DUF4130 - PFAM28P - GREMLIN Contacts

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DUF4130 - Domain of unknown function (DUF4130

PFAM:	PF13566	Sequences: PEREALLYRYLWRGLRGGPRLLEDLADPDVLRLLKLAKKVRREAHKMKAFVRFREVEDGVYVAWIEPDHNILPLLAPHFADRFADMRWSIYDPKRKLALHYDDAPDEDAYEELWKTYYKSIFIPARLNPKLQRQEMPKRYWKNLPE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	146 (145)
Sequences:	6089 (4064)
Seq/√Len:	337.5
META:	0.828

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_K	75_L	3.215	1.00
133_R	138_K	3.172	1.00
9_R	29_D	2.969	1.00
70_N	97_L	2.887	1.00
44_A	48_K	2.705	1.00
76_A	99_L	2.483	1.00
118_Y	132_Q	2.480	1.00
13_R	27_D	2.424	1.00
54_R	111_E	2.328	1.00
62_V	91_Y	2.309	1.00
66_E	142_K	2.266	1.00
66_E	143_N	2.158	1.00
31_L	35_K	2.150	1.00
66_E	93_P	2.010	1.00
136_M	141_W	1.985	1.00
131_L	134_Q	1.955	1.00
122_F	127_L	1.950	1.00
68_D	139_R	1.916	1.00
64_W	93_P	1.903	1.00
131_L	135_E	1.885	1.00
55_E	61_Y	1.833	1.00
138_K	141_W	1.812	1.00
44_A	74_L	1.806	1.00
51_V	65_I	1.798	1.00
61_Y	86_M	1.796	1.00
129_P	133_R	1.727	1.00
10_Y	33_L	1.687	1.00
130_K	133_R	1.623	1.00
10_Y	22_L	1.608	1.00
6_L	32_R	1.584	1.00
45_H	48_K	1.501	1.00
37_A	41_R	1.495	1.00
44_A	75_L	1.485	1.00
124_P	127_L	1.460	1.00
112_E	115_K	1.446	1.00
45_H	49_A	1.389	1.00
51_V	63_A	1.346	1.00
32_R	35_K	1.346	1.00
32_R	36_L	1.342	1.00
116_T	120_S	1.255	1.00
5_A	9_R	1.233	1.00
39_K	68_D	1.231	1.00
20_R	23_E	1.224	1.00
40_V	69_H	1.222	1.00
43_E	71_I	1.217	1.00
92_D	95_R	1.197	1.00
128_N	131_L	1.189	1.00
47_M	71_I	1.188	1.00
33_L	37_A	1.187	1.00
93_P	143_N	1.172	1.00
43_E	139_R	1.164	1.00
39_K	69_H	1.159	1.00
132_Q	141_W	1.150	1.00
8_Y	12_W	1.141	1.00
130_K	134_Q	1.139	1.00
55_E	59_G	1.135	1.00
87_R	102_D	1.122	1.00
50_F	144_L	1.104	1.00
89_S	100_H	1.086	1.00
98_A	101_Y	1.085	1.00
70_N	95_R	1.085	1.00
18_G	21_L	1.081	1.00
51_V	90_I	1.080	1.00
106_D	109_A	1.051	1.00
11_L	15_L	1.042	1.00
89_S	98_A	1.030	1.00
54_R	64_W	1.029	1.00
107_E	111_E	1.026	1.00
66_E	94_K	1.019	1.00
6_L	33_L	1.016	1.00
55_E	104_A	1.001	1.00
9_R	12_W	0.996	1.00
95_R	101_Y	0.993	1.00
96_K	99_L	0.992	1.00
2_E	32_R	0.992	1.00
95_R	98_A	0.989	1.00
132_Q	136_M	0.982	1.00
34_L	37_A	0.979	1.00
56_V	60_V	0.977	1.00
13_R	29_D	0.974	1.00
63_A	90_I	0.973	1.00
140_Y	143_N	0.966	1.00
12_W	16_R	0.961	1.00
79_F	90_I	0.947	1.00
111_E	145_P	0.945	1.00
14_G	21_L	0.939	1.00
46_K	49_A	0.935	1.00
46_K	135_E	0.934	1.00
121_I	128_N	0.929	1.00
14_G	17_G	0.929	1.00
110_Y	113_L	0.928	1.00
47_M	65_I	0.922	1.00
64_W	143_N	0.913	1.00
46_K	140_Y	0.910	1.00
116_T	119_K	0.889	1.00
46_K	50_F	0.884	1.00
48_K	78_H	0.884	1.00
42_R	49_A	0.876	1.00
7_L	33_L	0.871	1.00
47_M	75_L	0.863	1.00
42_R	46_K	0.854	1.00
10_Y	30_V	0.853	1.00
117_Y	121_I	0.839	1.00
92_D	102_D	0.827	1.00
59_G	87_R	0.826	1.00
6_L	36_L	0.821	1.00
56_V	62_V	0.810	1.00
76_A	88_W	0.807	1.00
35_K	39_K	0.797	1.00
61_Y	85_D	0.796	1.00
