Gly_rich - PFAM28P - GREMLIN Contacts

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Gly_rich - Glycine rich protein

PFAM:	PF12810	Sequences: TPQFVVPPTGTYKIEVWGAQGGGGSSSGGTGGKGGYSSGTITLTPGTTLYIYVGGQGGSGSSGSGGAGGYNGGGSGSGGGGGGGGGGATDIRGGTSLSSRIIVAGGGGGGGGSGGNGGAGGGLTGGNGGSGSGSGGGGGTQTAGGAGGTGGSFGQGGNGGSGGGGGGGGGGGGYYGGGGGGGGGGGGGGGSSYIGGSTTHTGGSTHYSGYYFTNTSTIAGNASMPSNSGNGYARITYLSSFKC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	243 (223)
Sequences:	3195 (2907)
Seq/√Len:	194.7
META:	0.829

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
152_S	155_Q	3.909	1.00
90_D	100_R	3.258	1.00
17_W	36_Y	3.146	1.00
89_T	233_A	3.146	1.00
15_E	38_S	3.132	1.00
15_E	36_Y	3.128	1.00
51_I	233_A	3.066	1.00
92_R	100_R	3.030	1.00
13_K	38_S	2.784	1.00
55_G	69_G	2.761	1.00
153_F	174_Y	2.589	1.00
37_S	192_S	2.582	1.00
94_G	98_S	2.549	1.00
97_L	100_R	2.510	1.00
14_I	91_I	2.394	1.00
13_K	40_T	2.215	1.00
94_G	99_S	2.114	1.00
197_S	215_T	2.046	1.00
195_G	198_T	2.045	1.00
20_Q	33_K	2.040	1.00
218_I	221_N	2.009	1.00
106_G	172_G	1.967	1.00
127_N	137_G	1.938	1.00
35_G	122_G	1.925	1.00
227_N	232_Y	1.917	1.00
23_G	31_G	1.898	1.00
20_Q	31_G	1.870	1.00
119_A	126_G	1.828	1.00
88_A	92_R	1.825	1.00
92_R	97_L	1.810	1.00
7_P	46_G	1.784	1.00
35_G	192_S	1.777	1.00
11_T	42_T	1.758	1.00
35_G	105_G	1.758	1.00
37_S	102_I	1.744	1.00
16_V	91_I	1.723	1.00
137_G	146_A	1.664	1.00
11_T	40_T	1.662	1.00
16_V	233_A	1.635	1.00
44_T	47_T	1.621	1.00
20_Q	227_N	1.605	1.00
52_Y	90_D	1.562	1.00
40_T	214_N	1.555	1.00
52_Y	70_Y	1.551	1.00
175_Y	191_S	1.545	1.00
69_G	84_G	1.542	1.00
100_R	103_V	1.534	1.00
66_G	84_G	1.529	1.00
17_W	232_Y	1.519	1.00
32_G	107_G	1.504	1.00
14_I	49_L	1.501	1.00
37_S	217_T	1.493	1.00
20_Q	56_Q	1.487	1.00
20_Q	228_S	1.463	1.00
155_Q	158_N	1.451	1.00
16_V	102_I	1.447	1.00
31_G	110_G	1.445	1.00
90_D	97_L	1.438	1.00
49_L	91_I	1.433	1.00
16_V	104_A	1.406	1.00
205_T	211_Y	1.395	1.00
88_A	103_V	1.376	1.00
206_H	209_G	1.355	1.00
9_T	46_G	1.330	1.00
20_Q	229_G	1.323	1.00
140_T	143_A	1.317	1.00
71_N	90_D	1.293	1.00
72_G	88_A	1.289	1.00
57_G	84_G	1.281	1.00
15_E	234_R	1.273	1.00
52_Y	92_R	1.264	1.00
105_G	192_S	1.264	1.00
24_G	83_G	1.258	1.00
15_E	236_T	1.258	1.00
204_S	207_Y	1.253	1.00
193_Y	196_G	1.244	1.00
96_S	99_S	1.243	1.00
93_G	100_R	1.219	1.00
57_G	83_G	1.218	1.00
71_N	88_A	1.216	1.00
102_I	194_I	1.203	1.00
94_G	97_L	1.202	1.00
122_G	192_S	1.176	1.00
52_Y	100_R	1.160	1.00
93_G	97_L	1.159	1.00
13_K	238_L	1.151	1.00
95_T	98_S	1.140	1.00
33_K	119_A	1.139	1.00
12_Y	43_L	1.138	1.00
33_K	228_S	1.127	1.00
24_G	110_G	1.104	1.00
56_Q	59_S	1.101	1.00
123_L	141_Q	1.100	1.00
58_G	84_G	1.096	1.00
194_I	197_S	1.081	1.00
139_G	188_G	1.072	1.00
17_W	37_S	1.067	1.00
9_T	44_T	1.066	1.00
217_T	221_N	1.066	1.00
153_F	157_G	1.057	1.00
156_G	176_G	1.054	1.00
91_I	233_A	1.046	1.00
14_I	233_A	1.042	1.00
