DUF4835 - PFAM28P - GREMLIN Contacts

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DUF4835 - Domain of unknown function (DUF4835)

PFAM:	PF16119	Sequences: QELNCTVTVNAQQIQGTNKQVFKTLQTALTEFMNNRKWTNDVFKPNERIECNFLITITEYPSSNEFKATLQVQSSRPVYNSSYNTPLLNFNDKDFSFKYVEFQPLEFNENSFDSNLTSVLAFYAYIILGLDYDSFSPLGGTPYFQKAQNIVNNAQSSGEIKGWKAFDGNRNRYWLIENLLNPRYKPFREALYDYHRLGLDLMAENPDEGRANILEALELLQKVNRRRPNSYLLQVFFDAKSDEIVNIFSGAPPEEKTRVYEILSKIDPSNSSKYEKI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	277 (275)
Sequences:	4732 (3228)
Seq/√Len:	194.7
META:	0.902

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_E	67_K	4.241	1.00
87_L	134_S	3.677	1.00
33_M	124_A	3.566	1.00
29_L	120_L	3.303	1.00
205_N	208_E	3.067	1.00
41_D	132_Y	2.976	1.00
214_L	248_F	2.928	1.00
105_L	117_T	2.665	1.00
33_M	120_L	2.591	1.00
95_F	119_V	2.548	1.00
5_C	53_F	2.517	1.00
55_I	95_F	2.496	1.00
109_E	146_K	2.471	1.00
137_P	189_E	2.253	1.00
138_L	185_K	2.185	1.00
3_L	124_A	2.149	1.00
193_D	197_L	2.108	1.00
136_S	139_G	2.055	1.00
74_S	127_I	1.994	1.00
4_N	50_E	1.971	1.00
50_E	84_N	1.925	1.00
43_F	132_Y	1.915	1.00
5_C	51_C	1.913	1.00
201_L	209_G	1.901	1.00
134_S	191_L	1.901	1.00
74_S	87_L	1.900	1.00
267_D	274_Y	1.900	1.00
141_T	188_R	1.873	1.00
129_G	144_F	1.867	1.00
70_L	95_F	1.851	1.00
201_L	212_N	1.833	1.00
133_D	188_R	1.830	1.00
126_I	176_I	1.816	1.00
70_L	119_V	1.808	1.00
3_L	128_L	1.806	1.00
177_E	181_N	1.796	1.00
5_C	33_M	1.790	1.00
190_A	236_F	1.790	1.00
164_K	167_D	1.788	1.00
218_E	258_R	1.776	1.00
112_F	118_S	1.752	1.00
8_T	26_Q	1.707	1.00
90_F	231_Y	1.688	1.00
13_Q	58_T	1.680	1.00
55_I	70_L	1.678	1.00
221_Q	225_R	1.674	1.00
221_Q	265_K	1.664	1.00
57_I	68_A	1.663	1.00
65_E	98_K	1.646	1.00
11_A	19_K	1.642	1.00
7_V	29_L	1.631	1.00
198_G	213_I	1.577	1.00
126_I	175_L	1.567	1.00
189_E	193_D	1.528	1.00
267_D	270_N	1.523	1.00
24_T	101_E	1.506	1.00
176_I	180_L	1.504	1.00
32_F	121_A	1.489	1.00
23_K	26_Q	1.489	1.00
138_L	189_E	1.458	1.00
126_I	179_L	1.455	1.00
26_Q	30_T	1.453	1.00
124_A	128_L	1.449	1.00
144_F	191_L	1.434	1.00
138_L	141_T	1.429	1.00
197_L	212_N	1.425	1.00
78_V	85_T	1.425	1.00
151_V	176_I	1.412	1.00
3_L	33_M	1.407	1.00
67_K	96_S	1.399	1.00
186_P	189_E	1.397	1.00
244_I	263_L	1.394	1.00
213_I	247_I	1.363	1.00
187_F	232_L	1.358	1.00
193_D	219_L	1.347	1.00
270_N	273_K	1.339	1.00
53_F	70_L	1.336	1.00
260_Y	264_S	1.331	1.00
51_C	127_I	1.327	1.00
120_L	124_A	1.323	1.00
33_M	53_F	1.320	1.00
60_Y	66_F	1.306	1.00
126_I	147_A	1.301	1.00
2_E	43_F	1.301	1.00
190_A	216_A	1.290	1.00
218_E	221_Q	1.289	1.00
199_L	247_I	1.286	1.00
141_T	145_Q	1.285	1.00
214_L	259_V	1.283	1.00
