DUF2695 - PFAM28P - GREMLIN Contacts

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DUF2695 - Protein of unknown function (DUF2695)

PFAM:	PF10905	Sequences: LFDYLDRELEEEGCDHTLRLTRRWLDERGLDVEAVLAWLEENGGYCDCEVLAN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (52)
Sequences:	2556 (1898)
Seq/√Len:	263.2
META:	0.953

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_L	40_E	2.751	1.00
25_L	35_V	2.404	1.00
24_W	28_R	2.295	1.00
38_W	42_N	2.158	1.00
21_T	50_V	2.156	1.00
15_D	19_R	1.872	1.00
40_E	45_Y	1.783	1.00
18_L	50_V	1.722	1.00
26_D	32_V	1.693	1.00
18_L	36_L	1.622	1.00
25_L	32_V	1.606	1.00
9_L	13_G	1.534	1.00
22_R	32_V	1.462	1.00
14_C	46_C	1.375	1.00
22_R	36_L	1.358	1.00
18_L	44_G	1.346	1.00
36_L	40_E	1.292	1.00
35_V	39_L	1.242	1.00
14_C	48_C	1.236	1.00
23_R	27_E	1.226	1.00
44_G	49_E	1.183	1.00
45_Y	49_E	1.176	1.00
7_R	11_E	1.148	1.00
32_V	36_L	1.108	1.00
49_E	53_N	1.107	1.00
21_T	39_L	1.070	1.00
24_W	38_W	1.031	1.00
2_F	38_W	1.029	1.00
5_L	9_L	0.987	1.00
33_E	37_A	0.980	1.00
21_T	25_L	0.970	1.00
38_W	52_A	0.940	1.00
4_Y	8_E	0.937	1.00
22_R	26_D	0.931	1.00
25_L	36_L	0.914	1.00
6_D	10_E	0.899	1.00
45_Y	53_N	0.893	1.00
4_Y	24_W	0.887	1.00
34_A	38_W	0.875	1.00
32_V	35_V	0.830	0.99
3_D	7_R	0.829	0.99
8_E	23_R	0.779	0.99
8_E	11_E	0.759	0.99
2_F	6_D	0.748	0.99
25_L	39_L	0.741	0.99
8_E	12_E	0.735	0.99
33_E	45_Y	0.734	0.99
25_L	30_L	0.706	0.98
30_L	35_V	0.697	0.98
3_D	10_E	0.697	0.98
6_D	11_E	0.687	0.98
18_L	45_Y	0.680	0.98
8_E	20_L	0.676	0.98
23_R	26_D	0.667	0.97
22_R	40_E	0.667	0.97
14_C	17_T	0.662	0.97
9_L	51_L	0.653	0.97
5_L	51_L	0.644	0.97
24_W	30_L	0.634	0.96
31_D	37_A	0.632	0.96
31_D	34_A	0.598	0.95
5_L	20_L	0.597	0.95
19_R	31_D	0.584	0.94
21_T	24_W	0.581	0.94
5_L	10_E	0.580	0.94
12_E	20_L	0.576	0.94
19_R	23_R	0.570	0.94
15_D	20_L	0.565	0.93
38_W	41_E	0.563	0.93
44_G	53_N	0.557	0.93
3_D	6_D	0.556	0.93
33_E	41_E	0.527	0.91
44_G	50_V	0.527	0.91
12_E	23_R	0.526	0.91
25_L	38_W	0.519	0.90
5_L	8_E	0.515	0.90
37_A	40_E	0.501	0.88
4_Y	20_L	0.500	0.88

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
4xlgB	1	0.9057	6.8	0.864	Contact Map
1urjA	1	1	6.8	0.864	Contact Map
1z96A	1	0.6604	6.7	0.864	Contact Map
2z14A	2	0.6226	6.4	0.866	Contact Map
1pdnC	1	0.717	5.2	0.872	Contact Map
1rw1A	1	0.8302	5	0.872	Contact Map
3j7yg	1	0.8113	4.7	0.874	Contact Map
2dakA	1	0.7925	4.7	0.874	Contact Map
1o7dA	1	0.6981	4.4	0.875	Contact Map
2h21A	3	0.5094	4.2	0.877	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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