00
82_T	88_D	2.194	1.00
126_T	131_T	2.180	1.00
120_D	135_T	2.163	1.00
122_T	135_T	2.116	1.00
53_K	81_D	2.045	1.00
110_T	124_D	2.036	1.00
132_K	165_D	2.012	1.00
160_K	178_E	2.008	1.00
121_I	138_A	1.983	1.00
164_K	177_Q	1.966	1.00
162_K	165_D	1.953	1.00
76_N	104_Q	1.951	1.00
122_T	133_P	1.943	1.00
162_K	177_Q	1.943	1.00
94_A	98_N	1.858	1.00
90_H	95_D	1.835	1.00
24_D	60_T	1.833	1.00
72_N	106_T	1.824	1.00
113_K	122_T	1.811	1.00
86_E	89_K	1.803	1.00
113_K	120_D	1.800	1.00
102_Y	128_N	1.775	1.00
65_N	68_A	1.774	1.00
77_T	99_T	1.749	1.00
111_S	122_T	1.690	1.00
108_T	124_D	1.665	1.00
58_T	72_N	1.661	1.00
59_F	187_G	1.641	1.00
85_A	89_K	1.596	1.00
124_D	133_P	1.558	1.00
160_K	180_D	1.548	1.00
156_E	184_S	1.531	1.00
71_V	109_S	1.454	1.00
125_L	134_V	1.401	1.00
157_A	183_I	1.387	1.00
36_V	55_F	1.380	1.00
39_R	47_W	1.367	1.00
38_F	50_G	1.354	1.00
34_A	185_V	1.333	1.00
56_D	74_T	1.328	1.00
136_L	157_A	1.319	1.00
132_K	166_F	1.315	1.00
70_K	108_T	1.304	1.00
136_L	159_G	1.301	1.00
28_D	33_H	1.296	1.00
40_I	179_V	1.274	1.00
115_D	118_E	1.259	1.00
92_R	99_T	1.208	1.00
102_Y	129_G	1.208	1.00
27_I	57_G	1.206	1.00
75_I	105_A	1.200	1.00
82_T	87_R	1.163	1.00
159_G	181_L	1.160	1.00
40_I	175_A	1.153	1.00
115_D	120_D	1.139	1.00
80_V	91_L	1.131	1.00
112_V	121_I	1.123	1.00
152_R	188_V	1.122	1.00
110_T	133_P	1.118	1.00
114_K	119_L	1.111	1.00
128_N	168_I	1.107	1.00
158_E	182_I	1.107	1.00
60_T	70_K	1.099	1.00
57_G	73_V	1.083	1.00
108_T	126_T	1.082	1.00
143_Q	153_A	1.066	1.00
52_F	75_I	1.063	1.00
37_N	49_Y	1.048	1.00
152_R	186_E	1.044	1.00
20_A	23_A	1.043	1.00
91_L	97_L	1.042	1.00
54_D	79_S	1.038	1.00
81_D	88_D	1.028	1.00
24_D	58_T	1.025	1.00
162_K	178_E	1.012	1.00
89_K	92_R	1.007	1.00
158_E	180_D	0.998	1.00
105_A	127_L	0.984	1.00
136_L	183_I	0.971	1.00
170_T	175_A	0.964	1.00
48_L	87_R	0.964	1.00
109_S	112_V	0.963	1.00
171_D	174_P	0.957	1.00
78_T	92_R	0.941	1.00
90_H	96_F	0.940	1.00
29_K	56_D	0.936	1.00
53_K	79_S	0.935	1.00
25_Y	153_A	0.934	1.00
145_D	151_K	0.933	1.00
36_V	183_I	0.919	1.00
59_F	71_V	0.908	1.00
33_H	186_E	0.902	1.00
32_Q	84_H	0.901	1.00
94_A	101_K	0.899	1.00
114_K	117_D	0.898	1.00
62_D	68_A	0.898	1.00
126_T	129_G	0.894	1.00
51_T	83_N	0.891	1.00
161_I	181_L	0.888	1.00
134_V	159_G	0.886	1.00
39_R	49_Y	0.872	0.99
77_T	97_L	0.871	0.99
88_D	92_R	0.865	0.99
107_F	135_T	0.856	0.99
118_E	139_K	0.853	0.99
112_V	119_L	0.843	0.99
27_I	185_V	0.834	0.99
74_T	106_T	0.833	0.99
73_V	183_I	0.831	0.99
133_P	137_E	0.830	0.99
66_P	69_D	0.829	0.99
137_E	159_G	0.824	0.99
25_Y	187_G	0.822	0.99
62_D	65_N	0.819	0.99
98_N	102_Y	0.818	0.99
39_R	182_I	0.814	0.99
96_F	175_A	0.813	0.99
33_H	42_H	0.809	0.99
37_N	182_I	0.806	0.99
61_F	119_L	0.804	0.99
140_L	143_Q	0.801	0.99
52_F	79_S	0.795	0.99
34_A	55_F	0.790	0.99
130_V	167_N	0.789	0.99
33_H	154_G	0.783	0.99
155_F	185_V	0.779	0.99
40_I	48_L	0.774	0.99
97_L	163_L	0.770	0.99
97_L	168_I	0.763	0.99
49_Y	184_S	0.760	0.99
89_K	93_S	0.759	0.99