194_I	215_T	1.030	1.00
55_G	71_N	1.014	1.00
188_G	191_S	1.013	1.00
37_S	194_I	1.011	1.00
127_N	138_G	1.009	1.00
136_G	188_G	1.007	1.00
137_G	188_G	1.001	1.00
145_G	157_G	0.989	1.00
95_T	99_S	0.980	0.99
105_G	139_G	0.978	0.99
22_G	57_G	0.977	0.99
39_G	198_T	0.976	0.99
94_G	100_R	0.968	0.99
93_G	101_I	0.964	0.99
55_G	68_G	0.963	0.99
93_G	98_S	0.957	0.99
88_A	100_R	0.955	0.99
206_H	212_F	0.955	0.99
195_G	212_F	0.934	0.99
16_V	37_S	0.929	0.99
227_N	234_R	0.928	0.99
41_I	101_I	0.916	0.99
22_G	109_G	0.909	0.99
109_G	169_G	0.908	0.99
193_Y	204_S	0.903	0.99
23_G	59_S	0.896	0.99
17_W	234_R	0.892	0.99
216_S	219_A	0.889	0.99
11_T	238_L	0.886	0.99
118_G	186_G	0.880	0.99
7_P	12_Y	0.877	0.99
204_S	209_G	0.875	0.99
90_D	103_V	0.875	0.99
7_P	47_T	0.875	0.99
172_G	176_G	0.874	0.99
204_S	211_Y	0.873	0.99
7_P	43_L	0.872	0.99
43_L	49_L	0.872	0.99
8_P	11_T	0.870	0.99
125_G	141_Q	0.866	0.99
118_G	128_G	0.865	0.99
8_P	237_Y	0.862	0.99
7_P	45_P	0.859	0.99
139_G	143_A	0.854	0.99
194_I	217_T	0.853	0.99
123_L	192_S	0.849	0.98
71_N	92_R	0.846	0.98
202_G	207_Y	0.845	0.98
153_F	156_G	0.845	0.98
202_G	205_T	0.845	0.98
203_G	206_H	0.842	0.98
203_G	207_Y	0.838	0.98
108_G	186_G	0.833	0.98
233_A	237_Y	0.833	0.98
52_Y	97_L	0.833	0.98
207_Y	210_Y	0.830	0.98
187_G	190_G	0.826	0.98
97_L	154_G	0.816	0.98
88_A	172_G	0.811	0.98
52_Y	95_T	0.810	0.98
154_G	157_G	0.810	0.98
117_G	186_G	0.810	0.98
31_G	107_G	0.797	0.98
53_V	89_T	0.791	0.98
9_T	42_T	0.790	0.98
39_G	197_S	0.788	0.98
119_A	221_N	0.788	0.98
19_A	55_G	0.786	0.97
175_Y	192_S	0.786	0.97
47_T	210_Y	0.785	0.97
32_G	117_G	0.782	0.97
196_G	212_F	0.781	0.97
124_T	127_N	0.781	0.97
51_I	91_I	0.777	0.97
221_N	232_Y	0.773	0.97
108_G	189_G	0.768	0.97
220_G	227_N	0.764	0.97
204_S	210_Y	0.760	0.97
49_L	101_I	0.757	0.97
39_G	102_I	0.756	0.97
19_A	57_G	0.754	0.97
7_P	11_T	0.751	0.97
206_H	211_Y	0.747	0.97
204_S	208_S	0.744	0.97
93_G	99_S	0.737	0.96
35_G	191_S	0.735	0.96
125_G	128_G	0.734	0.96
30_T	116_N	0.733	0.96
204_S	212_F	0.732	0.96
215_T	218_I	0.731	0.96
70_Y	74_G	0.728	0.96
88_A	97_L	0.727	0.96
14_I	235_I	0.726	0.96
68_G	84_G	0.726	0.96
232_Y	236_T	0.724	0.96
93_G	96_S	0.723	0.96
83_G	109_G	0.721	0.96
156_G	159_G	0.717	0.96
9_T	43_L	0.716	0.96
171_G	175_Y	0.713	0.96
9_T	12_Y	0.711	0.95
98_S	174_Y	0.711	0.95
138_G	188_G	0.708	0.95
169_G	172_G	0.706	0.95
22_G	59_S	0.702	0.95
55_G	230_N	0.701	0.95
192_S	195_G	0.699	0.95
56_Q	230_N	0.698	0.95
125_G	139_G	0.693	0.95
30_T	33_K	0.689	0.95
168_G	187_G	0.688	0.95
72_G	172_G	0.686	0.95
174_Y	206_H	0.680	0.94
96_S	100_R	0.676	0.94
193_Y	203_G	0.672	0.94
33_K	56_Q	0.672	0.94
171_G	174_Y	0.671	0.94
126_G	219_A	0.671	0.94
85_G	169_G	0.671	0.94
108_G	187_G	0.670	0.94
70_Y	90_D	0.666	0.94
40_T	238_L	0.664	0.94
144_G	152_S	0.664	0.94
100_R	174_Y	0.661	0.93
138_G	141_Q	0.660	0.93
205_T	208_S	0.660	0.93
21_G	107_G	0.656	0.93
