RDGB - ECOLI - GREMLIN Contacts

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RDGB - dITP/XTP pyrophosphatase

UniProt:	P52061	Sequences: MQKVVLATGNVGKVRELASLLSDFGLDIVAQTDLGVDSAEETGLTFIENAILKARHAAKVTALPAIADDSGLAVDVLGGAPGIYSARYSGEDATDQKNLQKLLETMKDVPDDQRQARFHCVLVYLRHAEDPTPLVCHGSWPGVITREPAGTGGFGYDPIFFVPSEGKTAAELTREEKSAISHRGQALKLLLDALRNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12982
Length:	197 (188)
Sequences:	4639 (3242)
Seq/√Len:	236.4

ECOLI - RDGB
BACSU - NTPA
HALSA - Q9HNL8
SULSO - NTPA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_G	48_E	3.382	1.00
140_W	169_A	3.058	1.00
149_A	171_E	2.974	1.00
80_A	105_T	2.691	1.00
99_L	159_I	2.651	1.00
173_T	176_E	2.430	1.00
73_A	117_R	2.428	1.00
101_K	105_T	2.381	1.00
3_K	27_D	2.373	1.00
42_T	52_L	2.367	1.00
117_R	139_S	2.323	1.00
145_T	168_T	2.303	1.00
50_A	123_V	2.288	1.00
117_R	141_P	2.249	1.00
167_K	176_E	2.248	1.00
3_K	29_V	2.242	1.00
75_D	115_Q	2.200	1.00
136_C	193_A	2.122	1.00
111_D	146_R	2.117	1.00
75_D	117_R	2.032	1.00
47_I	137_H	2.004	1.00
73_A	119_H	1.975	1.00
96_Q	100_Q	1.917	1.00
12_G	15_R	1.916	1.00
145_T	161_F	1.898	1.00
74_V	102_L	1.878	1.00
88_Y	105_T	1.871	1.00
104_E	107_K	1.832	1.00
119_H	137_H	1.819	1.00
3_K	63_L	1.796	1.00
100_Q	148_P	1.781	1.00
94_T	97_K	1.777	1.00
96_Q	148_P	1.756	1.00
51_I	55_R	1.732	1.00
14_V	30_A	1.731	1.00
165_E	176_E	1.650	1.00
19_S	178_S	1.636	1.00
75_D	113_Q	1.618	1.00
55_R	133_P	1.592	1.00
184_G	188_K	1.556	1.00
99_L	148_P	1.544	1.00
123_V	135_V	1.528	1.00
9_G	32_T	1.520	1.00
64_P	124_Y	1.460	1.00
51_I	133_P	1.450	1.00
185_Q	188_K	1.446	1.00
44_L	48_E	1.410	1.00
6_L	17_L	1.409	1.00
51_I	135_V	1.396	1.00
39_A	52_L	1.386	1.00
55_R	59_K	1.379	1.00
145_T	149_A	1.375	1.00
80_A	88_Y	1.366	1.00
39_A	56_H	1.364	1.00
54_A	123_V	1.352	1.00
143_V	163_P	1.348	1.00
126_R	129_E	1.337	1.00
5_V	57_A	1.317	1.00
134_L	193_A	1.315	1.00
29_V	34_L	1.307	1.00
46_F	73_A	1.303	1.00
161_F	166_G	1.303	1.00
143_V	161_F	1.273	1.00
47_I	135_V	1.273	1.00
100_Q	104_E	1.265	1.00
8_T	14_V	1.239	1.00
176_E	179_A	1.229	1.00
56_H	60_V	1.208	1.00
93_A	97_K	1.205	1.00
124_Y	190_L	1.197	1.00
58_A	125_L	1.184	1.00
46_F	70_S	1.169	1.00
116_A	144_I	1.151	1.00
162_V	172_L	1.149	1.00
92_D	97_K	1.147	1.00
172_L	176_E	1.144	1.00
126_R	130_D	1.135	1.00
103_L	159_I	1.125	1.00
108_D	146_R	1.115	1.00
47_I	123_V	1.113	1.00
167_K	172_L	1.106	1.00
89_S	98_N	1.104	1.00
161_F	164_S	1.101	1.00
189_L	192_D	1.101	1.00
51_I	123_V	1.082	1.00
