DUF748 - PFAM28P - GREMLIN Contacts

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DUF748 - Domain of Unknown Function (DUF748)

PFAM:	PF05359	Sequences: WPVSIGRLALEDGRVDFTDRSVKPPFRLTLSDLNLTLTNLSTLPDAPAPVDLSARLNGGGPLSLSGTLNPLPLAADLKLKLKGLDLAPLQPYLPKYLGLDLASGKLSLDLEYRFAKGDGPKLTASGKLTLDDLALGDKVESEDLLKWKSLPV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	152 (144)
Sequences:	32555 (25017)
Seq/√Len:	2084.8
META:	0.922

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_K	111_E	2.800	1.00
51_D	65_S	2.682	1.00
80_K	109_D	2.627	1.00
32_D	55_R	2.592	1.00
7_R	38_T	2.547	1.00
7_R	36_T	2.529	1.00
16_D	29_T	2.451	1.00
18_T	27_R	2.392	1.00
53_S	63_S	2.277	1.00
9_A	36_T	2.235	1.00
78_K	109_D	2.152	1.00
63_S	80_K	2.141	1.00
14_R	29_T	2.138	1.00
83_G	105_K	2.069	1.00
11_E	34_N	2.066	1.00
76_D	113_R	2.009	1.00
12_D	32_D	1.985	1.00
107_S	131_D	1.977	1.00
50_V	66_G	1.905	1.00
38_T	49_P	1.885	1.00
16_D	27_R	1.867	1.00
65_S	78_K	1.837	1.00
49_P	67_T	1.831	1.00
55_R	61_P	1.722	1.00
51_D	63_S	1.666	1.00
111_E	125_S	1.607	1.00
103_S	132_D	1.602	1.00
47_P	67_T	1.593	1.00
79_L	110_L	1.592	1.00
14_R	31_S	1.576	1.00
34_N	53_S	1.574	1.00
5_I	8_L	1.570	1.00
102_A	136_G	1.524	1.00
85_D	105_K	1.491	1.00
61_P	82_K	1.491	1.00
54_A	62_L	1.477	1.00
64_L	77_L	1.461	1.00
35_L	52_L	1.438	1.00
3_V	42_T	1.436	1.00
81_L	84_L	1.428	1.00
85_D	88_P	1.377	1.00
113_R	123_T	1.348	1.00
6_G	39_N	1.328	1.00
50_V	77_L	1.318	1.00
22_V	92_Y	1.315	1.00
36_T	51_D	1.305	1.00
56_L	60_G	1.299	1.00
67_T	76_D	1.286	1.00
102_A	134_A	1.281	1.00
69_N	72_P	1.278	1.00
77_L	112_Y	1.275	1.00
110_L	114_F	1.263	1.00
82_K	107_S	1.251	1.00
10_L	13_G	1.217	1.00
105_K	132_D	1.217	1.00
26_F	92_Y	1.191	1.00
110_L	124_A	1.190	1.00
100_D	136_G	1.187	1.00
90_Q	94_P	1.179	1.00
20_R	25_P	1.176	1.00
76_D	111_E	1.166	1.00
83_G	131_D	1.132	1.00
103_S	134_A	1.125	1.00
12_D	34_N	1.116	1.00
19_D	92_Y	1.115	1.00
30_L	54_A	1.109	1.00
9_A	34_N	1.104	1.00
53_S	61_P	1.098	1.00
107_S	129_T	1.095	1.00
57_N	88_P	1.084	1.00
4_S	41_S	1.069	1.00
31_S	55_R	1.065	1.00
109_D	127_K	1.059	1.00
30_L	56_L	1.059	1.00
17_F	92_Y	1.043	1.00
124_A	128_L	1.041	1.00
13_G	33_L	1.027	1.00
38_T	51_D	1.019	1.00
85_D	103_S	1.015	1.00
47_P	69_N	0.999	1.00
130_L	133_L	0.998	1.00
94_P	100_D	0.986	1.00
90_Q	93_L	0.986	1.00
11_E	36_T	0.977	1.00
43_L	46_A	0.942	1.00
33_L	54_A	0.938	1.00
75_A	114_F	0.929	1.00
137_D	140_E	0.919	1.00
66_G	77_L	0.910	1.00
100_D	138_K	0.882	1.00
134_A	143_D	0.880	1.00
83_G	107_S	0.874	1.00
24_P	94_P	0.873	1.00
81_L	108_L	0.872	1.00
29_T	57_N	0.860	1.00
60_G	84_L	0.849	1.00
37_L	50_V	0.842	1.00
108_L	112_Y	0.836	1.00
64_L	68_L	0.832	1.00
40_L	48_A	0.830	1.00
22_V	26_F	0.829	1.00
2_P	43_L	0.828	1.00
48_A	68_L	0.823	1.00
16_D	31_S	0.817	1.00
63_S	82_K	0.810	1.00
84_L	89_L	0.807	1.00
44_P	47_P	0.797	1.00
115_A	118_D	0.793	1.00
50_V	64_L	0.789	1.00