236_F	244_I	1.283	1.00
31_E	35_N	1.282	1.00
149_N	153_N	1.275	1.00
179_L	232_L	1.271	1.00
244_I	259_V	1.266	1.00
201_L	204_E	1.262	1.00
25_L	29_L	1.261	1.00
68_A	95_F	1.256	1.00
129_G	147_A	1.248	1.00
14_I	57_I	1.247	1.00
187_F	191_L	1.244	1.00
217_L	262_I	1.244	1.00
189_E	219_L	1.241	1.00
215_E	218_E	1.232	1.00
175_L	235_V	1.228	1.00
264_S	275_E	1.227	1.00
145_Q	148_Q	1.225	1.00
50_E	75_S	1.213	1.00
212_N	215_E	1.210	1.00
219_L	222_K	1.209	1.00
20_Q	101_E	1.208	1.00
64_N	98_K	1.190	1.00
237_F	263_L	1.188	1.00
193_D	212_N	1.185	1.00
2_E	39_T	1.182	1.00
132_Y	143_Y	1.177	1.00
107_F	121_A	1.177	1.00
72_V	127_I	1.166	1.00
122_F	126_I	1.165	1.00
262_I	266_I	1.139	1.00
210_R	255_E	1.125	1.00
65_E	96_S	1.125	1.00
220_L	233_L	1.124	1.00
58_T	69_T	1.117	1.00
171_N	174_W	1.117	1.00
206_P	209_G	1.117	1.00
241_S	270_N	1.099	1.00
270_N	274_Y	1.095	1.00
230_S	233_L	1.094	1.00
78_V	199_L	1.094	1.00
29_L	55_I	1.093	1.00
183_R	227_R	1.091	1.00
241_S	273_K	1.090	1.00
130_L	144_F	1.088	1.00
129_G	179_L	1.085	1.00
257_T	261_E	1.077	1.00
22_F	60_Y	1.075	1.00
242_D	273_K	1.075	1.00
185_K	189_E	1.074	1.00
3_L	51_C	1.071	1.00
146_K	150_I	1.070	1.00
3_L	127_I	1.055	1.00
182_P	185_K	1.053	1.00
210_R	251_A	1.051	1.00
138_L	188_R	1.046	1.00
39_T	128_L	1.039	1.00
225_R	265_K	1.038	1.00
197_L	201_L	1.035	1.00
193_D	215_E	1.034	1.00
128_L	132_Y	1.027	1.00
192_Y	196_R	1.023	1.00
75_S	84_N	1.023	1.00
142_P	145_Q	1.023	1.00
190_A	220_L	1.023	1.00
7_V	33_M	1.015	1.00
117_T	121_A	1.015	1.00
118_S	150_I	1.010	1.00
186_P	222_K	0.987	0.99
78_V	83_Y	0.986	0.99
24_T	99_Y	0.975	0.99
173_Y	177_E	0.969	0.99
246_N	249_S	0.960	0.99
69_T	91_N	0.955	0.99
126_I	130_L	0.953	0.99
248_F	259_V	0.950	0.99
130_L	179_L	0.949	0.99
174_W	178_N	0.941	0.99
28_A	99_Y	0.932	0.99
107_F	125_Y	0.932	0.99
201_L	205_N	0.927	0.99
141_T	180_L	0.926	0.99
88_L	235_V	0.924	0.99
36_R	106_E	0.923	0.99
132_Y	136_S	0.905	0.99
100_V	103_Q	0.905	0.99
218_E	262_I	0.898	0.99
112_F	154_A	0.889	0.99
25_L	57_I	0.887	0.99
145_Q	180_L	0.886	0.99
199_L	202_M	0.886	0.99
252_P	255_E	0.886	0.99
128_L	143_Y	0.885	0.99
57_I	66_F	0.880	0.99
211_A	215_E	0.876	0.99
254_E	258_R	0.872	0.99
122_F	176_I	0.867	0.99
258_R	261_E	0.867	0.99
39_T	143_Y	0.855	0.99
113_D	118_S	0.850	0.98
237_F	241_S	0.849	0.98
209_G	212_N	0.846	0.98
56_T	69_T	0.843	0.98
203_A	209_G	0.842	0.98
137_P	193_D	0.842	0.98
133_D	138_L	0.842	0.98
222_K	226_R	0.838	0.98
144_F	176_I	0.837	0.98
112_F	157_S	0.836	0.98
170_R	234_Q	0.835	0.98
115_N	119_V	0.829	0.98
209_G	213_I	0.823	0.98
201_L	208_E	0.823	0.98
24_T	102_F	0.819	0.98
146_K	149_N	0.817	0.98
