ATPD - ECOLI - GREMLIN Contacts

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ATPD - ATP synthase subunit delta

UniProt:	P0ABA4	Sequences: MSEFITVARPYAKAAFDFAVEHQSVERWQDMLAFAAEVTKNEQMAELLSGALAPETLAESFIAVCGEQLDENGQNLIRVMAENGRLNALPDVLEQFIHLRAVSEATAEVDVISAAALSEQQLAKISAAMEKRLSRKVKLNCKIDKSVMAGVIIRAGDMVIDGSVRGRLERLADVLQS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10105
Length:	177 (169)
Sequences:	4174 (3207)
Seq/√Len:	246.7

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
20_V	103_S	3.811	1.00
80_M	92_V	3.053	1.00
110_D	142_K	2.727	1.00
122_L	141_C	2.588	1.00
130_E	136_K	2.577	1.00
112_I	144_D	2.460	1.00
152_I	163_S	2.355	1.00
110_D	140_N	2.319	1.00
31_M	70_D	2.284	1.00
119_E	123_A	2.244	1.00
119_E	122_L	2.197	1.00
62_I	78_R	2.120	1.00
58_A	82_E	2.005	1.00
123_A	127_A	1.991	1.00
123_A	126_S	1.988	1.00
118_S	121_Q	1.971	1.00
32_L	93_L	1.957	1.00
24_S	70_D	1.850	1.00
31_M	73_G	1.795	1.00
110_D	154_R	1.770	1.00
95_Q	98_H	1.765	1.00
26_E	104_E	1.657	1.00
108_E	138_K	1.641	1.00
59_E	63_A	1.626	1.00
112_I	142_K	1.605	1.00
100_R	104_E	1.596	1.00
113_S	141_C	1.588	1.00
56_T	59_E	1.559	1.00
122_L	126_S	1.545	1.00
147_V	163_S	1.530	1.00
62_I	66_G	1.528	1.00
166_G	170_R	1.521	1.00
113_S	151_V	1.470	1.00
109_V	155_A	1.455	1.00
113_S	117_L	1.443	1.00
19_A	28_W	1.427	1.00
114_A	143_I	1.424	1.00
107_A	135_R	1.410	1.00
24_S	27_R	1.403	1.00
149_A	164_V	1.391	1.00
127_A	131_K	1.387	1.00
36_A	94_E	1.384	1.00
16_F	103_S	1.379	1.00
81_A	86_L	1.378	1.00
33_A	97_I	1.377	1.00
55_E	59_E	1.342	1.00
44_M	64_V	1.338	1.00
53_A	56_T	1.332	1.00
29_Q	97_I	1.328	1.00
111_V	139_L	1.326	1.00
29_Q	100_R	1.321	1.00
76_L	92_V	1.318	1.00
112_I	152_I	1.304	1.00
126_S	130_E	1.290	1.00
108_E	140_N	1.290	1.00
133_L	155_A	1.289	1.00
147_V	152_I	1.287	1.00
58_A	78_R	1.280	1.00
112_I	147_V	1.269	1.00
74_Q	78_R	1.250	1.00
47_L	60_S	1.244	1.00
151_V	162_G	1.238	1.00
101_A	108_E	1.227	1.00
128_A	131_K	1.214	1.00
111_V	117_L	1.192	1.00
65_C	77_I	1.191	1.00
65_C	69_L	1.191	1.00
62_I	74_Q	1.179	1.00
45_A	49_S	1.150	1.00
124_K	128_A	1.149	1.00
29_Q	104_E	1.148	1.00
127_A	130_E	1.145	1.00
128_A	132_R	1.127	1.00
111_V	153_I	1.119	1.00
106_T	136_K	1.104	1.00
107_A	137_V	1.098	1.00
126_S	139_L	1.094	1.00
28_W	73_G	1.089	1.00
125_I	151_V	1.088	1.00
101_A	106_T	1.079	1.00
116_A	122_L	1.073	1.00
18_F	72_N	1.066	1.00
69_L	74_Q	1.066	1.00
120_Q	123_A	1.061	1.00
29_Q	33_A	1.060	1.00
109_V	139_L	1.054	1.00
165_R	169_E	1.054	1.00
36_A	93_L	1.050	1.00
48_L	57_L	1.050	1.00
66_G	74_Q	1.045	1.00
16_F	20_V	1.043	1.00
116_A	143_I	1.040	1.00
25_V	96_F	1.031	1.00
26_E	30_D	1.026	1.00
13_K	17_D	1.026	1.00
30_D	33_A	1.024	1.00
27_R	31_M	1.008	1.00
43_Q	46_E	0.994	1.00
79_V	83_N	0.992	1.00
36_A	97_I	0.989	1.00
58_A	62_I	0.989	1.00
16_F	99_L	0.988	1.00
15_A	76_L	0.983	1.00
27_R	70_D	0.981	1.00
59_E	62_I	0.973	1.00
120_Q	124_K	0.971	1.00
71_E	74_Q	0.969	1.00
15_A	18_F	0.967	1.00
35_A	65_C	0.964	1.00
80_M	86_L	0.962	1.00
54_P	84_G	0.959	1.00
97_I	101_A	0.958	1.00
133_L	158_M	0.943	1.00
30_D	34_F	0.941	1.00
18_F	22_H	0.932	1.00
76_L	80_M	0.931	1.00
24_S	28_W	0.929	1.00
101_A	138_K	0.910	1.00
32_L	73_G	0.906	1.00
27_R	30_D	0.901	1.00
116_A	119_E	0.892	1.00
105_A	135_R	0.886	1.00
11_Y	85_R	0.882	1.00
22_H	72_N	0.872	0.99
112_I	154_R	0.869	0.99
36_A	40_K	0.865	0.99
24_S	72_N	0.864	0.99