38_F	82_T	0.754	0.98
106_T	129_G	0.754	0.98
156_E	182_I	0.744	0.98
142_G	155_F	0.743	0.98
154_G	184_S	0.743	0.98
134_V	166_F	0.742	0.98
29_K	54_D	0.736	0.98
119_L	138_A	0.726	0.98
35_F	51_T	0.725	0.98
60_T	69_D	0.712	0.98
114_K	118_E	0.710	0.98
183_I	187_G	0.707	0.98
138_A	157_A	0.707	0.98
27_I	187_G	0.705	0.98
115_D	139_K	0.705	0.98
19_S	23_A	0.703	0.98
154_G	186_E	0.699	0.97
115_D	119_L	0.699	0.97
140_L	155_F	0.698	0.97
112_V	138_A	0.697	0.97
28_D	42_H	0.690	0.97
50_G	87_R	0.681	0.97
41_Q	47_W	0.679	0.97
128_N	167_N	0.679	0.97
19_S	22_A	0.678	0.97
77_T	92_R	0.675	0.97
39_R	180_D	0.675	0.97
140_L	153_A	0.673	0.97
29_K	32_Q	0.673	0.97
91_L	96_F	0.671	0.97
45_Y	144_G	0.671	0.97
129_G	167_N	0.669	0.97
164_K	171_D	0.669	0.97
26_K	56_D	0.669	0.97
18_G	22_A	0.659	0.96
47_W	156_E	0.658	0.96
80_V	92_R	0.656	0.96
52_F	55_F	0.655	0.96
65_N	69_D	0.651	0.96
42_H	154_G	0.650	0.96
49_Y	83_N	0.647	0.96
41_Q	176_S	0.646	0.96
125_L	166_F	0.640	0.96
107_F	159_G	0.637	0.96
43_L	46_S	0.635	0.96
125_L	161_I	0.635	0.96
170_T	174_P	0.632	0.95
90_H	170_T	0.632	0.95
97_L	177_Q	0.629	0.95
42_H	46_S	0.626	0.95
143_Q	151_K	0.626	0.95
169_K	173_G	0.625	0.95
53_K	83_N	0.619	0.95
97_L	179_V	0.619	0.95
42_H	186_E	0.606	0.94
110_T	122_T	0.603	0.94
84_H	88_D	0.602	0.94
51_T	81_D	0.600	0.94
63_E	68_A	0.596	0.94
87_R	90_H	0.592	0.94
127_L	166_F	0.587	0.93
83_N	88_D	0.584	0.93
163_L	175_A	0.582	0.93
35_F	49_Y	0.580	0.93
77_T	168_I	0.577	0.93
77_T	102_Y	0.576	0.93
141_I	156_E	0.574	0.93
73_V	157_A	0.574	0.93
66_P	119_L	0.573	0.92
87_R	91_L	0.572	0.92
118_E	137_E	0.571	0.92
127_L	161_I	0.568	0.92
78_T	99_T	0.567	0.92
34_A	57_G	0.565	0.92
37_N	51_T	0.565	0.92
84_H	87_R	0.564	0.92
141_I	154_G	0.559	0.92
80_V	97_L	0.559	0.92
29_K	33_H	0.557	0.91
26_K	58_T	0.556	0.91
164_K	172_L	0.555	0.91
50_G	82_T	0.552	0.91
38_F	80_V	0.551	0.91
33_H	152_R	0.550	0.91
62_D	66_P	0.548	0.91
63_E	66_P	0.548	0.91
49_Y	182_I	0.546	0.91
46_S	154_G	0.545	0.90
69_D	112_V	0.538	0.90
109_S	121_I	0.534	0.90
27_I	73_V	0.530	0.89
126_T	130_V	0.529	0.89
161_I	168_I	0.529	0.89
57_G	185_V	0.529	0.89
62_D	69_D	0.528	0.89
168_I	171_D	0.526	0.89
110_T	131_T	0.524	0.89
94_A	128_N	0.523	0.89
33_H	142_G	0.519	0.88
164_K	169_K	0.517	0.88
127_L	168_I	0.516	0.88
26_K	188_V	0.514	0.88
144_G	152_R	0.512	0.88
108_T	131_T	0.512	0.88
29_K	55_F	0.509	0.87
82_T	91_L	0.507	0.87
33_H	46_S	0.504	0.87
40_I	176_S	0.503	0.87
23_A	63_E	0.500	0.86

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
1y0gA	2	0.8743	100	0.074	Contact Map
1wubA	1	0.8691	100	0.176	Contact Map
2fgsA	2	0.8691	100	0.19	Contact Map
3hpeA	2	0.8429	100	0.216	Contact Map
3q34A	2	0.822	100	0.3	Contact Map
2x32A	1	0.8272	100	0.318	Contact Map
4uu4A	1	0.6597	39.8	0.927	Contact Map
2qguA	1	0.822	14.5	0.941	Contact Map
4wrtA	1	0.6963	12.8	0.942	Contact Map
3nb3A	2	0.6073	11.9	0.943	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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