195_H	240_K	0.817	0.98
122_F	151_V	0.815	0.98
24_T	28_A	0.814	0.98
69_T	93_K	0.813	0.98
259_V	262_I	0.810	0.98
80_N	204_E	0.803	0.98
90_F	238_D	0.799	0.98
212_N	216_A	0.798	0.98
49_I	127_I	0.788	0.98
125_Y	150_I	0.787	0.98
61_P	65_E	0.785	0.97
112_F	115_N	0.784	0.97
38_W	121_A	0.782	0.97
92_D	172_R	0.781	0.97
241_S	245_V	0.781	0.97
59_E	62_S	0.779	0.97
245_V	273_K	0.774	0.97
53_F	72_V	0.772	0.97
2_E	37_K	0.770	0.97
144_F	179_L	0.770	0.97
20_Q	23_K	0.770	0.97
251_A	256_K	0.767	0.97
36_R	107_F	0.764	0.97
94_D	161_K	0.761	0.97
206_P	210_R	0.755	0.97
97_F	119_V	0.755	0.97
252_P	256_K	0.754	0.97
62_S	65_E	0.751	0.97
61_P	67_K	0.748	0.97
222_K	225_R	0.748	0.97
217_L	259_V	0.745	0.97
133_D	144_F	0.745	0.97
90_F	130_L	0.744	0.97
87_L	191_L	0.744	0.97
37_K	42_V	0.740	0.96
5_C	34_N	0.737	0.96
211_A	255_E	0.737	0.96
130_L	191_L	0.736	0.96
87_L	130_L	0.733	0.96
240_K	243_E	0.731	0.96
78_V	135_F	0.727	0.96
108_N	113_D	0.726	0.96
80_N	203_A	0.721	0.96
255_E	258_R	0.715	0.96
174_W	177_E	0.712	0.96
49_I	128_L	0.710	0.95
11_A	22_F	0.705	0.95
191_L	232_L	0.705	0.95
208_E	212_N	0.705	0.95
231_Y	235_V	0.704	0.95
25_L	60_Y	0.701	0.95
234_Q	238_D	0.701	0.95
176_I	179_L	0.701	0.95
220_L	266_I	0.700	0.95
64_N	100_V	0.698	0.95
121_A	150_I	0.696	0.95
6_T	52_N	0.690	0.95
55_I	120_L	0.689	0.95
184_Y	230_S	0.689	0.95
183_R	226_R	0.686	0.95
74_S	131_D	0.686	0.95
121_A	125_Y	0.684	0.94
259_V	263_L	0.679	0.94
130_L	232_L	0.679	0.94
21_V	66_F	0.678	0.94
253_P	257_T	0.677	0.94
271_S	275_E	0.677	0.94
264_S	271_S	0.675	0.94
9_V	26_Q	0.674	0.94
202_M	247_I	0.672	0.94
41_D	143_Y	0.671	0.94
88_L	123_Y	0.671	0.94
273_K	276_K	0.671	0.94
221_Q	262_I	0.667	0.94
6_T	30_T	0.663	0.93
148_Q	152_N	0.663	0.93
39_T	43_F	0.660	0.93
85_T	199_L	0.660	0.93
235_V	239_A	0.657	0.93
147_A	176_I	0.656	0.93
68_A	97_F	0.655	0.93
11_A	14_I	0.651	0.93
71_Q	91_N	0.650	0.93
8_T	54_L	0.648	0.93
245_V	249_S	0.648	0.93
55_I	68_A	0.646	0.93
139_G	142_P	0.646	0.93
14_I	17_T	0.643	0.92
190_A	219_L	0.642	0.92
7_V	55_I	0.641	0.92
119_V	172_R	0.640	0.92
162_G	167_D	0.639	0.92
224_N	230_S	0.639	0.92
12_Q	57_I	0.635	0.92
186_P	219_L	0.634	0.92
27_T	31_E	0.632	0.92
272_S	275_E	0.632	0.92
269_S	272_S	0.631	0.92
112_F	159_E	0.631	0.92
213_I	216_A	0.629	0.92
198_G	216_A	0.629	0.92
257_T	260_Y	0.628	0.92
208_E	211_A	0.627	0.91
260_Y	276_K	0.627	0.91
260_Y	275_E	0.625	0.91
241_S	267_D	0.624	0.91
55_I	119_V	0.622	0.91
223_V	233_L	0.621	0.91
7_V	53_F	0.621	0.91
54_L	71_Q	0.621	0.91
61_P	96_S	0.619	0.91
224_N	233_L	0.619	0.91
207_D	211_A	0.618	0.91
184_Y	223_V	0.617	0.91
109_E	149_N	0.611	0.90
148_Q	180_L	0.609	0.90
