SHR-BD - PFAM28P - GREMLIN Contacts

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SHR-BD - SHR-binding domain of vacuolar-sorting associated protein 13

PFAM:	PF06650	Sequences: FKVSIYSPYWIINKTGLPLQYRSKGSSGSAAGQAGEHEEARKALPLLFSFSDDDRKNRAQLRVGDSEWSKPFSLDAVGSSGEVVLPSSNGDSEYHVGVSVSEGEGKYKLTKVVTFTPRYVLKNKLSEDIEVREPGSSKWITLKPGELVPLHWLRNSKEKLLCLRFPGVNNQWSGPFNIDDIGSTHLKLRKEGGRQGLIRVEVLLEGATIFITFSDETKGAWPYRIENHSDVEITFYQKNPNVGEDGWKPIRYRLPPRSSMPYAWDDPAAKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	271 (266)
Sequences:	897 (670)
Seq/√Len:	41.1
META:	0.207

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_D	144_P	5.465	1.00
130_E	164_R	5.075	1.00
262_Y	265_D	3.563	1.00
225_I	254_L	3.545	1.00
11_I	115_F	3.388	1.00
121_L	213_F	3.355	1.00
47_L	50_F	3.284	1.00
163_L	213_F	3.202	1.00
235_F	254_L	3.126	1.00
97_G	118_R	3.016	1.00
198_I	213_F	2.963	1.00
202_V	225_I	2.921	1.00
174_G	266_D	2.859	1.00
96_V	115_F	2.810	1.00
10_W	110_T	2.730	1.00
202_V	219_G	2.641	1.00
143_K	146_E	2.586	1.00
187_K	265_D	2.460	1.00
224_R	228_H	2.439	1.00
45_P	48_F	2.337	1.00
255_P	258_S	2.260	1.00
227_N	237_Q	2.234	1.00
222_P	265_D	2.221	1.00
14_K	114_T	2.179	0.99
252_Y	265_D	2.132	0.99
8_P	109_L	2.115	0.99
78_G	81_G	2.018	0.99
48_F	59_A	1.985	0.99
209_I	213_F	1.966	0.99
130_E	141_T	1.943	0.99
126_S	215_D	1.902	0.99
29_S	33_Q	1.896	0.99
236_Y	251_R	1.850	0.98
57_N	75_D	1.821	0.98
50_F	59_A	1.775	0.98
97_G	207_A	1.739	0.97
201_E	235_F	1.722	0.97
102_E	111_K	1.696	0.97
121_L	187_K	1.678	0.97
45_P	49_S	1.678	0.97
22_R	68_W	1.670	0.97
29_S	32_G	1.659	0.97
77_V	100_V	1.653	0.96
14_K	22_R	1.607	0.96
128_D	143_K	1.600	0.96
74_L	115_F	1.595	0.96
197_L	221_W	1.582	0.95
15_T	256_P	1.553	0.95
235_F	260_M	1.544	0.95
82_E	95_H	1.495	0.94
118_R	207_A	1.493	0.94
258_S	261_P	1.484	0.94
173_S	225_I	1.481	0.94
176_F	186_L	1.471	0.93
131_V	146_E	1.458	0.93
110_T	198_I	1.458	0.93
12_I	121_L	1.434	0.92
174_G	186_L	1.381	0.91
182_G	185_H	1.379	0.91
108_K	148_V	1.366	0.90
10_W	221_W	1.354	0.90
44_L	47_L	1.353	0.90
13_N	18_P	1.348	0.90
211_I	219_G	1.340	0.90
90_G	113_V	1.328	0.89
95_H	106_K	1.328	0.89
110_T	152_W	1.326	0.89
7_S	19_L	1.318	0.89
46_L	53_D	1.300	0.88
19_L	50_F	1.291	0.88
7_S	114_T	1.273	0.87
133_E	174_G	1.271	0.87
74_L	235_F	1.255	0.86
111_K	210_F	1.251	0.86
239_N	243_G	1.239	0.85
50_F	57_N	1.235	0.85
11_I	19_L	1.230	0.85
54_D	61_L	1.229	0.85
171_Q	188_L	1.229	0.85
102_E	105_G	1.221	0.85
62_R	68_W	1.217	0.84
8_P	133_E	1.204	0.84
205_E	210_F	1.198	0.83
90_G	159_K	1.189	0.83
