DUF4297 - PFAM28P - GREMLIN Contacts

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DUF4297 - Domain of unknown function (DUF4297)

PFAM:	PF14130	Sequences: REKGGSDARNRFDYQDHWALCKLLELHEDGDDYLVFCEYHDDIVVLDSESSPTKIEFYQVKTKESGKWTLKELTKRKKGKKGKPSSILGKLLKNKKDFPDEISSLRFVSNAGFSLKLKDLKKSLDSRKEICLSDLDKELLKKIKKKLKKELSLSGEDVEEWLDLSKLEFIRSDLSLEDHETHLIGKLAEFLEKLFPDSKSNANAIYRALIDEIRRKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	217 (212)
Sequences:	1003 (888)
Seq/√Len:	61.0
META:	0.754

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_A	12_F	5.589	1.00
4_G	8_A	4.121	1.00
27_H	33_Y	4.039	1.00
11_R	62_T	3.419	1.00
32_D	45_V	3.188	1.00
19_A	37_C	3.123	1.00
19_A	43_I	3.080	1.00
8_A	11_R	2.998	1.00
68_W	107_F	2.853	1.00
9_R	16_D	2.799	1.00
175_S	182_H	2.473	1.00
175_S	178_D	2.469	1.00
14_Y	172_S	2.417	1.00
7_D	11_R	2.413	1.00
69_T	72_E	2.378	1.00
4_G	7_D	2.296	1.00
4_G	11_R	2.245	1.00
18_W	22_K	2.244	1.00
212_E	215_R	2.217	1.00
18_W	108_V	2.198	1.00
137_K	141_K	2.137	1.00
28_E	193_K	2.069	1.00
40_H	44_V	2.032	1.00
15_Q	41_D	2.018	1.00
63_K	66_G	2.009	1.00
178_D	182_H	1.969	1.00
46_L	55_I	1.913	1.00
41_D	94_N	1.891	1.00
10_N	179_H	1.890	1.00
25_E	186_K	1.831	1.00
74_T	143_I	1.824	1.00
207_R	211_D	1.819	1.00
58_Y	106_R	1.813	1.00
211_D	215_R	1.811	1.00
15_Q	19_A	1.810	1.00
87_I	107_F	1.762	0.99
187_L	206_Y	1.721	0.99
2_E	94_N	1.664	0.99
210_I	213_I	1.642	0.99
95_K	105_L	1.588	0.99
181_T	189_E	1.577	0.99
54_K	103_S	1.556	0.99
71_K	75_K	1.546	0.99
11_R	16_D	1.507	0.98
184_I	187_L	1.450	0.98
22_K	26_L	1.440	0.98
72_E	75_K	1.428	0.98
20_L	23_L	1.419	0.97
32_D	48_S	1.416	0.97
14_Y	38_E	1.403	0.97
171_R	174_L	1.401	0.97
18_W	43_I	1.389	0.97
20_L	213_I	1.389	0.97
162_L	165_S	1.388	0.97
37_C	43_I	1.374	0.97
14_Y	60_V	1.359	0.97
178_D	181_T	1.350	0.96
2_E	40_H	1.349	0.96
140_L	144_K	1.316	0.96
56_E	103_S	1.310	0.96
56_E	104_S	1.297	0.96
141_K	145_K	1.293	0.96
41_D	57_F	1.267	0.95
79_G	84_P	1.254	0.95
37_C	213_I	1.252	0.95
180_E	184_I	1.235	0.94
15_Q	38_E	1.226	0.94
118_K	137_K	1.188	0.93
165_S	169_F	1.186	0.93
26_L	45_V	1.179	0.93
40_H	57_F	1.162	0.92
26_L	32_D	1.161	0.92
17_H	179_H	1.156	0.92
57_F	63_K	1.156	0.92
182_H	185_G	1.154	0.92
135_L	139_L	1.152	0.92
41_D	44_V	1.142	0.91
9_R	12_F	1.129	0.91
77_K	80_K	1.124	0.91
2_E	5_G	1.123	0.91
203_N	208_A	1.111	0.90
141_K	144_K	1.110	0.90
107_F	113_F	1.110	0.90
34_L	38_E	1.109	0.90
12_F	15_Q	1.091	0.89
38_E	115_L	1.087	0.89
6_S	38_E	1.084	0.89
174_L	190_F	1.083	0.89
79_G	83_K	1.034	0.87
40_H	98_F	1.026	0.86
6_S	11_R	1.005	0.85
6_S	14_Y	0.987	0.84
36_F	40_H	0.987	0.84
22_K	58_Y	0.982	0.84
11_R	17_H	0.978	0.84
197_D	200_S	0.969	0.83
11_R	176_L	0.968	0.83
146_K	149_K	0.965	0.83