119_H	139_S	1.079	1.00
43_G	52_L	1.077	1.00
40_E	52_L	1.067	1.00
61_T	65_A	1.064	1.00
11_V	15_R	1.063	1.00
17_L	122_L	1.046	1.00
5_V	63_L	1.043	1.00
57_A	65_A	1.043	1.00
37_D	60_V	1.030	1.00
72_L	144_I	1.028	1.00
141_P	163_P	1.026	1.00
165_E	180_I	1.025	1.00
36_V	61_T	1.019	1.00
164_S	185_Q	1.017	1.00
66_I	122_L	1.003	1.00
52_L	56_H	0.998	1.00
102_L	159_I	0.987	1.00
162_V	165_E	0.985	1.00
66_I	190_L	0.976	1.00
125_L	133_P	0.968	1.00
136_C	190_L	0.954	1.00
45_T	83_I	0.944	1.00
75_D	79_G	0.943	1.00
23_D	191_L	0.943	1.00
51_I	125_L	0.940	1.00
89_S	97_K	0.935	1.00
95_D	98_N	0.930	1.00
122_L	190_L	0.923	1.00
111_D	143_V	0.922	1.00
54_A	125_L	0.921	1.00
9_G	31_Q	0.911	1.00
5_V	65_A	0.910	1.00
89_S	93_A	0.904	1.00
152_G	173_T	0.901	1.00
115_Q	141_P	0.900	1.00
55_R	125_L	0.897	1.00
103_L	114_R	0.892	0.99
189_L	193_A	0.891	0.99
169_A	172_L	0.890	0.99
64_P	126_R	0.884	0.99
70_S	120_C	0.882	0.99
121_V	137_H	0.875	0.99
97_K	100_Q	0.874	0.99
58_A	129_E	0.874	0.99
98_N	101_K	0.869	0.99
126_R	131_P	0.867	0.99
85_S	156_Y	0.863	0.99
165_E	172_L	0.862	0.99
39_A	57_A	0.859	0.99
14_V	18_A	0.851	0.99
99_L	158_P	0.848	0.99
122_L	187_L	0.844	0.99
162_V	180_I	0.834	0.99
136_C	189_L	0.832	0.99
12_G	17_L	0.832	0.99
188_K	191_L	0.831	0.99
150_G	170_A	0.827	0.99
121_V	135_V	0.825	0.99
140_W	185_Q	0.801	0.99
49_N	83_I	0.789	0.99
19_S	174_R	0.785	0.99
108_D	111_D	0.779	0.99
91_E	94_T	0.778	0.99
106_M	144_I	0.773	0.99
145_T	159_I	0.764	0.98
157_D	177_K	0.764	0.98
29_V	33_D	0.762	0.98
19_S	22_S	0.757	0.98
6_L	66_I	0.757	0.98
188_K	192_D	0.755	0.98
140_W	180_I	0.755	0.98
56_H	59_K	0.751	0.98
162_V	166_G	0.745	0.98
162_V	169_A	0.740	0.98
72_L	118_F	0.737	0.98
98_N	102_L	0.736	0.98
14_V	28_I	0.734	0.98
111_D	115_Q	0.732	0.98
17_L	187_L	0.723	0.98
103_L	106_M	0.722	0.98
126_R	132_T	0.720	0.98
5_V	61_T	0.713	0.98
17_L	21_L	0.712	0.97
151_T	171_E	0.708	0.97
45_T	48_E	0.706	0.97
6_L	28_I	0.689	0.97
107_K	146_R	0.688	0.97
168_T	171_E	0.688	0.97
115_Q	143_V	0.687	0.97
44_L	84_Y	0.684	0.97
177_K	181_S	0.683	0.97
15_R	19_S	0.682	0.97
12_G	20_L	0.680	0.97
89_S	101_K	0.677	0.97
75_D	141_P	0.675	0.97
83_I	87_R	0.674	0.97
185_Q	189_L	0.672	0.96
15_R	18_A	0.667	0.96
121_V	136_C	0.667	0.96
99_L	102_L	0.665	0.96
12_G	95_D	0.664	0.96
31_Q	57_A	0.664	0.96
101_K	104_E	0.663	0.96
108_D	114_R	0.659	0.96
44_L	83_I	0.658	0.96
107_K	111_D	0.656	0.96
11_V	32_T	0.654	0.96
149_A	161_F	0.652	0.96
88_Y	101_K	0.650	0.96
90_G	93_A	0.646	0.96
