DUF4178 - PFAM28P - GREMLIN Contacts

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DUF4178 - Domain of unknown function (DUF4178)

PFAM:	PF13785	Sequences: QLGTRGTYDGVDFEVIGRLQYSYEDGYFWNEYLLYDGRSGRWLSEEEDQGEYVLSFWSPVPPLPPARPGQTVTYDGRTYRVFERAAATYVGEGEWPVRVGETVRVADYVAPPGGRFLSIEYSGDGEPTWSLGEYVEP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	137 (132)
Sequences:	7992 (5841)
Seq/√Len:	508.4
META:	0.889

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_R	115_R	3.209	1.00
9_D	133_E	3.049	1.00
71_T	78_T	2.835	1.00
7_T	12_D	2.721	1.00
5_R	12_D	2.690	1.00
30_N	45_E	2.654	1.00
5_R	14_E	2.647	1.00
15_V	34_L	2.435	1.00
20_Q	30_N	2.255	1.00
11_V	39_S	2.254	1.00
119_I	129_W	2.249	1.00
73_T	78_T	2.085	1.00
22_S	88_T	1.884	1.00
18_R	30_N	1.881	1.00
17_G	93_G	1.880	1.00
86_A	90_V	1.871	1.00
85_A	89_Y	1.839	1.00
81_V	106_A	1.822	1.00
32_Y	45_E	1.770	1.00
16_I	35_Y	1.696	1.00
20_Q	28_F	1.685	1.00
77_R	110_A	1.663	1.00
22_S	28_F	1.646	1.00
7_T	10_G	1.622	1.00
87_A	90_V	1.609	1.00
87_A	91_G	1.600	1.00
115_R	133_E	1.579	1.00
84_R	104_R	1.540	1.00
104_R	121_Y	1.507	1.00
75_D	131_L	1.470	1.00
34_L	43_L	1.466	1.00
86_A	102_T	1.408	1.00
23_Y	27_Y	1.391	1.00
84_R	91_G	1.386	1.00
54_L	57_W	1.379	1.00
119_I	127_P	1.368	1.00
36_D	39_S	1.354	1.00
85_A	91_G	1.352	1.00
121_Y	127_P	1.327	1.00
85_A	105_V	1.310	1.00
18_R	32_Y	1.231	1.00
51_E	54_L	1.228	1.00
56_F	59_P	1.224	1.00
11_V	36_D	1.222	1.00
115_R	131_L	1.211	1.00
53_V	56_F	1.206	1.00
105_V	108_Y	1.190	1.00
79_Y	117_L	1.181	1.00
52_Y	55_S	1.168	1.00
33_L	42_W	1.162	1.00
79_Y	131_L	1.150	1.00
51_E	55_S	1.147	1.00
101_E	105_V	1.133	1.00
41_R	56_F	1.113	1.00
106_A	119_I	1.106	1.00
58_S	62_P	1.084	1.00
93_G	97_V	1.060	1.00
107_D	111_P	1.060	1.00
60_V	63_L	1.059	1.00
84_R	88_T	1.046	1.00
95_W	100_G	1.044	1.00
18_R	92_E	1.043	1.00
82_F	109_V	1.038	1.00
19_L	42_W	1.029	1.00
11_V	38_R	1.027	1.00
103_V	108_Y	1.023	1.00
107_D	118_S	1.015	1.00
88_T	91_G	1.003	1.00
79_Y	115_R	0.993	1.00
92_E	95_W	0.980	1.00
37_G	40_G	0.976	1.00
71_T	80_R	0.974	1.00
57_W	60_V	0.966	1.00
97_V	100_G	0.959	1.00
59_P	62_P	0.957	1.00
85_A	88_T	0.938	1.00
49_Q	53_V	0.935	1.00
77_R	113_G	0.934	1.00
103_V	109_V	0.931	1.00
36_D	40_G	0.916	1.00
61_P	64_P	0.906	1.00
93_G	96_P	0.903	1.00
52_Y	57_W	0.900	1.00
101_E	108_Y	0.898	1.00
62_P	65_P	0.888	1.00
53_V	57_W	0.885	1.00
117_L	129_W	0.883	1.00
112_P	115_R	0.879	1.00
35_Y	40_G	0.878	1.00
108_Y	111_P	0.872	1.00
22_S	90_V	0.862	1.00
52_Y	56_F	0.857	1.00
61_P	65_P	0.855	1.00
51_E	56_F	0.843	1.00
106_A	121_Y	0.829	1.00
86_A	91_G	0.827	1.00
4_T	15_V	0.804	1.00
67_R	70_Q	0.803	1.00
23_Y	26_G	0.803	1.00
85_A	90_V	0.799	1.00
