SPY - ECOLI - GREMLIN Contacts

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SPY - Spheroplast protein Y

UniProt:	P77754	Sequences: MRKLTALFVASTLALGAANLAHAADTTTAAPADAKPMMHHKGKFGPHQDMMFKDLNLTDAQKQQIREIMKGQRDQMKRPPLEERRAMHDIIASDTFDKVKAEAQIAKMEEQRKANMLAHMETQNKIYNILTPEQKKQFNANFEKRLTERPAAKGKMPATAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13490
Length:	161 (144)
Sequences:	409 (307)
Seq/√Len:	25.6

ECOLI - SPY CPXP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_I	126_I	5.991	1.00
98_K	121_E	3.871	1.00
105_I	109_E	3.769	1.00
54_D	141_N	3.401	1.00
68_I	122_T	3.273	1.00
98_K	102_E	2.999	1.00
68_I	129_I	2.777	0.99
124_N	128_N	2.655	0.99
59_D	62_K	2.533	0.99
101_A	120_M	2.439	0.99
101_A	117_L	2.257	0.98
115_N	119_H	2.187	0.97
71_G	125_K	2.185	0.97
83_E	107_K	2.102	0.96
96_F	101_A	2.093	0.96
63_Q	66_R	2.085	0.96
63_Q	67_E	1.937	0.94
93_S	97_D	1.932	0.94
127_Y	135_K	1.859	0.93
97_D	100_K	1.832	0.92
140_A	143_E	1.780	0.91
56_N	137_Q	1.774	0.91
105_I	117_L	1.651	0.88
91_I	120_M	1.649	0.88
65_I	68_I	1.630	0.87
96_F	120_M	1.617	0.87
97_D	133_E	1.569	0.85
18_A	132_P	1.567	0.85
21_A	145_R	1.551	0.84
78_R	86_A	1.484	0.81
88_H	124_N	1.481	0.81
57_L	130_L	1.454	0.80
100_K	125_K	1.436	0.79
21_A	27_T	1.423	0.79
53_K	56_N	1.379	0.76
102_E	106_A	1.365	0.76
61_Q	134_Q	1.305	0.72
105_I	112_R	1.273	0.70
109_E	113_K	1.270	0.70
137_Q	141_N	1.247	0.69
14_A	17_A	1.224	0.67
143_E	147_T	1.142	0.62
72_Q	122_T	1.141	0.62
136_K	140_A	1.135	0.61
130_L	134_Q	1.125	0.61
61_Q	130_L	1.125	0.61
113_K	116_M	1.117	0.60
105_I	128_N	1.111	0.60
91_I	96_F	1.108	0.59
13_L	128_N	1.097	0.59
125_K	129_I	1.087	0.58
128_N	135_K	1.075	0.57
58_T	91_I	1.072	0.57
8_F	115_N	1.060	0.56
64_Q	97_D	1.051	0.55
52_F	65_I	1.046	0.55
132_P	138_F	1.040	0.54
99_V	131_T	1.025	0.53
115_N	118_A	1.018	0.53
25_D	103_A	1.014	0.53
95_T	123_Q	1.001	0.52
80_P	111_Q	0.991	0.51
59_D	76_M	0.989	0.51
138_F	142_F	0.983	0.50
68_I	136_K	0.965	0.49
81_L	85_R	0.957	0.48
65_I	129_I	0.954	0.48
55_L	141_N	0.953	0.48
24_A	27_T	0.952	0.48
101_A	142_F	0.952	0.48
112_R	115_N	0.952	0.48
18_A	147_T	0.949	0.48
47_H	52_F	0.941	0.47
68_I	118_A	0.933	0.47
65_I	103_A	0.907	0.45
9_V	105_I	0.907	0.45
21_A	84_R	0.902	0.44
17_A	22_H	0.900	0.44
65_I	119_H	0.895	0.44
48_Q	69_M	0.888	0.43
13_L	97_D	0.883	0.43
106_A	113_K	0.882	0.43
57_L	134_Q	0.879	0.43
57_L	61_Q	0.879	0.43
46_P	150_P	0.879	0.43
6_A	28_T	0.877	0.43
23_A	58_T	0.872	0.42
62_K	138_F	0.869	0.42
60_A	64_Q	0.860	0.41
13_L	140_A	0.855	0.41
108_M	128_N	0.853	0.41
11_S	129_I	0.845	0.40
109_E	121_E	0.845	0.40
14_A	128_N	0.845	0.40
53_K	98_K	0.842	0.40
70_K	74_D	0.830	0.39
92_A	124_N	0.826	0.39
39_H	42_G	0.825	0.39
141_N	144_K	0.823	0.39
72_Q	133_E	0.823	0.39
66_R	137_Q	0.817	0.38
89_D	101_A	0.816	0.38
102_E	105_I	0.810	0.38
105_I	113_K	0.809	0.38
66_R	77_K	0.808	0.38
76_M	110_E	0.793	0.37
7_L	11_S	0.790	0.36
50_M	98_K	0.788	0.36
