ATPD - BACSU - GREMLIN Contacts

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ATPD - ATP synthase subunit delta

UniProt:	P37811	Sequences: MSGSAVSKRYASALFDIANESAQLNQVEEELIVVKQVFQNEKALNDVLNHPKVPAAKKKELIQNAFGSLSQSVLNTIFLLIDRHRAAIVPELTDEFIKLANVARQTEDAIVYSVKPLTDAEMLPLSQVFAKKAGVASLRIRNEVQTDLIGGIKVRIGNRIYDGSVSGKLQRIERQLAGENR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	181 (171)
Sequences:	4185 (3180)
Seq/√Len:	243.2

ECOLI - ATPD
BACSU - ATPD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_N	103_A	3.944	1.00
80_L	92_L	2.991	1.00
110_I	143_E	2.746	1.00
130_A	137_S	2.668	1.00
122_M	142_N	2.563	1.00
30_E	70_S	2.509	1.00
153_K	164_S	2.453	1.00
112_Y	145_Q	2.433	1.00
110_I	141_R	2.290	1.00
119_D	123_L	2.211	1.00
63_Q	78_F	2.193	1.00
119_D	122_M	2.172	1.00
59_K	82_D	2.048	1.00
118_T	121_E	2.019	1.00
31_L	93_T	1.996	1.00
123_L	126_S	1.964	1.00
23_Q	70_S	1.958	1.00
123_L	127_Q	1.929	1.00
110_I	155_R	1.820	1.00
30_E	73_V	1.817	1.00
95_E	98_K	1.815	1.00
112_Y	143_E	1.688	1.00
108_D	139_R	1.665	1.00
60_E	64_N	1.650	1.00
148_L	164_S	1.648	1.00
25_N	104_R	1.646	1.00
100_A	104_R	1.637	1.00
107_E	135_V	1.622	1.00
113_S	152_I	1.619	1.00
113_S	142_N	1.588	1.00
57_K	60_E	1.587	1.00
122_M	126_S	1.564	1.00
167_G	171_R	1.557	1.00
36_Q	40_N	1.506	1.00
113_S	117_L	1.502	1.00
114_V	144_V	1.484	1.00
109_A	156_I	1.449	1.00
81_I	86_A	1.445	1.00
127_Q	131_K	1.439	1.00
23_Q	26_Q	1.434	1.00
111_V	140_I	1.423	1.00
35_K	94_D	1.416	1.00
18_A	27_V	1.381	1.00
54_P	57_K	1.378	1.00
150_G	165_V	1.378	1.00
15_F	103_A	1.374	1.00
32_I	97_I	1.359	1.00
28_E	97_I	1.354	1.00
112_Y	153_K	1.343	1.00
148_L	153_K	1.337	1.00
28_E	100_A	1.336	1.00
56_A	60_E	1.319	1.00
59_K	78_F	1.295	1.00
47_V	61_L	1.289	1.00
133_A	156_I	1.289	1.00
126_S	130_A	1.283	1.00
108_D	141_R	1.275	1.00
76_T	92_L	1.274	1.00
74_L	78_F	1.258	1.00
112_Y	148_L	1.246	1.00
111_V	117_L	1.245	1.00
101_N	108_D	1.237	1.00
44_L	65_A	1.232	1.00
66_F	69_L	1.211	1.00
152_I	163_G	1.204	1.00
128_V	131_K	1.194	1.00
28_E	104_R	1.165	1.00
106_T	137_S	1.163	1.00
124_P	128_V	1.160	1.00
45_N	49_N	1.158	1.00
63_Q	74_L	1.143	1.00
101_N	106_T	1.132	1.00
126_S	140_I	1.127	1.00
107_E	138_L	1.113	1.00
111_V	154_V	1.112	1.00
109_A	140_I	1.107	1.00
66_F	77_I	1.104	1.00