10_W	16_G	1.188	0.83
65_D	84_V	1.182	0.83
33_Q	36_E	1.175	0.82
120_V	175_P	1.172	0.82
185_H	188_L	1.161	0.81
19_L	115_F	1.151	0.81
176_F	200_V	1.148	0.81
121_L	131_V	1.147	0.81
11_I	52_D	1.135	0.80
112_V	126_S	1.130	0.80
118_R	172_W	1.118	0.79
232_E	256_P	1.115	0.79
94_Y	200_V	1.099	0.78
98_V	108_K	1.094	0.77
172_W	178_I	1.093	0.77
230_D	258_S	1.088	0.77
48_F	262_Y	1.084	0.77
65_D	129_I	1.084	0.77
118_R	197_L	1.083	0.77
45_P	59_A	1.080	0.77
32_G	35_G	1.077	0.76
18_P	130_E	1.073	0.76
172_W	223_Y	1.067	0.76
70_K	119_Y	1.065	0.75
172_W	237_Q	1.050	0.74
243_G	246_G	1.048	0.74
86_P	150_L	1.039	0.74
31_A	37_H	1.032	0.73
45_P	262_Y	1.028	0.73
109_L	133_E	1.027	0.73
27_S	53_D	1.022	0.72
94_Y	152_W	1.019	0.72
126_S	198_I	1.011	0.72
32_G	56_K	1.009	0.71
224_R	259_S	1.009	0.71
78_G	111_K	1.004	0.71
226_E	259_S	1.003	0.71
74_L	143_K	1.002	0.71
69_S	78_G	1.000	0.71
178_I	181_I	0.999	0.71
188_L	229_S	0.998	0.71
170_N	174_G	0.993	0.70
224_R	237_Q	0.993	0.70
176_F	229_S	0.985	0.70
41_R	44_L	0.984	0.70
146_E	158_E	0.981	0.69
80_S	99_S	0.976	0.69
68_W	99_S	0.974	0.69
167_G	170_N	0.974	0.69
133_E	189_R	0.973	0.69
50_F	119_Y	0.970	0.68
130_E	166_P	0.966	0.68
18_P	40_A	0.963	0.68
205_E	212_T	0.962	0.68
39_E	52_D	0.959	0.68
40_A	44_L	0.955	0.67
40_A	48_F	0.953	0.67
150_L	154_R	0.952	0.67
72_F	96_V	0.941	0.66
115_F	196_G	0.938	0.66
103_G	107_Y	0.938	0.66
38_E	47_L	0.934	0.65
121_L	124_K	0.933	0.65
27_S	33_Q	0.925	0.65
200_V	213_F	0.918	0.64
67_E	77_V	0.914	0.64
72_F	219_G	0.910	0.63
163_L	173_S	0.906	0.63
255_P	259_S	0.903	0.63
135_G	229_S	0.900	0.63
41_R	48_F	0.899	0.62
239_N	242_V	0.891	0.62
105_G	199_R	0.891	0.62
98_V	203_L	0.889	0.62
182_G	223_Y	0.882	0.61
8_P	48_F	0.881	0.61
223_Y	252_Y	0.879	0.61
21_Y	129_I	0.878	0.61
59_A	176_F	0.878	0.61
133_E	152_W	0.878	0.61
150_L	175_P	0.872	0.60
110_T	255_P	0.871	0.60
113_V	137_S	0.871	0.60
73_S	77_V	0.865	0.59
73_S	111_K	0.861	0.59
37_H	40_A	0.860	0.59
61_L	136_S	0.857	0.59
208_T	220_A	0.854	0.58
232_E	255_P	0.850	0.58
125_L	215_D	0.850	0.58
30_A	33_Q	0.846	0.58
11_I	60_Q	0.839	0.57
129_I	213_F	0.839	0.57
38_E	52_D	0.837	0.57
147_L	226_E	0.836	0.57
240_P	255_P	0.835	0.57
199_R	216_E	0.834	0.57
3_V	178_I	0.833	0.57
122_K	212_T	0.831	0.56
121_L	200_V	0.826	0.56
100_V	103_G	0.823	0.56
129_I	189_R	0.820	0.55
14_K	119_Y	0.818	0.55
19_L	98_V	0.814	0.55
118_R	181_I	0.811	0.55
77_V	80_S	0.804	0.54
237_Q	265_D	0.800	0.54
53_D	59_A	0.798	0.53
5_I	96_V	0.798	0.53
28_G	33_Q	0.796	0.53
92_S	96_V	0.791	0.53
225_I	235_F	0.787	0.52
44_L	49_S	0.784	0.52