206_H	210_Y	0.653	0.93
221_N	227_N	0.650	0.93
70_Y	88_A	0.649	0.93
195_G	206_H	0.645	0.93
84_G	169_G	0.639	0.92
38_S	216_S	0.639	0.92
140_T	144_G	0.637	0.92
143_A	146_A	0.636	0.92
116_N	119_A	0.633	0.92
174_Y	193_Y	0.633	0.92
70_Y	87_G	0.633	0.92
216_S	221_N	0.632	0.92
92_R	103_V	0.630	0.92
137_G	147_G	0.629	0.92
10_G	238_L	0.628	0.92
52_Y	71_N	0.628	0.92
218_I	227_N	0.628	0.92
234_R	237_Y	0.625	0.91
121_G	191_S	0.624	0.91
215_T	219_A	0.624	0.91
175_Y	202_G	0.624	0.91
181_G	184_G	0.623	0.91
195_G	204_S	0.621	0.91
50_Y	94_G	0.620	0.91
88_A	154_G	0.620	0.91
39_G	195_G	0.618	0.91
179_G	182_G	0.618	0.91
208_S	211_Y	0.614	0.91
203_G	210_Y	0.613	0.91
80_G	184_G	0.606	0.90
71_N	74_G	0.606	0.90
43_L	46_G	0.599	0.90
7_P	10_G	0.599	0.90
205_T	209_G	0.599	0.90
57_G	60_G	0.598	0.89
39_G	196_G	0.598	0.89
202_G	206_H	0.597	0.89
203_G	208_S	0.596	0.89
21_G	86_G	0.593	0.89
90_D	94_G	0.592	0.89
169_G	187_G	0.586	0.88
31_G	117_G	0.586	0.88
173_G	177_G	0.584	0.88
9_T	45_P	0.581	0.88
124_T	141_Q	0.580	0.88
18_G	21_G	0.574	0.87
126_G	129_G	0.573	0.87
43_L	47_T	0.571	0.87
95_T	100_R	0.571	0.87
94_G	101_I	0.571	0.87
32_G	110_G	0.570	0.87
55_G	87_G	0.569	0.87
193_Y	197_S	0.569	0.87
207_Y	212_F	0.568	0.87
108_G	118_G	0.566	0.87
141_Q	145_G	0.565	0.87
42_T	47_T	0.562	0.86
197_S	212_F	0.560	0.86
131_G	135_G	0.560	0.86
46_G	49_L	0.558	0.86
170_G	177_G	0.556	0.86
130_S	136_G	0.551	0.85
203_G	213_T	0.549	0.85
72_G	90_D	0.548	0.85
209_G	212_F	0.548	0.85
35_G	125_G	0.548	0.85
125_G	138_G	0.547	0.85
175_Y	188_G	0.547	0.85
148_G	185_G	0.546	0.85
58_G	68_G	0.544	0.85
7_P	16_V	0.539	0.84
125_G	188_G	0.537	0.84
211_Y	214_N	0.536	0.84
202_G	209_G	0.536	0.84
194_I	198_T	0.536	0.84
29_G	110_G	0.533	0.83
23_G	83_G	0.530	0.83
23_G	30_T	0.529	0.83
14_I	212_F	0.529	0.83
23_G	110_G	0.529	0.83
22_G	31_G	0.526	0.83
17_W	56_Q	0.525	0.82
129_G	136_G	0.522	0.82
234_R	238_L	0.522	0.82
153_F	158_N	0.521	0.82
180_G	183_G	0.520	0.82
50_Y	95_T	0.520	0.82
205_T	212_F	0.519	0.82
139_G	145_G	0.517	0.81
20_Q	23_G	0.516	0.81
213_T	218_I	0.515	0.81
7_P	237_Y	0.515	0.81
10_G	237_Y	0.514	0.81
130_S	182_G	0.514	0.81
60_G	83_G	0.514	0.81
47_T	198_T	0.512	0.81
74_G	158_N	0.512	0.81
21_G	32_G	0.507	0.80
8_P	45_P	0.507	0.80
97_L	103_V	0.506	0.80
10_G	45_P	0.506	0.80
141_Q	144_G	0.505	0.80
153_F	175_Y	0.501	0.79
214_N	217_T	0.500	0.79

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
4dzgA	1	0.1523	11.7	0.94	Contact Map
2cqkA	1	0.2346	4.1	0.951	Contact Map
4douA	1	0.3292	3.9	0.952	Contact Map
4g9sB	1	0.1564	3.6	0.953	Contact Map
1o91A	3	0.3251	3.6	0.953	Contact Map
2wnvC	1	0.3169	3.2	0.954	Contact Map
2eeaA	1	0.1605	3.1	0.954	Contact Map
3sk7A	1	0.1399	3.1	0.954	Contact Map
1j3eA	1	0.1399	3	0.954	Contact Map
4qqhA	3	0.3169	2.7	0.956	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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