YGAP - ECOLI - GREMLIN Contacts

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YGAP - Inner membrane protein YgaP

UniProt:	P55734	Sequences: MALTTISPHDAQELIARGAKLIDIRDADEYLREHIPEADLAPLSVLEQSGLPAKLRHEQIIFHCQAGKRTSNNADKLAAIAAPAEIFLLEDGIDGWKKAGLPVAVNKSQPLPLMRQVQIAAGGLILIGVVLGYTVNSGFFLLSGFVGAGLLFAGISGFCGMARLLDKMPWNQRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13288
Length:	174 (132)
Sequences:	1386 (1114)
Seq/√Len:	96.9

ECOLI - YGAP THTM
HALSA - Q9HMT6 Q9HMT7
SULSO - Q97XC6 Q97ZB1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_I	10_D	4.223	1.00
33_E	97_K	3.718	1.00
95_G	99_A	3.593	1.00
7_S	10_D	3.283	1.00
59_Q	87_F	3.111	1.00
30_Y	34_H	3.077	1.00
11_A	61_I	2.969	1.00
8_P	95_G	2.593	1.00
12_Q	101_L	2.438	1.00
8_P	99_A	2.284	1.00
20_K	58_E	2.155	1.00
14_L	17_R	2.100	1.00
50_G	113_L	1.952	1.00
8_P	101_L	1.936	1.00
25_R	65_Q	1.913	1.00
10_D	14_L	1.897	1.00
9_H	13_E	1.821	1.00
22_I	39_D	1.812	1.00
27_A	31_L	1.777	1.00
5_T	90_E	1.776	1.00
126_L	129_V	1.763	1.00
127_I	131_L	1.692	1.00
33_E	105_V	1.686	1.00
61_I	89_L	1.685	1.00
73_N	76_K	1.661	1.00
26_D	44_S	1.575	1.00
11_A	89_L	1.552	1.00
93_I	103_V	1.550	1.00
84_A	120_A	1.521	1.00
49_S	52_P	1.516	1.00
72_N	76_K	1.499	1.00
49_S	54_K	1.489	1.00
75_D	79_A	1.484	1.00
14_L	59_Q	1.440	1.00
36_P	104_A	1.387	0.99
73_N	78_A	1.369	0.99
24_I	62_F	1.352	0.99
104_A	108_S	1.329	0.99
35_I	96_W	1.328	0.99
49_S	78_A	1.308	0.99
125_I	129_V	1.278	0.99
6_I	14_L	1.275	0.99
29_E	69_R	1.273	0.99
125_I	133_Y	1.195	0.98
56_R	116_Q	1.163	0.98
34_H	104_A	1.151	0.98
35_I	61_I	1.141	0.98
55_L	113_L	1.135	0.98
130_V	134_T	1.116	0.97
27_A	40_L	1.109	0.97
104_A	107_K	1.098	0.97
55_L	58_E	1.098	0.97
11_A	19_A	1.091	0.97
6_I	11_A	1.083	0.97
30_Y	40_L	1.064	0.96
80_I	119_I	1.059	0.96
130_V	135_V	1.053	0.96
125_I	130_V	1.050	0.96
62_F	74_A	1.042	0.96
59_Q	85_E	1.019	0.96
91_D	95_G	1.018	0.95
12_Q	16_A	1.016	0.95
49_S	53_A	1.004	0.95
19_A	61_I	0.989	0.95
70_T	74_A	0.988	0.95
114_M	118_Q	0.986	0.95
25_R	66_A	0.982	0.95
12_Q	102_P	0.975	0.94
131_L	134_T	0.956	0.94
9_H	99_A	0.954	0.94
33_E	93_I	0.925	0.93
66_A	94_D	0.922	0.92
89_L	96_W	0.916	0.92
72_N	79_A	0.909	0.92
47_E	76_K	0.908	0.92
50_G	114_M	0.907	0.92
65_Q	94_D	0.905	0.92
30_Y	108_S	0.896	0.91
9_H	101_L	0.895	0.91
122_G	128_G	0.888	0.91
62_F	70_T	0.886	0.91
63_H	93_I	0.880	0.91
78_A	86_I	0.877	0.90
64_C	69_R	0.844	0.89
44_S	67_G	0.840	0.88
112_P	115_R	0.836	0.88
34_H	38_A	0.835	0.88
97_K	103_V	0.823	0.87
22_I	54_K	0.816	0.87
24_I	73_N	0.816	0.87
50_G	54_K	0.807	0.86
129_V	132_G	0.801	0.86
60_I	83_P	0.797	0.86
6_I	87_F	0.795	0.86
29_E	66_A	0.792	0.85
70_T	88_L	0.787	0.85
33_E	38_A	0.786	0.85
120_A	123_G	0.785	0.85