37_L	40_L	0.788	1.00
105_K	131_D	0.785	1.00
99_L	144_L	0.778	1.00
22_V	25_P	0.774	1.00
82_K	109_D	0.768	1.00
39_N	49_P	0.766	1.00
52_L	64_L	0.757	1.00
137_D	144_L	0.751	1.00
136_G	143_D	0.745	1.00
73_L	76_D	0.743	1.00
17_F	28_L	0.739	1.00
49_P	65_S	0.735	1.00
99_L	135_L	0.727	1.00
87_A	90_Q	0.727	1.00
31_S	57_N	0.723	1.00
18_T	25_P	0.718	1.00
30_L	33_L	0.715	1.00
90_Q	100_D	0.714	1.00
65_S	80_K	0.710	1.00
93_L	97_L	0.708	1.00
54_A	57_N	0.707	1.00
37_L	48_A	0.706	1.00
120_P	124_A	0.703	1.00
39_N	46_A	0.703	1.00
62_L	81_L	0.701	1.00
110_L	126_G	0.696	1.00
69_N	74_A	0.694	1.00
8_L	35_L	0.692	1.00
17_F	26_F	0.684	1.00
34_N	51_D	0.683	1.00
86_L	106_L	0.679	1.00
54_A	58_G	0.677	1.00
110_L	113_R	0.672	1.00
89_L	93_L	0.669	1.00
41_S	44_P	0.664	1.00
93_L	101_L	0.655	1.00
124_A	127_K	0.655	1.00
72_P	75_A	0.654	1.00
39_N	48_A	0.653	1.00
31_S	58_G	0.653	1.00
28_L	88_P	0.644	1.00
74_A	113_R	0.642	1.00
88_P	91_P	0.635	1.00
22_V	91_P	0.634	1.00
32_D	35_L	0.634	1.00
64_L	79_L	0.633	1.00
2_P	41_S	0.631	1.00
61_P	64_L	0.629	1.00
4_S	39_N	0.627	1.00
55_R	59_G	0.624	1.00
108_L	124_A	0.622	1.00
41_S	46_A	0.617	1.00
60_G	89_L	0.617	1.00
90_Q	98_G	0.616	1.00
60_G	88_P	0.614	1.00
87_A	103_S	0.610	1.00
101_L	133_L	0.608	1.00
49_P	52_L	0.602	1.00
108_L	128_L	0.602	1.00
115_A	119_G	0.600	1.00
4_S	43_L	0.598	1.00
77_L	81_L	0.596	1.00
7_R	39_N	0.589	1.00
37_L	66_G	0.588	1.00
32_D	53_S	0.582	1.00
44_P	71_L	0.581	1.00
98_G	138_K	0.577	1.00
10_L	35_L	0.572	1.00
68_L	73_L	0.571	1.00
137_D	142_E	0.571	1.00
125_S	128_L	0.565	1.00
95_K	98_G	0.565	1.00
91_P	94_P	0.564	1.00
28_L	89_L	0.564	1.00
91_P	96_Y	0.562	1.00
114_F	120_P	0.560	1.00
140_E	143_D	0.560	1.00
50_V	54_A	0.558	1.00
75_A	112_Y	0.556	1.00
28_L	92_Y	0.555	1.00
68_L	75_A	0.554	1.00
141_S	144_L	0.548	1.00
22_V	95_K	0.547	1.00
3_V	40_L	0.547	1.00
115_A	120_P	0.545	1.00
34_N	37_L	0.545	1.00
90_Q	97_L	0.544	1.00
58_G	88_P	0.543	1.00
79_L	108_L	0.542	1.00
68_L	72_P	0.536	1.00
13_G	32_D	0.536	1.00
73_L	114_F	0.533	1.00
29_T	58_G	0.532	1.00
2_P	5_I	0.528	1.00
28_L	57_N	0.527	1.00
21_S	25_P	0.524	1.00
142_E	145_L	0.524	1.00
118_D	121_K	0.523	1.00
86_L	93_L	0.519	1.00
87_A	102_A	0.518	1.00
23_K	95_K	0.516	1.00
48_A	70_P	0.515	1.00
116_K	121_K	0.512	1.00
59_G	83_G	0.510	1.00
93_L	96_Y	0.507	1.00
139_V	144_L	0.507	1.00
94_P	138_K	0.500	1.00

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
4kh9A	1	0.8421	11.3	0.891	Contact Map
1evlA	2	0.3355	6.4	0.903	Contact Map
1qf6A	1	0.3355	6.1	0.904	Contact Map
1vl4A	2	0.3882	3.7	0.913	Contact Map
3iklA	2	0.3092	3.6	0.914	Contact Map
4yguA	3	0.5855	3.3	0.916	Contact Map
1vpbA	2	0.4013	2.9	0.918	Contact Map
2mxaA	1	0.1382	2.7	0.919	Contact Map
3do6A	3	0.3355	2.6	0.92	Contact Map
2cfuA	2	0.5658	2.2	0.923	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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