ATPF - BACSU - GREMLIN Contacts

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ATPF - ATP synthase subunit b

UniProt:	P37814	Sequences: MSQLPLELGLSFNGGDILFQLLAMLILLALLKKYALGPLLNIMKQREDHIAGEITSAEEKNKEAQQLIEEQRVLLKEARQESQTLIENAKKLGEKQKEEIIQAARAESERLKEAARTEIVKEKEQAVSALREQVASLSVMIASKVIEKELDEQAQEKLIQDYLKEVGESR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	170 (152)
Sequences:	4056 (2863)
Seq/√Len:	232.2

ECOLI - ATPF
BACSU - ATPF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_N	45_Q	2.926	1.00
51_A	55_T	2.574	1.00
59_E	63_E	2.532	1.00
44_K	48_D	2.320	1.00
84_T	88_N	2.260	1.00
58_E	62_K	2.242	1.00
151_D	154_A	2.236	1.00
48_D	52_G	2.144	1.00
104_A	108_S	2.116	1.00
99_E	103_A	2.104	1.00
52_G	56_S	1.996	1.00
68_I	72_R	1.878	1.00
66_Q	70_E	1.871	1.00
103_A	107_E	1.849	1.00
55_T	59_E	1.822	1.00
109_E	113_E	1.784	1.00
120_V	124_E	1.760	1.00
113_E	117_T	1.744	1.00
25_L	29_A	1.717	1.00
108_S	111_L	1.689	1.00
44_K	47_E	1.667	1.00
94_E	98_E	1.659	1.00
29_A	33_K	1.625	1.00
138_S	142_A	1.623	1.00
73_V	77_E	1.609	1.00
69_E	72_R	1.603	1.00
69_E	73_V	1.565	1.00
112_K	116_R	1.559	1.00
98_E	102_Q	1.557	1.00
157_K	161_D	1.545	1.00
81_E	84_T	1.532	1.00
154_A	157_K	1.506	1.00
70_E	74_L	1.499	1.00
62_K	66_Q	1.485	1.00
148_K	154_A	1.477	1.00
96_Q	99_E	1.445	1.00
77_E	81_E	1.444	1.00
87_E	90_K	1.424	1.00
47_E	51_A	1.416	1.00
87_E	91_K	1.402	1.00
55_T	58_E	1.400	1.00
91_K	95_K	1.399	1.00
123_K	127_V	1.389	1.00
38_P	41_N	1.386	1.00
102_Q	105_R	1.378	1.00
102_Q	106_A	1.364	1.00
71_Q	74_L	1.364	1.00
97_K	100_I	1.357	1.00
153_Q	156_E	1.353	1.00
45_Q	49_H	1.351	1.00
29_A	32_K	1.346	1.00
105_R	109_E	1.342	1.00
77_E	80_Q	1.334	1.00
62_K	65_Q	1.334	1.00
152_E	156_E	1.320	1.00
65_Q	69_E	1.259	1.00
49_H	53_E	1.258	1.00
106_A	109_E	1.256	1.00
56_S	60_K	1.246	1.00
122_E	125_Q	1.229	1.00
97_K	101_I	1.217	1.00
138_S	141_I	1.217	1.00
72_R	76_K	1.174	1.00
115_A	119_I	1.171	1.00
65_Q	68_I	1.159	1.00
61_N	65_Q	1.150	1.00
106_A	110_R	1.140	1.00
129_A	133_Q	1.136	1.00
111_L	119_I	1.130	1.00
45_Q	48_D	1.110	1.00
73_V	76_K	1.109	1.00
88_N	92_L	1.102	1.00
156_E	160_Q	1.093	1.00
94_E	97_K	1.089	1.00
28_L	32_K	1.077	1.00
96_Q	101_I	1.050	1.00
103_A	106_A	1.046	1.00
90_K	94_E	1.040	1.00
161_D	165_E	1.036	1.00
74_L	77_E	1.033	1.00
95_K	99_E	1.032	1.00
74_L	79_R	1.024	1.00
110_R	114_A	1.023	1.00
63_E	66_Q	1.012	1.00
149_E	155_Q	1.003	1.00
83_Q	87_E	1.002	1.00
124_E	128_S	1.002	1.00
67_L	70_E	0.997	1.00
80_Q	83_Q	0.994	1.00
16_D	20_Q	0.990	1.00
121_K	125_Q	0.985	1.00
16_D	19_F	0.982	1.00
67_L	71_Q	0.975	1.00
70_E	73_V	0.972	1.00
153_Q	157_K	0.972	1.00
66_Q	69_E	0.971	1.00
116_R	120_V	0.966	1.00
143_S	147_E	0.965	1.00
101_I	105_R	0.964	1.00
64_A	68_I	0.953	1.00
119_I	126_A	0.950	1.00
99_E	102_Q	0.947	1.00
96_Q	100_I	0.944	1.00
17_I	20_Q	0.944	1.00
134_V	138_S	0.932	1.00
53_E	61_N	0.930	1.00
92_L	95_K	0.925	1.00
116_R	122_E	0.917	1.00
78_A	82_S	0.913	1.00
120_V	123_K	0.909	1.00
114_A	117_T	0.903	0.99
59_E	62_K	0.898	0.99
33_K	37_G	0.898	0.99
93_G	97_K	0.891	0.99