69_L	74_L	1.103	1.00
127_Q	130_A	1.103	1.00
166_S	170_Q	1.099	1.00
27_V	73_V	1.077	1.00
125_L	152_I	1.076	1.00
116_P	122_M	1.066	1.00
35_K	93_T	1.064	1.00
116_P	144_V	1.061	1.00
128_V	132_K	1.057	1.00
15_F	19_N	1.054	1.00
17_I	72_S	1.052	1.00
29_E	32_I	1.051	1.00
28_E	32_I	1.045	1.00
120_A	123_L	1.038	1.00
67_G	74_L	1.035	1.00
14_L	76_T	1.033	1.00
35_K	97_I	1.027	1.00
120_A	124_P	1.017	1.00
48_L	58_K	1.014	1.00
59_K	63_Q	1.011	1.00
116_P	119_D	0.998	1.00
60_E	63_Q	0.988	1.00
25_N	29_E	0.987	1.00
24_L	96_F	0.980	1.00
12_S	16_D	0.979	1.00
26_Q	30_E	0.979	1.00
71_Q	74_L	0.969	1.00
14_L	17_I	0.969	1.00
15_F	99_L	0.954	1.00
43_A	46_D	0.944	1.00
23_Q	27_V	0.944	1.00
97_I	101_N	0.936	1.00
17_I	21_S	0.932	1.00
26_Q	70_S	0.927	1.00
133_A	159_R	0.921	1.00
55_A	84_H	0.918	1.00
96_F	100_A	0.909	1.00
79_L	83_R	0.908	1.00
23_Q	72_S	0.904	1.00
80_L	86_A	0.898	1.00
112_Y	155_R	0.897	1.00
26_Q	29_E	0.891	1.00
34_V	69_L	0.891	1.00
21_S	72_S	0.890	1.00
35_K	39_Q	0.888	1.00
153_K	160_I	0.883	1.00
31_L	73_V	0.878	0.99
173_E	177_A	0.873	0.99
29_E	33_V	0.858	0.99
34_V	66_F	0.855	0.99
102_V	135_V	0.845	0.99
11_A	99_L	0.842	0.99
35_K	90_P	0.840	0.99
10_Y	85_R	0.840	0.99
76_T	80_L	0.839	0.99
75_N	78_F	0.834	0.99
106_T	139_R	0.826	0.99
58_K	84_H	0.826	0.99
129_F	138_L	0.825	0.99
109_A	129_F	0.823	0.99
37_V	66_F	0.822	0.99
21_S	71_Q	0.819	0.99
101_N	139_R	0.816	0.99
33_V	36_Q	0.812	0.99
162_D	167_G	0.809	0.99
71_Q	75_N	0.798	0.99
6_V	88_I	0.788	0.99
34_V	77_I	0.788	0.99
125_L	129_F	0.783	0.99
24_L	103_A	0.781	0.99
147_D	166_S	0.780	0.99
107_E	133_A	0.778	0.99
45_N	90_P	0.776	0.99
8_K	95_E	0.761	0.99
155_R	160_I	0.757	0.98
129_F	133_A	0.756	0.98
135_V	138_L	0.754	0.98
124_P	127_Q	0.753	0.98
88_I	91_E	0.747	0.98
131_K	134_G	0.741	0.98
99_L	102_V	0.737	0.98
55_A	59_K	0.736	0.98
149_I	165_V	0.718	0.98
170_Q	174_R	0.717	0.98
69_L	73_V	0.714	0.98
42_K	45_N	0.708	0.98
129_F	161_Y	0.708	0.98
113_S	148_L	0.708	0.98
33_V	37_V	0.707	0.98
18_A	24_L	0.705	0.98
27_V	70_S	0.705	0.98
7_S	95_E	0.703	0.98
126_S	137_S	0.700	0.97
24_L	104_R	0.683	0.97
53_V	57_K	0.680	0.97
42_K	46_D	0.676	0.97
160_I	163_G	0.674	0.97
95_E	99_L	0.674	0.97
49_N	87_A	0.671	0.97
62_I	81_I	0.663	0.96
116_P	142_N	0.663	0.96
