DUF4234 - PFAM28P - GREMLIN Contacts

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DUF4234 - Domain of unknown function (DUF4234)

PFAM:	PF14018	Sequences: RSIGLVILLSIVTLGIYGLYWYYKTNEELKRYSGDGPGGSGGLVVLLLGLLTLGIVPIVWFYKTGKRLNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (66)
Sequences:	7826 (5503)
Seq/√Len:	677.4
META:	0.941

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_Y	24_K	3.490	1.00
10_S	18_G	3.055	1.00
5_L	9_L	2.455	1.00
9_L	12_V	2.397	1.00
27_E	31_R	2.328	1.00
3_I	6_V	1.880	1.00
3_I	7_I	1.872	1.00
51_L	54_G	1.847	1.00
52_T	56_V	1.846	1.00
5_L	8_L	1.824	1.00
6_V	10_S	1.818	1.00
4_G	8_L	1.806	1.00
53_L	56_V	1.779	1.00
2_S	5_L	1.715	1.00
39_G	44_V	1.674	1.00
8_L	12_V	1.508	1.00
41_G	44_V	1.410	1.00
40_S	43_L	1.361	1.00
51_L	56_V	1.331	1.00
16_I	20_Y	1.321	1.00
62_Y	65_G	1.307	1.00
29_L	33_S	1.258	1.00
40_S	44_V	1.179	1.00
24_K	27_E	1.177	1.00
17_Y	20_Y	1.143	1.00
6_V	17_Y	1.141	1.00
24_K	28_E	1.094	1.00
58_I	62_Y	1.085	1.00
62_Y	66_K	1.072	1.00
22_Y	26_N	1.067	1.00
36_G	39_G	1.054	1.00
55_I	59_V	1.045	1.00
54_G	57_P	1.038	1.00
61_F	65_G	1.020	1.00
37_P	41_G	0.993	1.00
63_K	67_R	0.984	1.00
23_Y	27_E	0.982	1.00
39_G	43_L	0.950	1.00
36_G	41_G	0.940	1.00
7_I	10_S	0.896	1.00
52_T	55_I	0.893	1.00
56_V	60_W	0.877	1.00
4_G	7_I	0.866	1.00
65_G	68_L	0.866	1.00
25_T	64_T	0.860	1.00
14_L	53_L	0.849	1.00
59_V	63_K	0.832	1.00
39_G	42_G	0.825	1.00
60_W	67_R	0.812	1.00
19_L	23_Y	0.808	1.00
48_L	52_T	0.804	1.00
22_Y	60_W	0.804	1.00
29_L	64_T	0.772	1.00
23_Y	46_L	0.750	1.00
9_L	13_T	0.746	1.00
49_G	52_T	0.730	1.00
36_G	40_S	0.729	1.00
48_L	51_L	0.728	1.00
37_P	42_G	0.717	1.00
38_G	41_G	0.701	1.00
38_G	44_V	0.695	1.00
57_P	61_F	0.694	1.00
21_W	25_T	0.693	1.00
19_L	22_Y	0.688	1.00
26_N	30_K	0.685	1.00
17_Y	24_K	0.679	1.00
31_R	34_G	0.677	1.00
6_V	25_T	0.666	1.00
46_L	50_L	0.664	1.00
53_L	57_P	0.650	1.00
15_G	19_L	0.638	1.00
60_W	63_K	0.619	1.00
46_L	49_G	0.604	1.00
5_L	17_Y	0.603	1.00
25_T	28_E	0.603	1.00
38_G	42_G	0.588	1.00
8_L	16_I	0.586	1.00
2_S	6_V	0.584	1.00
60_W	65_G	0.578	1.00
37_P	40_S	0.575	1.00
5_L	10_S	0.572	1.00
64_T	68_L	0.561	1.00
22_Y	64_T	0.560	1.00
25_T	29_L	0.553	1.00
26_N	64_T	0.552	1.00
28_E	32_Y	0.547	1.00
50_L	54_G	0.542	1.00
61_F	64_T	0.541	1.00
30_K	38_G	0.539	1.00
36_G	42_G	0.535	1.00
6_V	21_W	0.533	1.00
26_N	33_S	0.532	1.00
63_K	66_K	0.519	0.99
30_K	39_G	0.516	0.99
48_L	53_L	0.509	0.99
30_K	34_G	0.507	0.99
32_Y	35_D	0.503	0.99
64_T	67_R	0.502	0.99
18_G	22_Y	0.500	0.99

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
3qnqA	2	0.5714	11.6	0.843	Contact Map
5a63B	1	0.8	4.3	0.871	Contact Map
3w4tA	1	0.4571	4	0.874	Contact Map
4n6hA	1	1	3.3	0.878	Contact Map
3wt9A	1	0.8714	3.3	0.879	Contact Map
3rzeA	1	0.9429	3.2	0.88	Contact Map
2xq2A	2	0.7286	3	0.881	Contact Map
4z35A	1	0.9429	3	0.881	Contact Map
3dh4A	3	0.3571	2.9	0.882	Contact Map
3j8eG	3	0.8286	2.7	0.883	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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