21_L	63_H	0.779	0.84
94_D	97_K	0.770	0.84
11_A	14_L	0.767	0.83
50_G	112_P	0.759	0.83
134_T	137_S	0.759	0.83
36_P	96_W	0.757	0.83
31_L	106_N	0.754	0.82
35_I	89_L	0.749	0.82
111_L	116_Q	0.741	0.81
76_K	79_A	0.736	0.81
127_I	133_Y	0.736	0.81
20_K	39_D	0.734	0.81
116_Q	122_G	0.720	0.79
70_T	73_N	0.718	0.79
38_A	93_I	0.713	0.79
93_I	97_K	0.710	0.78
113_L	117_V	0.704	0.78
95_G	98_K	0.692	0.77
111_L	119_I	0.692	0.77
34_H	40_L	0.691	0.77
65_Q	112_P	0.686	0.76
38_A	63_H	0.674	0.75
29_E	65_Q	0.673	0.75
69_R	117_V	0.665	0.74
36_P	97_K	0.664	0.74
25_R	69_R	0.662	0.73
71_S	124_L	0.661	0.73
26_D	40_L	0.651	0.72
12_Q	99_A	0.650	0.72
7_S	90_E	0.649	0.72
73_N	79_A	0.648	0.72
67_G	70_T	0.645	0.72
52_P	55_L	0.645	0.72
11_A	15_I	0.643	0.71
68_K	74_A	0.639	0.71
96_W	101_L	0.636	0.70
63_H	89_L	0.636	0.70
54_K	60_I	0.634	0.70
50_G	55_L	0.627	0.69
71_S	75_D	0.627	0.69
21_L	58_E	0.623	0.69
11_A	21_L	0.621	0.69
72_N	78_A	0.618	0.68
6_I	90_E	0.617	0.68
4_T	87_F	0.616	0.68
54_K	78_A	0.616	0.68
30_Y	63_H	0.612	0.68
51_L	57_H	0.607	0.67
64_C	75_D	0.602	0.66
35_I	63_H	0.602	0.66
33_E	103_V	0.592	0.65
4_T	85_E	0.587	0.64
57_H	85_E	0.587	0.64
74_A	78_A	0.585	0.64
43_L	48_Q	0.583	0.64
49_S	55_L	0.580	0.63
108_S	115_R	0.578	0.63
11_A	35_I	0.577	0.63
60_I	86_I	0.577	0.63
18_G	84_A	0.573	0.63
11_A	96_W	0.572	0.62
95_G	101_L	0.572	0.62
23_D	29_E	0.565	0.61
9_H	16_A	0.564	0.61
111_L	128_G	0.558	0.60
111_L	115_R	0.558	0.60
43_L	125_I	0.557	0.60
23_D	92_G	0.556	0.60
71_S	74_A	0.555	0.60
92_G	95_G	0.554	0.60
24_I	69_R	0.553	0.60
56_R	83_P	0.551	0.60
20_K	109_Q	0.549	0.59
60_I	94_D	0.545	0.59
117_V	121_A	0.542	0.58
43_L	64_C	0.540	0.58
38_A	96_W	0.539	0.58
25_R	77_L	0.537	0.58
51_L	60_I	0.537	0.58
5_T	95_G	0.536	0.57
10_D	17_R	0.536	0.57
61_I	96_W	0.535	0.57
54_K	127_I	0.535	0.57
63_H	97_K	0.533	0.57
67_G	77_L	0.532	0.57
58_E	71_S	0.532	0.57
34_H	63_H	0.529	0.56
26_D	29_E	0.528	0.56
32_R	112_P	0.527	0.56
43_L	122_G	0.526	0.56
111_L	118_Q	0.526	0.56
130_V	133_Y	0.525	0.56
68_K	72_N	0.525	0.56
69_R	77_L	0.525	0.56
32_R	110_P	0.518	0.55
46_L	124_L	0.516	0.55
73_N	77_L	0.511	0.54
14_L	61_I	0.504	0.53
74_A	77_L	0.502	0.53
119_I	122_G	0.500	0.52

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
1rhsA	1	0.9713	100	0.489	Contact Map
1urhA	1	0.9655	100	0.498	Contact Map
4jgtA	1	0.977	100	0.5	Contact Map
1e0cA	1	0.9713	100	0.504	Contact Map
1okgA	1	0.8966	100	0.508	Contact Map
3aayA	1	0.9253	100	0.511	Contact Map
1uarA	1	0.9885	100	0.512	Contact Map
3utnX	1	0.9598	100	0.515	Contact Map
3hzuA	2	0.9253	99.9	0.528	Contact Map
1yt8A	1	0.9655	99.9	0.539	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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