DUF4148 - PFAM28P - GREMLIN Contacts

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DUF4148 - Domain of unknown function (DUF4148)

PFAM:	PF13663	Sequences: AAALAAPAAAFAQAQSTPLTRAQVRAELVQLEQAGYNPAGGDDTYPADIQAAEARVAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	58 (53)
Sequences:	3024 (2059)
Seq/√Len:	282.9
META:	0.64

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_L	27_E	2.813	1.00
25_R	29_V	2.567	1.00
27_E	30_Q	2.526	1.00
27_E	31_L	2.347	1.00
28_L	32_E	2.005	1.00
29_V	33_Q	1.832	1.00
23_Q	26_A	1.715	1.00
53_E	57_A	1.653	1.00
40_G	43_D	1.635	1.00
29_V	32_E	1.495	1.00
44_T	48_D	1.428	1.00
7_P	10_A	1.401	1.00
30_Q	34_A	1.387	1.00
19_L	23_Q	1.377	1.00
31_L	36_Y	1.352	1.00
31_L	53_E	1.347	1.00
31_L	49_I	1.288	1.00
8_A	11_F	1.282	1.00
30_Q	33_Q	1.277	1.00
31_L	37_N	1.262	1.00
23_Q	27_E	1.255	1.00
51_A	55_R	1.243	1.00
21_R	24_V	1.238	1.00
52_A	55_R	1.175	1.00
21_R	25_R	1.093	1.00
5_A	9_A	1.089	1.00
26_A	30_Q	1.084	1.00
7_P	11_F	1.051	1.00
6_A	9_A	1.049	1.00
11_F	15_Q	1.014	1.00
47_A	50_Q	1.011	1.00
44_T	47_A	1.010	1.00
39_A	42_D	1.006	1.00
37_N	40_G	0.995	1.00
32_E	38_P	0.991	1.00
19_L	24_V	0.888	1.00
11_F	14_A	0.874	1.00
31_L	34_A	0.852	1.00
6_A	10_A	0.837	1.00
32_E	37_N	0.821	1.00
4_L	9_A	0.819	1.00
34_A	56_V	0.814	0.99
38_P	42_D	0.783	0.99
41_G	48_D	0.774	0.99
42_D	48_D	0.770	0.99
26_A	29_V	0.763	0.99
14_A	17_T	0.757	0.99
7_P	15_Q	0.722	0.99
5_A	8_A	0.713	0.99
22_A	26_A	0.710	0.99
53_E	56_V	0.686	0.98
38_P	43_D	0.681	0.98
49_I	53_E	0.680	0.98
54_A	57_A	0.677	0.98
40_G	48_D	0.673	0.98
6_A	11_F	0.666	0.98
22_A	25_R	0.649	0.97
19_L	31_L	0.648	0.97
52_A	56_V	0.630	0.97
39_A	48_D	0.619	0.97
10_A	14_A	0.609	0.96
40_G	44_T	0.608	0.96
37_N	44_T	0.599	0.96
18_P	21_R	0.592	0.96
6_A	16_S	0.588	0.96
48_D	52_A	0.588	0.96
49_I	52_A	0.585	0.95
25_R	32_E	0.581	0.95
4_L	7_P	0.564	0.94
47_A	54_A	0.563	0.94
28_L	45_Y	0.560	0.94
47_A	51_A	0.556	0.94
8_A	15_Q	0.550	0.94
32_E	39_A	0.540	0.93
34_A	37_N	0.539	0.93
46_P	49_I	0.535	0.93
31_L	46_P	0.532	0.93
36_Y	50_Q	0.509	0.91
33_Q	56_V	0.501	0.90
3_A	8_A	0.500	0.90

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
3go6A	4	0.5345	8.3	0.816	Contact Map
3i4eA	4	0.6724	4.1	0.841	Contact Map
4rhjA	3	0.1897	3.3	0.848	Contact Map
2nocA	1	0.931	2.8	0.853	Contact Map
3oi8A	2	0.7069	2.7	0.855	Contact Map
1rp3B	1	0.9138	2.1	0.864	Contact Map
2jnaA	2	0.9655	2	0.865	Contact Map
2ma4A	1	0.7241	1.9	0.866	Contact Map
2jerA	4	1	1.9	0.866	Contact Map
2dcnA	5	0.5345	1.8	0.868	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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