DUF1998 - PFAM28P - GREMLIN Contacts

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DUF1998 - Domain of unknown function (DUF1998)

PFAM:	PF09369	Sequences: ALAHALIRAAPLLLMCDRRDLGGRSYPRHPDGRPTIFLYDAYPGGAGLLERLFERLEELLRAALELIASCPCEDGCPSCV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (80)
Sequences:	28118 (15563)
Seq/√Len:	1740.0
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
9_A	66_L	3.041	1.00
3_A	23_G	2.949	1.00
10_A	52_L	2.625	1.00
55_R	58_E	2.610	1.00
13_L	62_A	2.600	1.00
5_A	67_I	2.417	1.00
64_L	68_A	2.333	1.00
13_L	58_E	2.267	1.00
5_A	63_A	2.203	1.00
51_R	55_R	2.145	1.00
62_A	65_E	2.094	1.00
65_E	69_S	1.772	1.00
13_L	55_R	1.757	1.00
7_I	23_G	1.753	1.00
22_G	41_A	1.642	1.00
51_R	54_E	1.641	1.00
22_G	39_Y	1.561	1.00
58_E	62_A	1.499	1.00
57_E	61_R	1.424	1.00
42_Y	46_A	1.418	1.00
8_R	11_P	1.404	1.00
3_A	25_S	1.312	1.00
9_A	62_A	1.296	1.00
61_R	65_E	1.282	1.00
12_L	66_L	1.278	1.00
26_Y	29_H	1.267	1.00
56_L	60_L	1.253	1.00
8_R	18_R	1.248	1.00
8_R	66_L	1.192	1.00
12_L	62_A	1.144	1.00
26_Y	35_T	1.106	1.00
65_E	68_A	1.103	1.00
24_R	37_F	1.086	1.00
58_E	61_R	1.080	1.00
4_H	8_R	1.078	1.00
16_C	48_L	1.059	1.00
7_I	18_R	1.034	1.00
28_R	33_R	1.028	1.00
10_A	21_L	1.009	1.00
26_Y	30_P	0.978	1.00
8_R	12_L	0.977	1.00
61_R	64_L	0.965	1.00
1_A	80_V	0.957	1.00
6_L	63_A	0.938	1.00
75_G	80_V	0.915	1.00
7_I	11_P	0.910	1.00
9_A	13_L	0.904	1.00
27_P	33_R	0.882	1.00
50_E	54_E	0.865	1.00
4_H	7_I	0.864	1.00
76_C	79_C	0.863	1.00
62_A	66_L	0.855	1.00
10_A	14_L	0.851	1.00
1_A	4_H	0.844	1.00
4_H	23_G	0.843	1.00
5_A	8_R	0.840	1.00
2_L	60_L	0.839	1.00
13_L	59_L	0.837	1.00
56_L	59_L	0.834	1.00
26_Y	37_F	0.834	1.00
9_A	59_L	0.834	1.00
3_A	36_I	0.821	1.00
52_L	56_L	0.818	1.00
6_L	60_L	0.783	1.00
2_L	6_L	0.782	1.00
6_L	38_L	0.777	1.00
29_H	33_R	0.775	1.00
71_P	78_S	0.770	1.00
27_P	34_P	0.760	1.00
2_L	36_I	0.741	1.00
26_Y	31_D	0.728	1.00
52_L	59_L	0.723	1.00
64_L	67_I	0.720	1.00
49_L	53_F	0.699	1.00
16_C	20_D	0.689	1.00
12_L	43_P	0.683	1.00
25_S	34_P	0.675	1.00
40_D	45_G	0.675	1.00
14_L	55_R	0.675	1.00
26_Y	32_G	0.673	1.00
28_R	32_G	0.662	1.00
11_P	16_C	0.657	1.00
15_M	19_R	0.649	1.00
48_L	78_S	0.645	1.00
22_G	25_S	0.645	1.00
6_L	59_L	0.627	1.00
28_R	35_T	0.621	1.00
23_G	38_L	0.621	1.00
2_L	64_L	0.613	1.00
53_F	57_E	0.609	1.00
40_D	44_G	0.595	1.00
9_A	63_A	0.586	1.00
19_R	22_G	0.585	1.00
46_A	52_L	0.581	1.00
7_I	25_S	0.578	1.00
27_P	31_D	0.577	1.00
40_D	49_L	0.573	1.00
50_E	53_F	0.571	1.00
28_R	31_D	0.569	1.00
43_P	46_A	0.567	1.00
14_L	48_L	0.563	1.00
27_P	32_G	0.560	1.00
66_L	69_S	0.546	1.00
42_Y	48_L	0.541	1.00
75_G	78_S	0.540	1.00
44_G	47_G	0.538	1.00
10_A	38_L	0.531	1.00
10_A	59_L	0.526	1.00
3_A	7_I	0.525	1.00
69_S	73_E	0.519	1.00
38_L	59_L	0.517	1.00
34_P	39_Y	0.513	1.00
32_G	35_T	0.513	1.00
15_M	80_V	0.511	1.00
17_D	46_A	0.505	1.00
10_A	48_L	0.505	1.00
6_L	36_I	0.504	1.00
60_L	64_L	0.502	1.00
25_S	36_I	0.502	1.00
49_L	52_L	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
4ekfA	1	0.875	29.8	0.84	Contact Map
2pa8D	1	0.85	10.8	0.87	Contact Map
3hrdA	2	0.775	8.5	0.876	Contact Map
1twfC	1	0.8375	7.4	0.879	Contact Map
3h0gC	1	0.9	5.7	0.885	Contact Map
3mb2B	3	0.5	5.3	0.887	Contact Map
1b63A	2	0.6625	5	0.888	Contact Map
1sqsA	2	0.5875	4.9	0.889	Contact Map
1rypG	1	0.75	3.7	0.895	Contact Map
4cpyA	2	0.925	3.2	0.899	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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