68_D	94_K	0.792	1.00
99_L	102_D	0.783	1.00
31_L	34_L	0.782	1.00
104_A	107_E	0.781	1.00
2_E	5_A	0.773	1.00
3_R	69_H	0.772	1.00
109_A	112_E	0.771	1.00
18_G	24_D	0.771	1.00
96_K	100_H	0.770	1.00
134_Q	139_R	0.764	1.00
4_E	8_Y	0.764	1.00
13_R	21_L	0.763	1.00
133_R	141_W	0.763	1.00
60_V	87_R	0.763	1.00
77_P	81_D	0.760	1.00
92_D	101_Y	0.757	1.00
25_L	34_L	0.756	1.00
38_K	42_R	0.750	1.00
65_I	143_N	0.747	1.00
80_A	101_Y	0.745	0.99
65_I	72_L	0.740	0.99
96_K	101_Y	0.737	0.99
64_W	91_Y	0.736	0.99
43_E	68_D	0.734	0.99
93_P	96_K	0.731	0.99
6_L	29_D	0.726	0.99
36_L	40_V	0.725	0.99
91_Y	104_A	0.710	0.99
83_F	99_L	0.708	0.99
37_A	40_V	0.707	0.99
21_L	30_V	0.704	0.99
20_R	24_D	0.702	0.99
73_P	97_L	0.698	0.99
95_R	99_L	0.697	0.99
72_L	99_L	0.695	0.99
141_W	144_L	0.694	0.99
136_M	144_L	0.682	0.99
12_W	15_L	0.681	0.99
76_A	80_A	0.681	0.99
112_E	119_K	0.677	0.99
34_L	38_K	0.675	0.99
38_K	41_R	0.670	0.99
96_K	102_D	0.669	0.99
49_A	75_L	0.669	0.99
97_L	101_Y	0.668	0.99
41_R	44_A	0.666	0.99
3_R	36_L	0.664	0.99
73_P	77_P	0.662	0.99
47_M	50_F	0.660	0.99
98_A	102_D	0.653	0.99
49_A	135_E	0.649	0.99
44_A	71_I	0.647	0.99
65_I	140_Y	0.642	0.98
77_P	99_L	0.641	0.98
13_R	16_R	0.638	0.98
47_M	51_V	0.626	0.98
42_R	135_E	0.617	0.98
129_P	132_Q	0.615	0.98
70_N	73_P	0.615	0.98
29_D	32_R	0.615	0.98
25_L	31_L	0.615	0.98
118_Y	122_F	0.613	0.98
62_V	89_S	0.608	0.98
42_R	45_H	0.605	0.98
58_D	87_R	0.604	0.98
104_A	108_D	0.603	0.98
13_R	24_D	0.600	0.98
108_D	111_E	0.597	0.98
115_K	119_K	0.588	0.97
72_L	97_L	0.586	0.97
26_A	31_L	0.584	0.97
74_L	77_P	0.583	0.97
80_A	88_W	0.583	0.97
136_M	140_Y	0.581	0.97
114_W	141_W	0.579	0.97
65_I	90_I	0.575	0.97
92_D	98_A	0.574	0.97
70_N	94_K	0.571	0.97
46_K	68_D	0.569	0.97
97_L	100_H	0.567	0.97
112_E	116_T	0.561	0.97
113_L	118_Y	0.560	0.96
50_F	136_M	0.555	0.96
40_V	44_A	0.554	0.96
54_R	103_D	0.554	0.96
108_D	112_E	0.550	0.96
70_N	74_L	0.549	0.96
131_L	136_M	0.549	0.96
21_L	24_D	0.547	0.96
78_H	90_I	0.546	0.96
45_H	52_R	0.542	0.96
60_V	89_S	0.540	0.96
27_D	32_R	0.540	0.96
3_R	6_L	0.537	0.96
103_D	108_D	0.531	0.95
17_G	24_D	0.531	0.95
29_D	33_L	0.530	0.95
17_G	22_L	0.529	0.95
45_H	50_F	0.526	0.95
61_Y	83_F	0.523	0.95
35_K	38_K	0.523	0.95
10_Y	15_L	0.523	0.95
13_R	17_G	0.516	0.94
122_F	132_Q	0.515	0.94
81_D	85_D	0.514	0.94
24_D	30_V	0.511	0.94
34_L	41_R	0.508	0.94
119_K	124_P	0.500	0.94

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
1yvlA	3	0.774	25.5	0.934	Contact Map
2xapA	4	0.8151	11.1	0.944	Contact Map
1bf5A	2	0.8493	7.4	0.948	Contact Map
2d8dA	2	0.2671	5.8	0.951	Contact Map
2r6iA	2	0.274	5.6	0.951	Contact Map
4um2A	1	0.6644	4.5	0.953	Contact Map
1y8qA	1	0.6712	4.3	0.954	Contact Map
2rioA	2	0.6849	3.2	0.956	Contact Map
3k8tA	2	0.7808	3.1	0.957	Contact Map
3hncA	2	0.7877	2.9	0.958	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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