5_R	38_R	0.796	1.00
19_L	89_Y	0.788	1.00
33_L	94_E	0.783	1.00
73_T	76_G	0.781	1.00
103_V	110_A	0.779	1.00
28_F	88_T	0.776	1.00
101_E	104_R	0.771	1.00
116_F	134_Y	0.763	1.00
116_F	132_G	0.762	1.00
109_V	134_Y	0.761	1.00
49_Q	55_S	0.760	1.00
56_F	62_P	0.759	1.00
2_L	16_I	0.756	1.00
44_S	132_G	0.755	1.00
57_W	61_P	0.754	1.00
27_Y	83_E	0.753	1.00
110_A	115_R	0.750	1.00
49_Q	56_F	0.750	1.00
80_R	83_E	0.745	1.00
103_V	111_P	0.740	1.00
123_G	128_T	0.736	1.00
98_R	101_E	0.735	1.00
105_V	109_V	0.735	1.00
13_F	39_S	0.727	1.00
81_V	84_R	0.727	1.00
23_Y	105_V	0.727	1.00
51_E	57_W	0.726	1.00
84_R	89_Y	0.726	1.00
43_L	54_L	0.724	1.00
46_E	83_E	0.720	1.00
33_L	39_S	0.714	1.00
14_E	35_Y	0.713	1.00
63_L	66_A	0.710	1.00
117_L	131_L	0.709	1.00
114_G	133_E	0.699	1.00
102_T	108_Y	0.694	1.00
42_W	94_E	0.680	1.00
22_S	86_A	0.677	1.00
100_G	103_V	0.673	1.00
54_L	59_P	0.671	1.00
45_E	48_D	0.666	1.00
19_L	93_G	0.665	1.00
122_S	125_G	0.662	1.00
122_S	128_T	0.653	1.00
58_S	63_L	0.650	1.00
35_Y	38_R	0.645	1.00
29_W	42_W	0.644	1.00
8_Y	56_F	0.640	1.00
54_L	60_V	0.638	1.00
121_Y	125_G	0.627	1.00
9_D	13_F	0.623	1.00
13_F	41_R	0.623	1.00
11_V	40_G	0.619	1.00
8_Y	13_F	0.611	1.00
51_E	134_Y	0.609	1.00
16_I	33_L	0.604	0.99
68_P	72_V	0.603	0.99
60_V	65_P	0.599	0.99
73_T	77_R	0.598	0.99
74_Y	117_L	0.594	0.99
86_A	89_Y	0.589	0.99
6_G	34_L	0.588	0.99
38_R	41_R	0.578	0.99
49_Q	52_Y	0.578	0.99
41_R	58_S	0.574	0.99
51_E	61_P	0.574	0.99
75_D	115_R	0.572	0.99
112_P	134_Y	0.572	0.99
102_T	111_P	0.571	0.99
42_W	130_S	0.567	0.99
111_P	114_G	0.563	0.99
18_R	89_Y	0.561	0.99
2_L	92_E	0.561	0.99
107_D	110_A	0.560	0.99
103_V	107_D	0.556	0.99
57_W	132_G	0.554	0.99
31_E	118_S	0.554	0.99
37_G	41_R	0.549	0.99
19_L	95_W	0.549	0.99
6_G	15_V	0.548	0.99
23_Y	83_E	0.542	0.99
12_D	37_G	0.540	0.99
19_L	87_A	0.539	0.99
56_F	64_P	0.538	0.99
23_Y	85_A	0.536	0.99
82_F	134_Y	0.530	0.99
84_R	87_A	0.526	0.99
84_R	90_V	0.521	0.99
105_V	110_A	0.521	0.99
62_P	66_A	0.520	0.98
33_L	40_G	0.519	0.98
95_W	98_R	0.514	0.98
59_P	65_P	0.513	0.98
60_V	64_P	0.512	0.98
55_S	58_S	0.506	0.98
77_R	114_G	0.502	0.98
60_V	74_Y	0.501	0.98
8_Y	11_V	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
3h43A	5	0.1679	20.5	0.883	Contact Map
2ls01	1	0.3869	16.5	0.888	Contact Map
2wfwA	3	0.6715	7.9	0.903	Contact Map
2oaiA	2	0.2263	7.8	0.903	Contact Map
1k0hA	1	0.3066	6.4	0.907	Contact Map
3er0A	1	0.9124	4.5	0.913	Contact Map
2f9hA	2	0.4818	3.9	0.916	Contact Map
2kz4A	1	0.2774	3.8	0.917	Contact Map
1ah9A	1	0.1752	3.2	0.919	Contact Map
1ed7A	1	0.2701	3.1	0.92	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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