42_K	51_S	0.782	0.52
150_L	153_L	0.780	0.52
77_V	111_K	0.779	0.52
102_E	109_L	0.777	0.51
234_T	251_R	0.777	0.51
28_G	34_A	0.774	0.51
5_I	252_Y	0.773	0.51
38_E	44_L	0.772	0.51
19_L	32_G	0.770	0.51
124_K	165_F	0.769	0.51
257_R	263_A	0.764	0.50
133_E	151_H	0.764	0.50
96_V	172_W	0.763	0.50
5_I	38_E	0.761	0.50
249_P	269_A	0.761	0.50
4_S	16_G	0.760	0.50
82_E	235_F	0.757	0.50
200_V	211_I	0.757	0.50
40_A	47_L	0.753	0.49
85_L	133_E	0.753	0.49
125_L	198_I	0.753	0.49
45_P	50_F	0.751	0.49
97_G	104_E	0.750	0.49
78_G	252_Y	0.748	0.49
75_D	262_Y	0.746	0.48
12_I	45_P	0.746	0.48
72_F	81_G	0.746	0.48
121_L	128_D	0.744	0.48
5_I	10_W	0.742	0.48
181_I	209_I	0.741	0.48
124_K	145_G	0.740	0.48
68_W	84_V	0.735	0.47
148_V	192_G	0.734	0.47
20_Q	179_D	0.733	0.47
5_I	80_S	0.733	0.47
113_V	163_L	0.732	0.47
259_S	266_D	0.732	0.47
200_V	261_P	0.731	0.47
140_I	150_L	0.730	0.47
216_E	219_G	0.729	0.47
114_T	222_P	0.726	0.47
253_R	256_P	0.724	0.46
38_E	41_R	0.720	0.46
77_V	81_G	0.719	0.46
116_T	208_T	0.718	0.46
15_T	70_K	0.717	0.46
9_Y	73_S	0.716	0.46
209_I	220_A	0.711	0.45
22_R	29_S	0.711	0.45
173_S	183_S	0.710	0.45
243_G	269_A	0.709	0.45
40_A	51_S	0.706	0.45
78_G	83_V	0.706	0.45
91_D	176_F	0.705	0.45
132_R	161_L	0.705	0.45
198_I	214_S	0.705	0.45
11_I	129_I	0.704	0.45
253_R	261_P	0.703	0.45
88_S	130_E	0.702	0.44
104_E	107_Y	0.701	0.44
89_N	243_G	0.701	0.44
182_G	187_K	0.698	0.44
103_G	106_K	0.693	0.44
31_A	235_F	0.688	0.43
221_W	261_P	0.684	0.43
164_R	224_R	0.683	0.43
97_G	107_Y	0.681	0.43
120_V	210_F	0.676	0.42
24_K	29_S	0.673	0.42
126_S	211_I	0.671	0.42
6_Y	145_G	0.670	0.42
10_W	152_W	0.670	0.42
130_E	258_S	0.660	0.41
38_E	50_F	0.660	0.41
107_Y	257_R	0.657	0.40
89_N	213_F	0.654	0.40
5_I	142_L	0.653	0.40
74_L	78_G	0.652	0.40
41_R	46_L	0.651	0.40
198_I	202_V	0.648	0.40
40_A	50_F	0.647	0.39
145_G	214_S	0.647	0.39
236_Y	254_L	0.647	0.39
224_R	255_P	0.645	0.39
121_L	201_E	0.645	0.39
43_A	47_L	0.645	0.39
27_S	31_A	0.642	0.39
174_G	181_I	0.641	0.39
181_I	187_K	0.641	0.39
11_I	98_V	0.640	0.39
233_I	257_R	0.638	0.39
47_L	58_R	0.637	0.39
22_R	41_R	0.637	0.39
40_A	163_L	0.636	0.38
52_D	219_G	0.633	0.38
65_D	116_T	0.632	0.38
38_E	46_L	0.632	0.38
115_F	173_S	0.632	0.38
107_Y	137_S	0.630	0.38
12_I	120_V	0.628	0.38
73_S	79_S	0.627	0.38
107_Y	236_Y	0.627	0.38
29_S	37_H	0.625	0.38
125_L	192_G	0.622	0.37
88_S	225_I	0.622	0.37
151_H	216_E	0.622	0.37
58_R	72_F	0.621	0.37
103_G	108_K	0.620	0.37
163_L	166_P	0.619	0.37
33_Q	63_V	0.619	0.37
63_V	204_L	0.618	0.37
97_G	116_T	0.618	0.37
17_L	42_K	0.618	0.37