91_K	94_E	0.886	0.99
48_D	51_A	0.862	0.99
80_Q	84_T	0.856	0.99
35_A	38_P	0.843	0.99
32_K	37_G	0.831	0.99
140_M	144_K	0.830	0.99
63_E	68_I	0.823	0.99
86_I	90_K	0.823	0.99
113_E	116_R	0.810	0.99
40_L	43_M	0.802	0.99
108_S	112_K	0.800	0.99
20_Q	23_A	0.798	0.99
82_S	86_I	0.795	0.99
148_K	161_D	0.790	0.99
89_A	93_G	0.783	0.99
15_G	18_L	0.771	0.98
136_S	140_M	0.771	0.98
32_K	36_L	0.768	0.98
31_L	35_A	0.762	0.98
93_G	100_I	0.760	0.98
118_E	122_E	0.755	0.98
117_T	120_V	0.753	0.98
150_L	155_Q	0.753	0.98
107_E	111_L	0.749	0.98
36_L	40_L	0.749	0.98
58_E	61_N	0.742	0.98
125_Q	129_A	0.741	0.98
24_M	28_L	0.741	0.98
119_I	130_L	0.741	0.98
57_A	64_A	0.735	0.98
20_Q	28_L	0.735	0.98
56_S	59_E	0.733	0.98
68_I	71_Q	0.727	0.98
100_I	104_A	0.717	0.97
82_S	85_L	0.713	0.97
128_S	131_R	0.713	0.97
130_L	134_V	0.709	0.97
150_L	154_A	0.708	0.97
76_K	80_Q	0.702	0.97
23_A	26_I	0.699	0.97
107_E	110_R	0.698	0.97
75_L	79_R	0.697	0.97
133_Q	136_S	0.695	0.97
81_E	85_L	0.688	0.97
159_I	163_L	0.684	0.97
112_K	118_E	0.684	0.97
140_M	143_S	0.679	0.96
42_I	45_Q	0.672	0.96
15_G	19_F	0.668	0.96
43_M	47_E	0.666	0.96
144_K	148_K	0.664	0.96
124_E	127_V	0.662	0.96
67_L	72_R	0.658	0.96
16_D	28_L	0.656	0.96
49_H	52_G	0.649	0.95
144_K	147_E	0.643	0.95
19_F	23_A	0.642	0.95
20_Q	24_M	0.637	0.95
160_Q	164_K	0.637	0.95
40_L	44_K	0.636	0.95
62_K	69_E	0.635	0.95
30_L	34_Y	0.632	0.95
128_S	132_E	0.630	0.95
63_E	67_L	0.625	0.94
20_Q	38_P	0.610	0.94
109_E	112_K	0.609	0.94
127_V	130_L	0.608	0.94
28_L	36_L	0.606	0.94
60_K	64_A	0.604	0.93
88_N	91_K	0.602	0.93
32_K	35_A	0.597	0.93
52_G	59_E	0.593	0.93
19_F	26_I	0.582	0.92
134_V	137_L	0.582	0.92
117_T	121_K	0.581	0.92
115_A	158_L	0.580	0.92
22_L	26_I	0.579	0.92
74_L	81_E	0.578	0.92
125_Q	128_S	0.577	0.92
79_R	82_S	0.577	0.92
31_L	36_L	0.576	0.92
48_D	56_S	0.575	0.92
161_D	164_K	0.573	0.91
60_K	63_E	0.568	0.91
53_E	56_S	0.564	0.91
19_F	22_L	0.561	0.91
100_I	108_S	0.552	0.90
121_K	124_E	0.550	0.90
50_I	53_E	0.550	0.90
23_A	36_L	0.550	0.90
95_K	98_E	0.541	0.89
92_L	135_A	0.538	0.89
88_N	95_K	0.538	0.89
79_R	83_Q	0.537	0.89
142_A	146_I	0.537	0.89
39_L	43_M	0.526	0.88
86_I	89_A	0.525	0.88
137_L	144_K	0.525	0.88
54_I	58_E	0.524	0.87
27_L	31_L	0.523	0.87
98_E	101_I	0.522	0.87
18_L	22_L	0.522	0.87
150_L	159_I	0.519	0.87
141_I	162_Y	0.517	0.87
50_I	54_I	0.512	0.86
133_Q	137_L	0.510	0.86
101_I	107_E	0.509	0.86
129_A	132_E	0.509	0.86
118_E	125_Q	0.509	0.86
32_K	41_N	0.507	0.86
93_G	103_A	0.503	0.85
119_I	123_K	0.503	0.85
34_Y	38_P	0.502	0.85
141_I	155_Q	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
2dm9A	2	0.2176	98.3	0.766	Contact Map
1b9uA	1	0.2	98	0.787	Contact Map
2khkA	1	0.3118	97.9	0.789	Contact Map
1l2pA	1	0.3588	97.8	0.793	Contact Map
3v6iA	1	0.6706	97.8	0.797	Contact Map
2clyA	1	0.5941	96.7	0.829	Contact Map
4efaE	1	0.7	92.9	0.864	Contact Map
4efaG	1	0.5412	83.8	0.886	Contact Map
2oarA	7	0.4118	77.5	0.893	Contact Map
3v6iB	1	0.5941	71.7	0.898	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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