107_F	146_K	0.605	0.90
245_V	276_K	0.602	0.90
256_K	260_Y	0.601	0.90
224_N	266_I	0.600	0.90
68_A	119_V	0.599	0.90
94_D	168_G	0.594	0.89
125_Y	146_K	0.588	0.89
248_F	251_A	0.587	0.89
242_D	246_N	0.586	0.88
21_V	24_T	0.583	0.88
77_P	135_F	0.582	0.88
57_I	60_Y	0.578	0.88
187_F	233_L	0.578	0.88
15_Q	18_N	0.577	0.88
167_D	171_N	0.575	0.88
187_F	190_A	0.575	0.88
133_D	139_G	0.574	0.87
144_F	188_R	0.572	0.87
260_Y	274_Y	0.572	0.87
107_F	117_T	0.571	0.87
133_D	141_T	0.570	0.87
19_K	23_K	0.569	0.87
33_M	51_C	0.566	0.87
106_E	113_D	0.566	0.87
114_S	117_T	0.562	0.86
20_Q	24_T	0.562	0.86
137_P	197_L	0.561	0.86
45_P	48_R	0.561	0.86
126_I	144_F	0.560	0.86
25_L	55_I	0.560	0.86
147_A	150_I	0.560	0.86
231_Y	234_Q	0.559	0.86
28_A	105_L	0.558	0.86
253_P	256_K	0.557	0.86
180_L	188_R	0.557	0.86
2_E	128_L	0.556	0.86
187_F	236_F	0.556	0.86
58_T	67_K	0.555	0.86
207_D	255_E	0.554	0.86
214_L	258_R	0.554	0.86
86_P	239_A	0.554	0.86
188_R	223_V	0.553	0.85
14_I	19_K	0.553	0.85
15_Q	19_K	0.553	0.85
214_L	251_A	0.553	0.85
53_F	120_L	0.548	0.85
242_D	245_V	0.545	0.85
109_E	117_T	0.545	0.85
114_S	118_S	0.544	0.85
187_F	223_V	0.541	0.84
75_S	86_P	0.539	0.84
237_F	266_I	0.536	0.84
76_R	200_D	0.536	0.84
150_I	153_N	0.536	0.84
17_T	21_V	0.536	0.84
16_G	22_F	0.536	0.84
9_V	55_I	0.534	0.83
260_Y	271_S	0.533	0.83
30_T	34_N	0.531	0.83
53_F	127_I	0.531	0.83
16_G	60_Y	0.530	0.83
96_S	161_K	0.529	0.83
256_K	259_V	0.527	0.83
251_A	274_Y	0.527	0.83
40_N	142_P	0.524	0.82
227_R	231_Y	0.524	0.82
90_F	175_L	0.523	0.82
29_L	116_L	0.522	0.82
237_F	274_Y	0.519	0.82
198_G	212_N	0.517	0.81
6_T	26_Q	0.515	0.81
33_M	38_W	0.513	0.81
25_L	97_F	0.513	0.81
25_L	99_Y	0.513	0.81
224_N	229_N	0.512	0.81
29_L	33_M	0.512	0.81
186_P	226_R	0.512	0.81
112_F	153_N	0.511	0.81
118_S	153_N	0.510	0.81
148_Q	176_I	0.510	0.81
165_A	174_W	0.510	0.81
88_L	127_I	0.509	0.80
81_S	203_A	0.509	0.80
33_M	128_L	0.507	0.80
106_E	114_S	0.507	0.80
202_M	206_P	0.507	0.80
32_F	120_L	0.507	0.80
61_P	64_N	0.506	0.80
259_V	274_Y	0.506	0.80
198_G	201_L	0.505	0.80
92_D	119_V	0.502	0.80
72_V	91_N	0.500	0.79
162_G	172_R	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
2ouxA	2	0.2383	19.5	0.963	Contact Map
4bujB	1	0.2744	19	0.963	Contact Map
1g1eB	1	0.2419	12.7	0.966	Contact Map
1e91A	1	0.231	9.3	0.968	Contact Map
2katA	1	0.2996	8.8	0.968	Contact Map
4c0aA	1	0.2816	8.5	0.969	Contact Map
2zy9A	2	0.1697	7.6	0.969	Contact Map
4bmaA	1	0.1769	7	0.97	Contact Map
2f05A	1	0.231	6.8	0.97	Contact Map
3uswA	1	0.4043	6.6	0.97	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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