38_E	42_K	0.617	0.37
97_G	161_L	0.611	0.36
121_L	151_H	0.607	0.36
208_T	256_P	0.607	0.36
100_V	169_N	0.605	0.36
123_N	227_N	0.602	0.36
11_I	116_T	0.601	0.35
26_S	191_E	0.599	0.35
58_R	71_P	0.595	0.35
47_L	53_D	0.595	0.35
27_S	30_A	0.594	0.35
83_V	134_P	0.594	0.35
10_W	81_G	0.592	0.35
174_G	189_R	0.591	0.35
199_R	207_A	0.588	0.34
135_G	138_K	0.583	0.34
129_I	165_F	0.583	0.34
195_Q	234_T	0.583	0.34
126_S	144_P	0.583	0.34
254_L	257_R	0.579	0.34
118_R	182_G	0.579	0.34
98_V	226_E	0.576	0.33
72_F	145_G	0.576	0.33
50_F	73_S	0.575	0.33
43_A	50_F	0.571	0.33
98_V	163_L	0.570	0.33
65_D	119_Y	0.570	0.33
7_S	128_D	0.567	0.33
33_Q	202_V	0.567	0.33
66_S	149_P	0.566	0.33
211_I	214_S	0.566	0.33
17_L	68_W	0.564	0.32
97_G	220_A	0.562	0.32
43_A	48_F	0.559	0.32
27_S	32_G	0.559	0.32
202_V	249_P	0.558	0.32
186_L	189_R	0.558	0.32
81_G	87_S	0.555	0.32
29_S	35_G	0.555	0.32
146_E	151_H	0.553	0.31
21_Y	168_V	0.550	0.31
62_R	100_V	0.548	0.31
165_F	212_T	0.547	0.31
75_D	92_S	0.547	0.31
34_A	37_H	0.546	0.31
204_L	265_D	0.545	0.31
236_Y	260_M	0.544	0.31
82_E	97_G	0.544	0.31
237_Q	264_W	0.542	0.31
5_I	51_S	0.541	0.31
113_V	256_P	0.540	0.30
34_A	200_V	0.539	0.30
89_N	233_I	0.539	0.30
133_E	154_R	0.538	0.30
182_G	221_W	0.537	0.30
129_I	156_S	0.536	0.30
218_K	238_K	0.535	0.30
251_R	258_S	0.534	0.30
52_D	88_S	0.533	0.30
4_S	164_R	0.533	0.30
129_I	246_G	0.531	0.30
131_V	234_T	0.530	0.30
64_G	229_S	0.527	0.29
23_S	97_G	0.524	0.29
86_P	115_F	0.524	0.29
6_Y	111_K	0.524	0.29
130_E	136_S	0.523	0.29
208_T	237_Q	0.522	0.29
13_N	21_Y	0.521	0.29
97_G	210_F	0.521	0.29
72_F	195_Q	0.520	0.29
10_W	17_L	0.520	0.29
54_D	60_Q	0.517	0.29
174_G	180_D	0.516	0.29
104_E	207_A	0.516	0.29
77_V	102_E	0.515	0.29
64_G	238_K	0.513	0.28
258_S	262_Y	0.510	0.28
175_P	178_I	0.509	0.28
129_I	138_K	0.509	0.28
121_L	186_L	0.509	0.28
54_D	58_R	0.507	0.28
140_I	146_E	0.506	0.28
226_E	261_P	0.504	0.28
212_T	235_F	0.504	0.28
241_N	244_E	0.504	0.28
39_E	232_E	0.504	0.28
264_W	268_A	0.500	0.27
201_E	206_G	0.500	0.27

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
4gioA	1	0.3506	4.4	0.965	Contact Map
4joxA	1	0.2952	3.8	0.966	Contact Map
3fsaA	1	0.3801	2.3	0.97	Contact Map
4jdeB	1	0.214	2.2	0.97	Contact Map
1g0yI	1	0.048	2	0.971	Contact Map
4h25C	1	0.0812	1.9	0.971	Contact Map
3isyA	1	0.2952	1.9	0.971	Contact Map
4jdeA	1	0.214	1.7	0.972	Contact Map
2ccwA	1	0.3985	1.6	0.972	Contact Map
1ncgA	2	0.3173	1.6	0.972	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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