DUF3791 - PFAM28P - GREMLIN Contacts

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DUF3791 - Protein of unknown function (DUF3791)

PFAM:	PF12668	Sequences: EFLVFCIEEYAERKGLSGKEAYRLLKKYGILDYIIECYDALHTQGDEYIVEDIDEYIKNN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (58)
Sequences:	6998 (3774)
Seq/√Len:	495.5
META:	0.959

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_K	54_D	3.725	1.00
29_G	32_D	2.807	1.00
37_C	40_A	2.021	1.00
9_E	46_D	1.969	1.00
44_Q	48_Y	1.872	1.00
17_S	20_E	1.721	1.00
3_L	35_I	1.715	1.00
16_L	21_A	1.707	1.00
23_R	27_K	1.684	1.00
16_L	20_E	1.604	1.00
8_E	18_G	1.572	1.00
16_L	24_L	1.549	1.00
40_A	43_T	1.515	1.00
9_E	12_E	1.461	1.00
13_R	54_D	1.454	1.00
19_K	23_R	1.366	1.00
45_G	48_Y	1.354	1.00
46_D	49_I	1.320	1.00
30_I	56_Y	1.302	1.00
22_Y	26_K	1.285	1.00
13_R	47_E	1.246	1.00
10_Y	14_K	1.221	1.00
32_D	36_E	1.221	1.00
55_E	58_K	1.216	1.00
22_Y	31_L	1.190	1.00
49_I	52_D	1.135	1.00
38_Y	42_H	1.122	1.00
9_E	50_V	1.115	1.00
20_E	23_R	1.114	1.00
33_Y	41_L	1.072	1.00
20_E	24_L	1.027	1.00
54_D	58_K	1.004	1.00
10_Y	53_I	1.002	1.00
40_A	44_Q	0.975	1.00
28_Y	57_I	0.967	1.00
5_F	9_E	0.932	1.00
56_Y	59_N	0.927	1.00
6_C	34_I	0.918	1.00
30_I	57_I	0.913	1.00
34_I	41_L	0.912	1.00
10_Y	54_D	0.899	1.00
25_L	31_L	0.887	1.00
2_F	49_I	0.863	1.00
13_R	50_V	0.844	1.00
11_A	18_G	0.825	1.00
3_L	31_L	0.807	1.00
31_L	35_I	0.804	1.00
33_Y	52_D	0.782	1.00
51_E	55_E	0.762	1.00
37_C	43_T	0.759	1.00
2_F	41_L	0.739	1.00
44_Q	49_I	0.735	1.00
41_L	52_D	0.723	1.00
13_R	51_E	0.719	1.00
47_E	51_E	0.716	1.00
7_I	22_Y	0.713	1.00
24_L	57_I	0.681	1.00
21_A	25_L	0.679	1.00
2_F	8_E	0.678	1.00
2_F	5_F	0.675	1.00
41_L	49_I	0.674	1.00
25_L	30_I	0.670	1.00
7_I	31_L	0.667	1.00
48_Y	51_E	0.666	1.00
30_I	53_I	0.636	1.00
55_E	59_N	0.635	1.00
23_R	26_K	0.628	1.00
5_F	46_D	0.621	1.00
24_L	30_I	0.617	1.00
6_C	41_L	0.602	0.99
26_K	31_L	0.592	0.99
8_E	11_A	0.592	0.99
4_V	8_E	0.565	0.99
38_Y	43_T	0.561	0.99
34_I	43_T	0.538	0.99
39_D	43_T	0.535	0.99
33_Y	56_Y	0.532	0.99
24_L	28_Y	0.531	0.99
42_H	45_G	0.524	0.98
10_Y	24_L	0.517	0.98
10_Y	25_L	0.516	0.98
6_C	49_I	0.514	0.98
52_D	55_E	0.513	0.98
5_F	8_E	0.512	0.98
24_L	27_K	0.512	0.98
45_G	49_I	0.502	0.98
33_Y	37_C	0.500	0.98

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
3i5qB	4	0.9833	20.6	0.813	Contact Map
3i5pA	1	0.9833	16.9	0.82	Contact Map
4jzaA	2	1	12.5	0.83	Contact Map
4u9bA	1	0.9833	10.3	0.836	Contact Map
3al0B	1	1	8.3	0.843	Contact Map
3ip4B	1	1	7.8	0.845	Contact Map
3j7aZ	1	0.5833	7	0.849	Contact Map
1yx3A	1	0.8667	6.7	0.849	Contact Map
3k1tA	2	0.8833	6.7	0.849	Contact Map
3h0lB	1	1	6.5	0.851	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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