211_D	214_R	0.963	0.83
76_R	89_G	0.960	0.82
67_K	72_E	0.957	0.82
91_L	94_N	0.955	0.82
57_F	94_N	0.951	0.82
195_F	198_S	0.950	0.82
131_C	134_D	0.940	0.81
147_L	150_E	0.933	0.81
89_G	150_E	0.933	0.81
73_L	107_F	0.929	0.80
68_W	72_E	0.926	0.80
115_L	169_F	0.921	0.80
77_K	81_K	0.921	0.80
40_H	86_S	0.920	0.80
69_T	114_S	0.917	0.79
20_L	32_D	0.915	0.79
42_D	59_Q	0.912	0.79
184_I	203_N	0.905	0.79
11_R	37_C	0.901	0.78
148_K	153_L	0.895	0.78
93_K	97_D	0.890	0.77
3_K	6_S	0.890	0.77
117_L	120_L	0.889	0.77
116_K	136_D	0.884	0.77
109_S	113_F	0.882	0.77
191_L	202_A	0.882	0.77
16_D	38_E	0.881	0.77
66_G	111_A	0.881	0.77
68_W	109_S	0.879	0.77
104_S	142_K	0.878	0.76
184_I	189_E	0.876	0.76
18_W	58_Y	0.862	0.75
106_R	167_L	0.861	0.75
192_E	203_N	0.856	0.75
63_K	72_E	0.855	0.75
181_T	186_K	0.853	0.74
9_R	15_Q	0.853	0.74
86_S	91_L	0.846	0.74
36_F	94_N	0.844	0.74
5_G	12_F	0.842	0.73
154_S	157_D	0.839	0.73
15_Q	42_D	0.838	0.73
17_H	206_Y	0.838	0.73
187_L	205_I	0.837	0.73
139_L	142_K	0.834	0.73
41_D	95_K	0.833	0.73
22_K	91_L	0.824	0.72
36_F	39_Y	0.816	0.71
60_V	76_R	0.815	0.71
194_L	198_S	0.809	0.70
200_S	208_A	0.809	0.70
186_K	213_I	0.805	0.70
199_K	204_A	0.802	0.70
207_R	212_E	0.802	0.70
57_F	86_S	0.784	0.68
205_I	213_I	0.771	0.67
147_L	151_L	0.769	0.66
141_K	146_K	0.766	0.66
6_S	10_N	0.763	0.66
13_D	18_W	0.759	0.65
11_R	102_I	0.758	0.65
210_I	215_R	0.757	0.65
37_C	105_L	0.756	0.65
123_S	126_S	0.754	0.65
38_E	44_V	0.754	0.65
21_C	183_L	0.753	0.65
18_W	21_C	0.752	0.65
131_C	138_E	0.752	0.65
32_D	60_V	0.751	0.65
23_L	182_H	0.751	0.65
39_Y	57_F	0.745	0.64
15_Q	40_H	0.745	0.64
145_K	154_S	0.741	0.64
179_H	183_L	0.737	0.63
62_T	110_N	0.737	0.63
189_E	203_N	0.734	0.63
14_Y	62_T	0.733	0.63
37_C	62_T	0.732	0.63
118_K	124_L	0.730	0.62
203_N	207_R	0.729	0.62
163_D	166_K	0.728	0.62
132_L	140_L	0.727	0.62
33_Y	185_G	0.724	0.62
149_K	152_S	0.723	0.62
92_L	111_A	0.721	0.61
11_R	40_H	0.715	0.61
5_G	15_Q	0.714	0.61
107_F	119_D	0.714	0.61
13_D	214_R	0.713	0.61
43_I	213_I	0.711	0.60
144_K	153_L	0.711	0.60
118_K	127_R	0.708	0.60
26_L	35_V	0.703	0.60
196_P	206_Y	0.698	0.59
109_S	171_R	0.695	0.59
156_E	160_E	0.695	0.59
63_K	110_N	0.694	0.59
80_K	152_S	0.694	0.59
49_E	52_P	0.694	0.59
8_A	16_D	0.692	0.58
202_A	205_I	0.692	0.58
2_E	57_F	0.692	0.58
179_H	182_H	0.688	0.58
12_F	176_L	0.685	0.58
60_V	85_S	0.679	0.57
109_S	201_N	0.678	0.57
38_E	113_F	0.675	0.56
22_K	45_V	0.675	0.56
145_K	149_K	0.672	0.56
184_I	188_A	0.672	0.56
192_E	207_R	0.669	0.56
198_S	207_R	0.667	0.56
5_G	8_A	0.666	0.55
36_F	46_L	0.664	0.55
69_T	82_G	0.664	0.55
71_K	74_T	0.663	0.55
42_D	61_K	0.663	0.55
205_I	212_E	0.662	0.55
78_K	84_P	0.662	0.55
41_D	46_L	0.658	0.55
45_V	56_E	0.651	0.54
140_L	143_I	0.648	0.53