44_L	61_L	0.659	0.96
114_V	148_L	0.654	0.96
39_Q	90_P	0.654	0.96
38_F	48_L	0.644	0.96
99_L	103_A	0.642	0.96
50_H	58_K	0.641	0.96
32_I	36_Q	0.640	0.96
118_T	122_M	0.639	0.96
57_K	64_N	0.635	0.96
150_G	162_D	0.631	0.95
14_L	27_V	0.625	0.95
153_K	166_S	0.621	0.95
171_R	174_R	0.620	0.95
19_N	24_L	0.615	0.95
77_I	89_V	0.612	0.95
91_E	95_E	0.603	0.94
34_V	38_F	0.602	0.94
17_I	27_V	0.601	0.94
30_E	33_V	0.600	0.94
37_V	41_E	0.600	0.94
109_A	133_A	0.599	0.94
17_I	20_E	0.598	0.94
107_E	129_F	0.595	0.94
9_R	173_E	0.593	0.94
100_A	106_T	0.593	0.94
72_S	75_N	0.588	0.93
44_L	47_V	0.586	0.93
132_K	159_R	0.581	0.93
38_F	89_V	0.572	0.92
126_S	139_R	0.571	0.92
47_V	53_V	0.569	0.92
113_S	121_E	0.568	0.92
122_M	140_I	0.565	0.92
94_D	98_K	0.565	0.92
113_S	144_V	0.561	0.92
165_V	169_L	0.561	0.92
142_N	148_L	0.557	0.91
34_V	73_V	0.556	0.91
174_R	177_A	0.555	0.91
105_Q	134_G	0.555	0.91
27_V	72_S	0.552	0.91
125_L	154_V	0.551	0.91
18_A	96_F	0.546	0.90
18_A	22_A	0.541	0.90
63_Q	67_G	0.540	0.90
111_V	142_N	0.540	0.90
132_K	161_Y	0.537	0.90
14_L	30_E	0.534	0.90
170_Q	173_E	0.533	0.89
15_F	24_L	0.533	0.89
50_H	53_V	0.532	0.89
107_E	157_G	0.530	0.89
171_R	177_A	0.530	0.89
62_I	74_L	0.527	0.89
105_Q	137_S	0.525	0.89
38_F	44_L	0.524	0.89
160_I	176_L	0.523	0.89
83_R	164_S	0.522	0.88
134_G	138_L	0.521	0.88
171_R	175_Q	0.521	0.88
105_Q	135_V	0.518	0.88
87_A	90_P	0.517	0.88
125_L	161_Y	0.516	0.88
27_V	30_E	0.516	0.88
145_Q	166_S	0.516	0.88
93_T	97_I	0.514	0.88
62_I	77_I	0.514	0.88
97_I	108_D	0.514	0.88
16_D	20_E	0.512	0.87
48_L	62_I	0.512	0.87
91_E	94_D	0.510	0.87
169_L	172_I	0.508	0.87
126_S	142_N	0.507	0.87
24_L	100_A	0.505	0.87
8_K	102_V	0.505	0.87
165_V	174_R	0.503	0.87
28_E	96_F	0.501	0.86
19_N	22_A	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
2wssS	1	0.8564	100	0.102	Contact Map
1abvA	1	0.5746	100	0.396	Contact Map
3lg8A	1	0.5304	93.8	0.869	Contact Map
3v6iA	1	0.8785	88.1	0.887	Contact Map
4efaE	1	0.9392	85.1	0.892	Contact Map
2dm9A	2	0.5912	72.6	0.904	Contact Map
2marA	1	0.4807	10.8	0.94	Contact Map
2nx4A	2	0.7293	8.4	0.943	Contact Map
2r9vA	1	0.7182	7.6	0.944	Contact Map
3he0A	2	0.7459	7.4	0.945	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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