2_R	90_I	0.787	0.36
86_A	100_K	0.787	0.36
91_I	113_K	0.784	0.36
41_K	60_A	0.776	0.36
63_Q	69_M	0.775	0.35
68_I	126_I	0.774	0.35
62_K	122_T	0.767	0.35
18_A	150_P	0.756	0.34
10_A	13_L	0.756	0.34
25_D	28_T	0.749	0.34
93_S	96_F	0.748	0.34
81_L	128_N	0.748	0.34
62_K	135_K	0.747	0.34
85_R	93_S	0.742	0.33
96_F	117_L	0.738	0.33
88_H	142_F	0.738	0.33
124_N	127_Y	0.730	0.32
3_K	14_A	0.728	0.32
77_K	84_R	0.715	0.32
8_F	11_S	0.712	0.31
4_L	73_R	0.707	0.31
53_K	144_K	0.707	0.31
8_F	21_A	0.707	0.31
4_L	46_P	0.706	0.31
136_K	147_T	0.705	0.31
79_P	111_Q	0.704	0.31
66_R	82_E	0.700	0.31
83_E	104_Q	0.698	0.30
54_D	62_K	0.695	0.30
137_Q	146_L	0.694	0.30
17_A	147_T	0.694	0.30
60_A	63_Q	0.693	0.30
56_N	131_T	0.691	0.30
74_D	77_K	0.689	0.30
86_A	115_N	0.686	0.30
113_K	117_L	0.685	0.30
124_N	135_K	0.683	0.30
125_K	139_N	0.682	0.29
121_E	138_F	0.682	0.29
81_L	84_R	0.677	0.29
108_M	124_N	0.671	0.29
69_M	144_K	0.665	0.28
10_A	112_R	0.661	0.28
92_A	127_Y	0.654	0.28
91_I	138_F	0.645	0.27
64_Q	67_E	0.643	0.27
59_D	88_H	0.642	0.27
21_A	48_Q	0.640	0.27
52_F	143_E	0.638	0.27
48_Q	105_I	0.628	0.26
105_I	119_H	0.627	0.26
121_E	125_K	0.625	0.26
88_H	135_K	0.615	0.26
108_M	115_N	0.613	0.25
85_R	142_F	0.611	0.25
48_Q	65_I	0.604	0.25
148_E	151_A	0.604	0.25
77_K	80_P	0.596	0.25
9_V	46_P	0.595	0.24
147_T	151_A	0.595	0.24
66_R	74_D	0.593	0.24
118_A	121_E	0.591	0.24
10_A	132_P	0.589	0.24
10_A	14_A	0.588	0.24
12_T	94_D	0.581	0.24
22_H	26_T	0.580	0.24
87_M	112_R	0.576	0.23
29_A	147_T	0.569	0.23
104_Q	142_F	0.568	0.23
24_A	29_A	0.568	0.23
98_K	118_A	0.568	0.23
114_A	123_Q	0.567	0.23
40_H	44_F	0.566	0.23
138_F	141_N	0.566	0.23
139_N	142_F	0.565	0.23
59_D	107_K	0.561	0.23
15_L	90_I	0.557	0.22
64_Q	96_F	0.553	0.22
83_E	118_A	0.552	0.22
82_E	114_A	0.551	0.22
95_T	132_P	0.548	0.22
138_F	146_L	0.548	0.22
135_K	147_T	0.546	0.22
63_Q	70_K	0.545	0.22
77_K	137_Q	0.544	0.22
23_A	130_L	0.544	0.22
6_A	29_A	0.544	0.22
87_M	101_A	0.544	0.22
108_M	117_L	0.543	0.22
17_A	50_M	0.539	0.22
38_M	98_K	0.538	0.22
67_E	89_D	0.536	0.21
26_T	29_A	0.536	0.21
89_D	97_D	0.535	0.21
100_K	104_Q	0.533	0.21
41_K	44_F	0.532	0.21
42_G	143_E	0.529	0.21
18_A	145_R	0.524	0.21
5_T	9_V	0.519	0.21
136_K	141_N	0.517	0.20
6_A	9_V	0.512	0.20
28_T	31_P	0.511	0.20
55_L	75_Q	0.509	0.20
102_E	107_K	0.507	0.20
22_H	143_E	0.504	0.20
12_T	24_A	0.501	0.20
2_R	14_A	0.500	0.20
58_T	123_Q	0.500	0.20

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
3o39A	2	0.5963	99.9	0.395	Contact Map
3oeoA	3	0.5652	99.9	0.4	Contact Map
3itfA	2	0.6894	99.9	0.41	Contact Map
3zg1A	2	0.6522	99.9	0.437	Contact Map
4wwfA	2	0.6708	99.8	0.534	Contact Map
3layA	5	0.4845	99.6	0.595	Contact Map
2qguA	1	0.5528	67	0.899	Contact Map
4q4gX	1	0	50.8	0.908	Contact Map
2zzsA	4	0.4907	46.7	0.911	Contact Map
2marA	1	0.6894	44.4	0.912	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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