199_K	205_I	0.645	0.53
13_D	210_I	0.645	0.53
54_K	102_I	0.641	0.53
180_E	187_L	0.638	0.52
170_I	173_D	0.637	0.52
157_D	160_E	0.635	0.52
198_S	210_I	0.633	0.52
24_L	187_L	0.632	0.52
7_D	10_N	0.630	0.51
204_A	208_A	0.628	0.51
125_D	140_L	0.627	0.51
112_G	169_F	0.626	0.51
198_S	205_I	0.623	0.51
9_R	17_H	0.622	0.50
57_F	70_L	0.622	0.50
99_P	148_K	0.620	0.50
86_S	90_K	0.620	0.50
81_K	84_P	0.620	0.50
32_D	49_E	0.617	0.50
197_D	205_I	0.615	0.50
43_I	175_S	0.613	0.49
132_L	167_L	0.611	0.49
172_S	175_S	0.610	0.49
20_L	105_L	0.603	0.48
38_E	94_N	0.598	0.48
56_E	106_R	0.597	0.48
113_F	169_F	0.596	0.48
44_V	55_I	0.592	0.47
66_G	105_L	0.592	0.47
103_S	154_S	0.592	0.47
90_K	105_L	0.591	0.47
68_W	87_I	0.588	0.47
55_I	102_I	0.588	0.47
4_G	10_N	0.584	0.46
31_D	142_K	0.583	0.46
5_G	62_T	0.580	0.46
195_F	201_N	0.577	0.45
199_K	202_A	0.574	0.45
136_D	139_L	0.574	0.45
62_T	94_N	0.570	0.45
93_K	124_L	0.570	0.45
127_R	156_E	0.569	0.44
32_D	56_E	0.568	0.44
15_Q	59_Q	0.566	0.44
204_A	211_D	0.565	0.44
14_Y	18_W	0.564	0.44
17_H	20_L	0.563	0.44
50_S	64_E	0.561	0.44
200_S	203_N	0.560	0.43
8_A	13_D	0.559	0.43
21_C	43_I	0.559	0.43
13_D	46_L	0.556	0.43
44_V	63_K	0.556	0.43
23_L	113_F	0.555	0.43
3_K	7_D	0.555	0.43
91_L	105_L	0.554	0.43
64_E	67_K	0.551	0.42
35_V	43_I	0.549	0.42
20_L	33_Y	0.549	0.42
71_K	144_K	0.548	0.42
196_P	199_K	0.547	0.42
23_L	90_K	0.547	0.42
88_L	109_S	0.543	0.42
135_L	149_K	0.542	0.41
11_R	179_H	0.542	0.41
80_K	83_K	0.541	0.41
71_K	142_K	0.541	0.41
60_V	71_K	0.541	0.41
29_D	133_S	0.540	0.41
13_D	17_H	0.539	0.41
99_P	102_I	0.535	0.41
107_F	160_E	0.531	0.40
77_K	134_D	0.530	0.40
132_L	147_L	0.530	0.40
19_A	66_G	0.527	0.40
55_I	162_L	0.527	0.40
79_G	82_G	0.525	0.40
6_S	17_H	0.523	0.39
26_L	91_L	0.523	0.39
17_H	92_L	0.522	0.39
40_H	62_T	0.521	0.39
150_E	163_D	0.516	0.39
33_Y	150_E	0.515	0.39
10_N	62_T	0.515	0.39
74_T	200_S	0.512	0.38
195_F	203_N	0.512	0.38
105_L	115_L	0.512	0.38
150_E	155_G	0.512	0.38
136_D	141_K	0.510	0.38
203_N	215_R	0.509	0.38
44_V	57_F	0.507	0.38
36_F	57_F	0.506	0.38
151_L	166_K	0.506	0.38
66_G	69_T	0.505	0.37
195_F	208_A	0.503	0.37
35_V	44_V	0.501	0.37
28_E	125_D	0.500	0.37
41_D	105_L	0.500	0.37

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
1wteA	2	0.8249	6.1	0.945	Contact Map
1ob8A	1	0.5622	5.2	0.947	Contact Map
1y88A	5	0.788	4.9	0.947	Contact Map
1nh2B	1	0.0876	3.5	0.951	Contact Map
1x4qA	1	0.3917	2.8	0.953	Contact Map
3p6zC	1	0	2.7	0.954	Contact Map
3wolA	2	0.6129	2.4	0.955	Contact Map
1nvpB	1	0.0783	2.3	0.956	Contact Map
2avaA	1	0.3548	2.2	0.956	Contact Map
2p7vA	1	0.3041	2.1	0.957	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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