DUF4250 - PFAM28P - GREMLIN Contacts

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DUF4250 - Domain of unknown function (DUF4250)

PFAM:	PF14056	Sequences: LPKDPVMLLSYVNTKLRDEYSSLDELCEDLDIDKEELEEKLAAIGYEYDEEQNQF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (55)
Sequences:	2385 (1811)
Seq/√Len:	244.1
META:	0.789

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_K	38_E	3.041	1.00
24_D	34_K	2.949	1.00
15_K	19_E	2.510	1.00
26_L	30_L	1.936	1.00
12_V	41_L	1.765	1.00
20_Y	29_D	1.733	1.00
42_A	47_E	1.662	1.00
15_K	30_L	1.662	1.00
25_E	29_D	1.643	1.00
11_Y	14_T	1.607	1.00
35_E	39_E	1.603	1.00
49_D	52_Q	1.574	1.00
25_E	28_E	1.535	1.00
3_K	40_K	1.527	1.00
6_V	44_I	1.490	1.00
23_L	55_F	1.477	1.00
1_L	11_Y	1.475	1.00
21_S	25_E	1.439	1.00
48_Y	53_N	1.364	1.00
12_V	26_L	1.361	1.00
38_E	55_F	1.280	1.00
11_Y	15_K	1.258	1.00
39_E	43_A	1.134	1.00
6_V	46_Y	1.130	1.00
33_D	36_E	1.122	1.00
9_L	46_Y	1.110	1.00
1_L	32_I	1.086	1.00
23_L	37_L	1.076	1.00
22_S	25_E	1.070	1.00
11_Y	30_L	1.054	1.00
7_M	10_S	1.033	1.00
6_V	9_L	1.022	1.00
35_E	38_E	0.992	1.00
7_M	14_T	0.986	1.00
16_L	53_N	0.915	1.00
8_L	41_L	0.898	1.00
39_E	42_A	0.859	0.99
9_L	44_I	0.854	0.99
36_E	40_K	0.850	0.99
5_P	40_K	0.839	0.99
19_E	29_D	0.830	0.99
40_K	43_A	0.823	0.99
20_Y	30_L	0.818	0.99
23_L	34_K	0.776	0.99
10_S	18_D	0.774	0.99
5_P	44_I	0.768	0.99
14_T	18_D	0.763	0.99
32_I	37_L	0.753	0.98
49_D	54_Q	0.728	0.98
14_T	19_E	0.708	0.98
19_E	30_L	0.705	0.98
6_V	54_Q	0.700	0.97
22_S	53_N	0.688	0.97
7_M	11_Y	0.647	0.96
11_Y	26_L	0.627	0.95
27_C	34_K	0.624	0.95
24_D	50_E	0.617	0.95
2_P	11_Y	0.612	0.95
2_P	5_P	0.607	0.94
28_E	31_D	0.601	0.94
14_T	26_L	0.590	0.93
40_K	44_I	0.586	0.93
39_E	47_E	0.583	0.93
32_I	40_K	0.577	0.93
15_K	20_Y	0.573	0.92
47_E	51_E	0.569	0.92
10_S	20_Y	0.551	0.91
39_E	50_E	0.550	0.91
36_E	39_E	0.549	0.91
15_K	29_D	0.544	0.90
22_S	50_E	0.539	0.90
14_T	52_Q	0.537	0.90
38_E	42_A	0.534	0.90
3_K	11_Y	0.533	0.90
19_E	22_S	0.532	0.89
4_D	45_G	0.523	0.89
6_V	45_G	0.518	0.88
31_D	45_G	0.512	0.88
20_Y	48_Y	0.505	0.87
10_S	15_K	0.503	0.87
7_M	15_K	0.502	0.87
50_E	53_N	0.500	0.86

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
2fi0A	1	0.9455	53.1	0.827	Contact Map
2k9sA	1	0.9636	29.7	0.851	Contact Map
2p22B	2	0.4364	25.1	0.856	Contact Map
3lsgA	2	0.9818	23.8	0.858	Contact Map
2f6mB	1	0.8	23	0.859	Contact Map
1rr7A	2	0.8727	22.5	0.859	Contact Map
3mn2A	1	0.9636	20	0.862	Contact Map
3oioA	1	0.9818	19.7	0.863	Contact Map
1d5yA	1	0.9455	16.4	0.868	Contact Map
3rkxA	1	0.9091	15.6	0.869	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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