167_K	171_E	0.645	0.96
103_L	145_T	0.644	0.96
46_F	119_H	0.644	0.96
11_V	18_A	0.642	0.95
66_I	124_Y	0.637	0.95
20_L	187_L	0.636	0.95
138_G	185_Q	0.629	0.95
30_A	33_D	0.629	0.95
20_L	174_R	0.624	0.95
20_L	122_L	0.624	0.95
18_A	27_D	0.623	0.95
102_L	105_T	0.623	0.95
169_A	180_I	0.623	0.95
118_F	159_I	0.623	0.95
161_F	167_K	0.622	0.95
125_L	129_E	0.621	0.95
120_C	186_A	0.615	0.94
16_E	177_K	0.607	0.94
143_V	146_R	0.604	0.94
154_F	157_D	0.604	0.94
179_A	184_G	0.603	0.94
16_E	178_S	0.602	0.94
15_R	174_R	0.599	0.93
62_A	65_A	0.598	0.93
154_F	177_K	0.594	0.93
18_A	22_S	0.592	0.93
36_V	57_A	0.590	0.93
105_T	108_D	0.587	0.93
124_Y	134_L	0.582	0.92
36_V	60_V	0.578	0.92
118_F	156_Y	0.577	0.92
118_F	169_A	0.574	0.92
113_Q	143_V	0.574	0.92
149_A	168_T	0.574	0.92
58_A	64_P	0.571	0.92
161_F	165_E	0.570	0.92
59_K	62_A	0.569	0.92
47_I	121_V	0.568	0.92
4_V	124_Y	0.567	0.91
46_F	71_G	0.566	0.91
129_E	132_T	0.563	0.91
114_R	145_T	0.561	0.91
50_A	135_V	0.554	0.90
112_D	143_V	0.552	0.90
178_S	181_S	0.550	0.90
74_V	116_A	0.544	0.90
137_H	189_L	0.543	0.90
148_P	158_P	0.542	0.90
74_V	159_I	0.539	0.89
78_G	81_P	0.537	0.89
58_A	126_R	0.536	0.89
29_V	32_T	0.534	0.89
103_L	144_I	0.533	0.89
22_S	25_G	0.531	0.89
17_L	66_I	0.529	0.88
34_L	37_D	0.529	0.88
167_K	173_T	0.528	0.88
121_V	138_G	0.527	0.88
126_R	134_L	0.525	0.88
19_S	175_E	0.524	0.88
190_L	194_L	0.524	0.88
90_G	94_T	0.523	0.88
95_D	99_L	0.523	0.88
114_R	144_I	0.522	0.88
150_G	154_F	0.521	0.88
16_E	183_R	0.521	0.88
70_S	85_S	0.520	0.88
70_S	99_L	0.519	0.87
170_A	178_S	0.519	0.87
58_A	65_A	0.518	0.87
38_S	41_E	0.517	0.87
20_L	178_S	0.517	0.87
4_V	66_I	0.516	0.87
115_Q	163_P	0.515	0.87
148_P	159_I	0.515	0.87
95_D	102_L	0.514	0.87
73_A	79_G	0.513	0.87
9_G	57_A	0.513	0.87
144_I	159_I	0.510	0.87
42_T	83_I	0.510	0.87
11_V	33_D	0.509	0.86
74_V	77_L	0.506	0.86
179_A	188_K	0.506	0.86
149_A	167_K	0.505	0.86
93_A	102_L	0.505	0.86
106_M	114_R	0.502	0.86
58_A	63_L	0.500	0.85

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
1k7kA	1	1	100	0.003	Contact Map
3tquA	2	1	100	0.046	Contact Map
1vp2A	3	0.9492	100	0.056	Contact Map
2carA	2	0.9391	100	0.088	Contact Map
1v7rA	1	0.9289	100	0.09	Contact Map
1b78A	2	0.9188	100	0.09	Contact Map
4bnqA	2	0.9645	100	0.111	Contact Map
4jhcA	2	0.7513	97.6	0.875	Contact Map
1ex2A	2	0.7513	97.1	0.884	Contact Map
2amhA	1	0.7716	96.9	0.888	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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