DUF1841 - PFAM28P - GREMLIN Contacts

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DUF1841 - Domain of unknown function (DUF1841)

PFAM:	PF08897	Sequences: SRDQVRRFFFDAWRKHRAGEPLTPLEALAADVIAEHPEYHALLEDPEAALDRDYTPEGGETNPFLHLSLHLAIREQLSIDQPPGIRAAYERLAARLGDAHEAEHAMMECLGEMLWEAQRSGRPPDEAAYLECLRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	135 (134)
Sequences:	4542 (2796)
Seq/√Len:	241.5
META:	0.928

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_D	101_E	2.888	1.00
15_K	26_E	2.727	1.00
116_E	120_S	2.461	1.00
109_C	132_C	2.423	1.00
12_A	30_A	2.398	1.00
16_H	34_A	2.249	1.00
106_M	133_L	2.206	1.00
5_V	9_F	2.200	1.00
14_R	18_A	2.135	1.00
96_L	105_A	2.097	1.00
7_R	11_D	2.089	1.00
80_D	86_R	2.081	1.00
17_R	44_E	2.076	1.00
74_R	103_E	2.039	1.00
73_I	106_M	2.029	1.00
112_E	116_E	1.992	1.00
88_A	133_L	1.931	1.00
32_V	67_L	1.879	1.00
86_R	90_E	1.773	1.00
88_A	134_R	1.765	1.00
89_Y	106_M	1.760	1.00
89_Y	99_A	1.751	1.00
87_A	91_R	1.674	1.00
88_A	91_R	1.667	1.00
30_A	34_A	1.666	1.00
28_L	71_L	1.610	1.00
99_A	103_E	1.609	1.00
8_F	29_A	1.595	1.00
4_Q	7_R	1.557	1.00
27_A	31_D	1.541	1.00
42_L	54_Y	1.539	1.00
11_D	14_R	1.534	1.00
69_L	107_M	1.531	1.00
131_E	134_R	1.477	1.00
89_Y	93_A	1.467	1.00
55_T	58_G	1.466	1.00
9_F	68_S	1.430	1.00
31_D	35_E	1.420	1.00
7_R	50_L	1.419	1.00
10_F	49_A	1.395	1.00
85_I	133_L	1.354	1.00
33_I	43_L	1.342	1.00
80_D	87_A	1.283	1.00
23_T	26_E	1.278	1.00
52_R	60_E	1.275	1.00
1_S	4_Q	1.265	1.00
16_H	30_A	1.264	1.00
77_L	89_Y	1.238	1.00
42_L	60_E	1.227	1.00
22_L	30_A	1.220	1.00
93_A	102_A	1.214	1.00
32_V	74_R	1.212	1.00
5_V	68_S	1.202	1.00
3_D	51_D	1.188	1.00
56_P	59_G	1.180	1.00
116_E	122_R	1.172	1.00
101_E	105_A	1.164	1.00
81_Q	126_E	1.149	1.00
113_M	132_C	1.149	1.00
1_S	5_V	1.145	1.00
14_R	20_E	1.145	1.00
116_E	132_C	1.135	1.00
46_P	50_L	1.131	1.00
41_A	44_E	1.121	1.00
93_A	99_A	1.117	1.00
28_L	74_R	1.116	1.00
45_D	48_A	1.076	1.00
76_Q	129_Y	1.076	1.00
90_E	94_A	1.072	1.00
24_P	27_A	1.067	1.00
73_I	107_M	1.033	1.00
13_W	16_H	1.014	1.00
69_L	111_G	1.007	1.00
35_E	99_A	1.006	1.00
31_D	74_R	1.002	1.00
24_P	28_L	0.982	1.00
87_A	90_E	0.980	1.00
31_D	34_A	0.958	1.00
117_A	124_P	0.955	1.00
54_Y	60_E	0.954	1.00
80_D	83_P	0.951	1.00
88_A	92_L	0.949	1.00
80_D	84_G	0.944	1.00
10_F	46_P	0.942	1.00
84_G	130_L	0.917	1.00
77_L	99_A	0.915	1.00
16_H	19_G	0.894	1.00
93_A	96_L	0.886	1.00
89_Y	103_E	0.885	0.99
127_A	134_R	0.882	0.99
2_R	53_D	0.881	0.99
115_W	119_R	0.871	0.99
35_E	74_R	0.864	0.99
28_L	79_I	0.861	0.99
113_M	124_P	0.859	0.99
8_F	12_A	0.843	0.99
22_L	27_A	0.837	0.99
42_L	49_A	0.829	0.99
112_E	132_C	0.824	0.99
12_A	16_H	0.824	0.99
7_R	46_P	0.823	0.99
5_V	29_A	0.821	0.99
71_L	79_I	0.805	0.99
