DUF4189 - PFAM28P - GREMLIN Contacts

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DUF4189 - Domain of unknown function (DUF4189)

PFAM:	PF13827	Sequences: WGAIAYSPSGGAYGYSYNYPSRAAAEAAALAECAAKGGGDCKVVVTFRNGCGALAVGPKGGGYGWAVGATREEAENAALAECRKAGGKDCKVRASAC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	97 (96)
Sequences:	7246 (5350)
Seq/√Len:	546.0
META:	0.914

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_R	26_E	3.418	1.00
71_R	75_E	3.044	1.00
26_E	46_T	2.777	1.00
28_A	32_E	2.705	1.00
21_S	24_A	2.266	1.00
82_C	90_C	2.243	1.00
19_Y	28_A	2.221	1.00
30_L	43_V	2.168	1.00
33_C	41_C	1.965	1.00
47_F	52_G	1.953	1.00
70_T	73_E	1.952	1.00
5_A	30_L	1.760	1.00
75_E	95_S	1.710	1.00
2_G	47_F	1.707	1.00
22_R	46_T	1.684	1.00
50_G	67_V	1.681	1.00
68_G	77_A	1.679	1.00
55_A	79_L	1.675	1.00
19_Y	24_A	1.656	1.00
41_C	51_C	1.639	1.00
55_A	78_A	1.625	1.00
16_S	19_Y	1.546	1.00
68_G	73_E	1.472	1.00
7_S	40_D	1.455	1.00
26_E	43_V	1.440	1.00
81_E	84_K	1.407	1.00
5_A	43_V	1.398	1.00
77_A	81_E	1.385	1.00
58_P	89_D	1.377	1.00
53_A	74_A	1.363	1.00
20_P	24_A	1.337	1.00
41_C	90_C	1.275	1.00
66_A	77_A	1.268	1.00
1_W	46_T	1.243	1.00
7_S	10_G	1.235	1.00
73_E	77_A	1.229	1.00
28_A	31_A	1.224	1.00
14_G	29_A	1.199	1.00
55_A	92_V	1.175	1.00
76_N	80_A	1.153	1.00
86_G	89_D	1.125	1.00
47_F	50_G	1.123	1.00
68_G	74_A	1.118	1.00
71_R	95_S	1.109	1.00
51_C	97_C	1.096	1.00
27_A	31_A	1.052	1.00
45_V	52_G	1.042	1.00
23_A	27_A	1.036	1.00
2_G	52_G	1.018	1.00
7_S	38_G	1.015	1.00
44_V	63_Y	1.011	1.00
72_E	76_N	0.995	1.00
5_A	29_A	0.990	1.00
79_L	92_V	0.979	1.00
53_A	75_E	0.975	1.00
53_A	92_V	0.958	1.00
15_Y	94_A	0.958	1.00
75_E	79_L	0.925	1.00
79_L	83_R	0.918	1.00
53_A	95_S	0.904	1.00
23_A	26_E	0.895	1.00
24_A	28_A	0.891	1.00
72_E	75_E	0.877	1.00
8_P	42_K	0.866	1.00
4_I	52_G	0.865	1.00
57_G	61_G	0.861	1.00
1_W	48_R	0.845	1.00
70_T	74_A	0.840	1.00
17_Y	96_A	0.839	1.00
26_E	30_L	0.837	1.00
13_Y	94_A	0.822	1.00
3_A	43_V	0.812	1.00
24_A	27_A	0.808	1.00
74_A	78_A	0.806	1.00
55_A	75_E	0.802	1.00
16_S	28_A	0.798	1.00
64_G	78_A	0.792	1.00
6_Y	44_V	0.779	1.00
80_A	84_K	0.773	1.00
56_V	93_R	0.766	1.00
69_A	73_E	0.751	1.00
56_V	91_K	0.735	1.00
57_G	86_G	0.722	1.00
32_E	36_K	0.716	1.00
9_S	40_D	0.712	1.00
1_W	22_R	0.710	1.00
41_C	52_G	0.705	1.00
3_A	25_A	0.703	1.00
80_A	83_R	0.701	1.00
3_A	46_T	0.695	1.00
15_Y	32_E	0.693	1.00
6_Y	10_G	0.672	1.00
47_F	96_A	0.670	1.00
55_A	64_G	0.667	1.00
37_G	40_D	0.664	1.00
54_L	63_Y	0.664	1.00
83_R	86_G	0.650	1.00
27_A	30_L	0.645	1.00
13_Y	54_L	0.643	1.00
45_V	65_W	0.640	1.00
35_A	38_G	0.639	1.00
31_A	35_A	0.638	1.00
19_Y	25_A	0.638	1.00
57_G	60_G	0.635	1.00
3_A	26_E	0.628	1.00
44_V	65_W	0.623	1.00
59_K	62_G	0.614	1.00
75_E	92_V	0.608	1.00
92_V	95_S	0.608	1.00
73_E	76_N	0.606	1.00
64_G	81_E	0.606	1.00
57_G	62_G	0.605	1.00
6_Y	54_L	0.596	1.00
45_V	67_V	0.585	1.00
5_A	14_G	0.581	0.99
77_A	80_A	0.575	0.99
12_A	37_G	0.568	0.99
57_G	87_G	0.562	0.99
66_A	81_E	0.561	0.99
13_Y	56_V	0.556	0.99
14_G	32_E	0.551	0.99
6_Y	56_V	0.549	0.99
16_S	29_A	0.545	0.99
6_Y	63_Y	0.544	0.99
19_Y	32_E	0.542	0.99
6_Y	11_G	0.531	0.99
1_W	6_Y	0.529	0.99
49_N	52_G	0.529	0.99
50_G	69_A	0.528	0.99
58_P	91_K	0.526	0.99
30_L	42_K	0.526	0.99
83_R	88_K	0.525	0.99
78_A	92_V	0.525	0.99
5_A	26_E	0.523	0.99
1_W	26_E	0.523	0.99
17_Y	95_S	0.522	0.99
18_N	96_A	0.521	0.99
50_G	95_S	0.519	0.99
65_W	77_A	0.509	0.99
8_P	12_A	0.503	0.99
51_C	90_C	0.502	0.98
54_L	94_A	0.502	0.98
58_P	88_K	0.501	0.98
17_Y	94_A	0.500	0.98

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
2w4lA	3	0.9588	8.7	0.866	Contact Map
2g6vA	2	0.9588	2.7	0.895	Contact Map
1z3aA	2	0.9897	1.9	0.904	Contact Map
3zpgA	2	0.9588	1.8	0.905	Contact Map
2b3zA	3	0.9485	1.6	0.906	Contact Map
4oh4F	1	0.1649	1.6	0.907	Contact Map
2hxvA	2	0.9485	1.6	0.907	Contact Map
1r02A	1	0.2165	1.4	0.911	Contact Map
2lzyA	1	0.1753	1.3	0.913	Contact Map
1fygA	1	0.1546	1	0.918	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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