152_I	159_V	0.860	0.99
75_N	78_R	0.859	0.99
35_A	69_L	0.838	0.99
7_V	88_A	0.834	0.99
96_F	100_R	0.828	0.99
45_A	90_P	0.825	0.99
12_A	99_L	0.820	0.99
161_D	166_G	0.818	0.99
9_R	95_Q	0.815	0.99
125_I	129_M	0.815	0.99
36_A	90_P	0.812	0.99
129_M	133_L	0.808	0.99
71_E	75_N	0.808	0.99
109_V	129_M	0.804	0.99
54_P	58_A	0.803	0.99
106_T	138_K	0.799	0.99
107_A	133_L	0.796	0.99
38_V	65_C	0.794	0.99
34_F	37_E	0.790	0.99
154_R	159_V	0.778	0.99
99_L	102_V	0.774	0.99
35_A	77_I	0.770	0.99
22_H	71_E	0.770	0.99
129_M	137_V	0.769	0.99
146_S	165_R	0.766	0.99
63_A	66_G	0.764	0.99
34_F	38_V	0.763	0.99
88_A	91_D	0.758	0.99
124_K	127_A	0.755	0.99
57_L	84_G	0.749	0.98
25_V	103_S	0.742	0.98
113_S	147_V	0.729	0.98
126_S	136_K	0.727	0.98
131_K	134_S	0.723	0.98
69_L	73_G	0.711	0.98
49_S	87_N	0.710	0.98
25_V	104_E	0.705	0.98
33_A	37_E	0.705	0.98
169_E	173_D	0.704	0.98
116_A	141_C	0.702	0.98
19_A	25_V	0.698	0.98
95_Q	99_L	0.697	0.98
8_A	95_Q	0.689	0.97
148_M	164_V	0.685	0.97
152_I	165_R	0.683	0.97
129_M	160_I	0.681	0.97
159_V	162_G	0.678	0.97
18_F	21_E	0.672	0.97
50_G	57_L	0.671	0.97
114_A	147_V	0.668	0.97
99_L	103_S	0.662	0.97
18_F	28_W	0.662	0.97
28_W	70_D	0.656	0.96
52_L	56_T	0.653	0.96
170_R	173_D	0.651	0.96
42_E	45_A	0.650	0.96
42_E	46_E	0.647	0.96
40_K	90_P	0.644	0.96
61_F	81_A	0.642	0.96
72_N	75_N	0.639	0.96
118_S	122_L	0.638	0.96
67_E	74_Q	0.638	0.96
35_A	73_G	0.638	0.96
39_T	44_M	0.634	0.96
44_M	60_S	0.614	0.95
113_S	143_I	0.613	0.95
94_E	98_H	0.613	0.95
126_S	138_K	0.607	0.95
107_A	129_M	0.606	0.94
125_I	153_I	0.606	0.94
56_T	63_A	0.604	0.94
31_M	34_F	0.601	0.94
77_I	89_L	0.601	0.94
68_Q	74_Q	0.599	0.94
107_A	156_G	0.598	0.94
132_R	158_M	0.595	0.94
91_D	95_Q	0.595	0.94
15_A	28_W	0.589	0.94
20_V	25_V	0.588	0.94
100_R	106_T	0.588	0.94
38_V	41_N	0.588	0.94
83_N	163_S	0.586	0.93
125_I	160_I	0.580	0.93
149_A	161_D	0.580	0.93
105_A	136_K	0.575	0.93
47_L	52_L	0.575	0.93
28_W	72_N	0.575	0.93
170_R	174_V	0.571	0.93
134_S	137_V	0.566	0.92
144_D	165_R	0.560	0.92
87_N	90_P	0.558	0.92
44_M	47_L	0.555	0.91
39_T	48_L	0.551	0.91
141_C	147_V	0.550	0.91
16_F	25_V	0.550	0.91
169_E	172_A	0.549	0.91
105_A	134_S	0.549	0.91
10_P	172_A	0.548	0.91
164_V	168_L	0.546	0.91
126_S	141_C	0.543	0.91
132_R	160_I	0.542	0.90
122_L	139_L	0.539	0.90
93_L	97_I	0.537	0.90
10_P	85_R	0.536	0.90
113_S	121_Q	0.531	0.90
50_G	163_S	0.530	0.90
19_A	96_F	0.530	0.90
111_V	141_C	0.529	0.89
15_A	31_M	0.529	0.89
111_V	125_I	0.525	0.89
48_L	156_G	0.524	0.89
97_I	108_E	0.521	0.89
142_K	147_V	0.521	0.89
25_V	100_R	0.520	0.89
15_A	73_G	0.520	0.89
29_Q	96_F	0.520	0.89
109_V	133_L	0.517	0.88
114_A	141_C	0.517	0.88
7_V	76_L	0.513	0.88
9_R	102_V	0.512	0.88
157_D	165_R	0.512	0.88
8_A	91_D	0.506	0.87
48_L	61_F	0.504	0.87
164_V	173_D	0.503	0.87
161_D	165_R	0.501	0.87
91_D	94_E	0.500	0.87
51_A	149_A	0.500	0.87

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	0.8757	100	0.116	Contact Map
1abvA	1	0.5932	100	0.383	Contact Map
3lg8A	1	0.5254	94.8	0.865	Contact Map
3v6iA	1	0.8588	91.3	0.881	Contact Map
4efaE	1	0.9379	83.1	0.895	Contact Map
2dm9A	2	0.6045	80.5	0.898	Contact Map
1pjhA	4	0.2825	16.3	0.936	Contact Map
4uera	1	0.791	14.1	0.938	Contact Map
1repC	1	0.5028	10.3	0.941	Contact Map
4l7mA	1	0.8079	6.7	0.946	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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