DUF4235 - PFAM28P - GREMLIN Contacts

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DUF4235 - Protein of unknown function (DUF4235)

PFAM:	PF14019	Sequences: YKPVGLVAGLLAGLLARKLFKQVWKLVDGEEPPADPTDPDVSWGEALAAAALQGAIFAVVRALVDRGAARGFRRLTG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (76)
Sequences:	6631 (3865)
Seq/√Len:	443.4
META:	0.899

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_Q	26_L	3.168	1.00
22_Q	25_K	2.909	1.00
44_G	48_A	2.595	1.00
18_K	22_Q	2.145	1.00
39_P	73_R	2.144	1.00
28_D	45_E	2.028	1.00
74_R	77_G	1.926	1.00
71_G	75_L	1.911	1.00
48_A	51_A	1.822	1.00
18_K	21_K	1.816	1.00
43_W	63_L	1.795	1.00
50_A	62_A	1.679	1.00
42_S	45_E	1.647	1.00
38_D	41_V	1.630	1.00
67_G	70_R	1.596	1.00
14_L	17_R	1.576	1.00
67_G	71_G	1.500	1.00
8_A	11_L	1.399	1.00
55_A	58_A	1.398	1.00
6_L	10_L	1.389	1.00
70_R	73_R	1.329	1.00
60_V	64_V	1.319	1.00
41_V	46_A	1.285	1.00
17_R	21_K	1.250	1.00
11_L	14_L	1.244	1.00
23_V	26_L	1.244	1.00
12_A	64_V	1.212	1.00
8_A	12_A	1.202	1.00
54_G	61_R	1.166	1.00
16_A	60_V	1.146	1.00
64_V	68_A	1.132	1.00
35_D	38_D	1.129	1.00
56_I	60_V	1.126	1.00
54_G	58_A	1.115	1.00
47_L	59_V	1.095	1.00
46_A	62_A	1.057	1.00
14_L	18_K	1.030	1.00
46_A	66_R	1.028	1.00
63_L	67_G	1.026	1.00
8_A	64_V	1.016	1.00
2_K	5_G	1.013	1.00
7_V	11_L	1.002	1.00
12_A	16_A	0.994	1.00
3_P	6_L	0.990	1.00
51_A	55_A	0.984	1.00
30_E	45_E	0.977	1.00
20_F	56_I	0.969	1.00
16_A	56_I	0.957	1.00
43_W	70_R	0.943	1.00
4_V	8_A	0.935	1.00
66_R	70_R	0.929	1.00
47_L	63_L	0.926	1.00
23_V	27_V	0.905	1.00
47_L	50_A	0.889	1.00
1_Y	7_V	0.868	1.00
20_F	49_A	0.859	1.00
72_F	75_L	0.855	1.00
51_A	59_V	0.853	1.00
41_V	45_E	0.853	1.00
25_K	31_E	0.844	1.00
32_P	39_P	0.822	1.00
25_K	29_G	0.811	1.00
49_A	53_Q	0.791	1.00
69_A	72_F	0.790	1.00
6_L	9_G	0.789	1.00
8_A	68_A	0.780	1.00
46_A	50_A	0.760	1.00
48_A	52_L	0.754	1.00
57_F	61_R	0.751	1.00
10_L	14_L	0.739	1.00
50_A	54_G	0.735	1.00
36_P	62_A	0.735	1.00
6_L	14_L	0.731	1.00
53_Q	57_F	0.728	1.00
61_R	65_D	0.719	1.00
16_A	20_F	0.708	1.00
43_W	47_L	0.661	1.00
1_Y	8_A	0.659	1.00
43_W	50_A	0.656	1.00
2_K	37_T	0.652	1.00
60_V	63_L	0.650	1.00
68_A	72_F	0.647	0.99
1_Y	68_A	0.633	0.99
8_A	14_L	0.631	0.99
9_G	56_I	0.621	0.99
71_G	74_R	0.621	0.99
62_A	66_R	0.616	0.99
19_L	23_V	0.616	0.99
56_I	59_V	0.611	0.99
32_P	49_A	0.603	0.99
14_L	22_Q	0.603	0.99
46_A	49_A	0.600	0.99
49_A	56_I	0.587	0.99
24_W	61_R	0.583	0.99
28_D	33_P	0.577	0.99
26_L	29_G	0.577	0.99
38_D	66_R	0.573	0.99
55_A	62_A	0.572	0.99
3_P	7_V	0.565	0.99
5_G	37_T	0.555	0.98
16_A	19_L	0.552	0.98
5_G	9_G	0.551	0.98
21_K	53_Q	0.551	0.98
9_G	24_W	0.549	0.98
1_Y	72_F	0.538	0.98
10_L	13_G	0.533	0.98
16_A	57_F	0.528	0.98
5_G	60_V	0.528	0.98
2_K	59_V	0.525	0.98
42_S	73_R	0.523	0.98
12_A	60_V	0.521	0.98
4_V	7_V	0.519	0.98
66_R	69_A	0.505	0.97
36_P	43_W	0.500	0.97

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
1vl8A	4	0.4935	22.2	0.841	Contact Map
4weoA	4	0.4805	18.2	0.847	Contact Map
2x9gA	4	0.4675	16.6	0.85	Contact Map
4nimA	4	0.4805	14.7	0.854	Contact Map
3f9iA	3	0.5195	14.2	0.855	Contact Map
3vtzA	4	0.5065	11.9	0.86	Contact Map
4nbuA	4	0.5325	11.4	0.861	Contact Map
4iqgC	3	0.4286	11	0.862	Contact Map
4ospA	4	0.5195	10.3	0.864	Contact Map
4zjuA	4	0.5195	9.4	0.866	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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