5_V	8_F	0.805	0.99
74_R	99_A	0.801	0.99
10_F	43_L	0.791	0.99
13_W	40_H	0.783	0.99
13_W	44_E	0.779	0.99
16_H	31_D	0.771	0.99
15_K	20_E	0.767	0.99
21_P	24_P	0.740	0.98
9_F	67_L	0.735	0.98
4_Q	11_D	0.735	0.98
54_Y	59_G	0.733	0.98
117_A	123_P	0.725	0.98
116_E	128_A	0.721	0.98
123_P	126_E	0.719	0.98
130_L	134_R	0.716	0.98
5_V	10_F	0.709	0.98
66_H	104_H	0.708	0.98
28_L	78_S	0.708	0.98
70_H	100_H	0.706	0.98
108_E	111_G	0.702	0.97
28_L	31_D	0.696	0.97
91_R	94_A	0.690	0.97
56_P	61_T	0.687	0.97
52_R	58_G	0.684	0.97
90_E	99_A	0.681	0.97
21_P	27_A	0.671	0.97
89_Y	102_A	0.661	0.96
85_I	106_M	0.658	0.96
8_F	23_T	0.657	0.96
58_G	61_T	0.655	0.96
74_R	89_Y	0.648	0.96
96_L	102_A	0.647	0.96
128_A	132_C	0.646	0.96
20_E	23_T	0.646	0.96
113_M	128_A	0.644	0.96
97_G	102_A	0.643	0.96
43_L	67_L	0.641	0.96
125_D	128_A	0.638	0.96
96_L	101_E	0.634	0.95
28_L	75_E	0.633	0.95
77_L	86_R	0.632	0.95
9_F	29_A	0.632	0.95
107_M	113_M	0.631	0.95
11_D	23_T	0.627	0.95
29_A	71_L	0.626	0.95
113_M	116_E	0.622	0.95
23_T	28_L	0.621	0.95
102_A	105_A	0.618	0.95
93_A	98_D	0.616	0.95
110_L	114_L	0.612	0.94
32_V	103_E	0.609	0.94
68_S	72_A	0.608	0.94
25_L	28_L	0.603	0.94
29_A	68_S	0.598	0.94
2_R	13_W	0.597	0.94
70_H	104_H	0.594	0.94
11_D	15_K	0.593	0.93
103_E	107_M	0.592	0.93
68_S	114_L	0.592	0.93
41_A	45_D	0.590	0.93
40_H	44_E	0.586	0.93
12_A	33_I	0.579	0.93
126_E	130_L	0.578	0.93
5_V	72_A	0.578	0.93
127_A	131_E	0.566	0.92
10_F	16_H	0.565	0.92
85_I	130_L	0.565	0.92
88_A	106_M	0.564	0.92
48_A	51_D	0.563	0.92
113_M	126_E	0.559	0.91
99_A	106_M	0.558	0.91
66_H	70_H	0.558	0.91
35_E	98_D	0.555	0.91
74_R	78_S	0.552	0.91
16_H	20_E	0.552	0.91
31_D	99_A	0.551	0.91
56_P	114_L	0.548	0.90
115_W	118_Q	0.547	0.90
72_A	77_L	0.545	0.90
74_R	100_H	0.545	0.90
111_G	124_P	0.543	0.90
94_A	134_R	0.543	0.90
35_E	103_E	0.541	0.90
83_P	113_M	0.533	0.89
113_M	117_A	0.531	0.89
81_Q	114_L	0.531	0.89
72_A	81_Q	0.529	0.89
45_D	49_A	0.528	0.89
14_R	46_P	0.527	0.89
48_A	52_R	0.525	0.89
93_A	131_E	0.525	0.89
33_I	67_L	0.522	0.88
69_L	103_E	0.522	0.88
7_R	10_F	0.518	0.88
55_T	60_E	0.508	0.87
15_K	19_G	0.505	0.87
39_Y	110_L	0.503	0.86
29_A	32_V	0.500	0.86

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
1ashA	1	0.9333	39.2	0.917	Contact Map
1mbaA	1	0.9185	32.2	0.921	Contact Map
4d0h0	3	0.8889	31.1	0.921	Contact Map
2zs0D	1	0.9185	22.4	0.927	Contact Map
1x9fD	3	0.8889	21.3	0.927	Contact Map
1ecaA	1	0.8815	21.2	0.927	Contact Map
1x9fB	1	0.8963	20.6	0.928	Contact Map
1yhuA	2	0.9037	19.5	0.929	Contact Map
3wctC	1	0.8815	19.2	0.929	Contact Map
3wctD	1	0.8889	18.1	0.93	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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