DUF1628 - PFAM28P - GREMLIN Contacts

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DUF1628 - Protein of unknown function (DUF1628)

PFAM:	PF07790	Sequences: RAVSPVIGVILMVAITVILAAVIGAFVLGLGGSPETAPQASFSVDVDSSGGTGGNTVTITHEGGDTIDASDLKITVDGDG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (75)
Sequences:	8376 (6222)
Seq/√Len:	718.5
META:	0.912

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_G	28_L	4.512	1.00
61_H	67_I	2.997	1.00
23_I	27_V	2.791	1.00
61_H	64_G	2.702	1.00
9_V	16_T	2.220	1.00
10_I	14_A	2.094	1.00
61_H	65_D	2.072	1.00
43_S	62_E	1.987	1.00
7_I	10_I	1.792	1.00
72_L	75_T	1.706	1.00
13_V	16_T	1.686	1.00
42_F	59_I	1.631	1.00
57_V	61_H	1.628	1.00
68_D	71_D	1.625	1.00
44_V	59_I	1.508	1.00
21_A	25_A	1.385	1.00
16_T	20_A	1.376	1.00
14_A	18_I	1.363	1.00
42_F	67_I	1.349	1.00
73_K	76_V	1.318	1.00
25_A	29_G	1.288	1.00
52_T	55_N	1.262	1.00
42_F	61_H	1.248	1.00
69_A	72_L	1.235	1.00
27_V	30_L	1.214	1.00
68_D	72_L	1.210	1.00
48_S	52_T	1.209	1.00
50_G	55_N	1.205	1.00
33_S	37_A	1.169	1.00
5_P	8_G	1.157	1.00
26_F	30_L	1.134	1.00
66_T	69_A	1.131	1.00
15_I	19_L	1.123	1.00
31_G	34_P	1.116	1.00
52_T	56_T	1.048	1.00
8_G	26_F	1.027	1.00
12_M	26_F	1.022	1.00
22_V	25_A	1.018	1.00
5_P	20_A	1.012	1.00
46_V	50_G	0.982	1.00
6_V	24_G	0.966	1.00
6_V	20_A	0.928	1.00
33_S	36_T	0.927	1.00
67_I	72_L	0.923	1.00
46_V	49_S	0.916	1.00
49_S	52_T	0.906	1.00
9_V	19_L	0.901	1.00
46_V	51_G	0.887	1.00
10_I	16_T	0.883	1.00
40_A	44_V	0.876	1.00
68_D	76_V	0.872	1.00
51_G	56_T	0.859	1.00
9_V	20_A	0.851	1.00
5_P	16_T	0.839	1.00
48_S	56_T	0.824	1.00
34_P	37_A	0.816	1.00
9_V	12_M	0.794	1.00
18_I	24_G	0.791	1.00
15_I	24_G	0.777	1.00
31_G	35_E	0.772	1.00
70_S	73_K	0.768	1.00
13_V	21_A	0.744	1.00
19_L	30_L	0.743	1.00
47_D	55_N	0.736	1.00
35_E	38_P	0.734	1.00
46_V	55_N	0.731	1.00
48_S	55_N	0.731	1.00
37_A	41_S	0.730	1.00
49_S	55_N	0.728	1.00
5_P	12_M	0.724	1.00
10_I	13_V	0.715	1.00
19_L	22_V	0.706	1.00
49_S	56_T	0.699	1.00
40_A	61_H	0.695	1.00
36_T	40_A	0.689	1.00
18_I	23_I	0.687	1.00
36_T	39_Q	0.684	1.00
43_S	60_T	0.676	1.00
58_T	62_E	0.674	1.00
13_V	20_A	0.673	1.00
16_T	30_L	0.668	1.00
57_V	60_T	0.664	1.00
57_V	63_G	0.637	1.00
47_D	50_G	0.633	1.00
22_V	28_L	0.632	1.00
44_V	57_V	0.616	1.00
17_V	26_F	0.600	1.00
50_G	56_T	0.596	1.00
9_V	23_I	0.591	1.00
4_S	8_G	0.586	1.00
26_F	41_S	0.583	1.00
10_I	24_G	0.575	1.00
72_L	76_V	0.565	1.00
4_S	12_M	0.555	1.00
11_L	19_L	0.549	1.00
1_R	5_P	0.548	1.00
19_L	29_G	0.538	1.00
23_I	26_F	0.537	1.00
31_G	36_T	0.534	1.00
5_P	18_I	0.531	1.00
24_G	27_V	0.530	1.00
51_G	57_V	0.525	1.00
16_T	19_L	0.525	1.00
5_P	26_F	0.519	1.00
31_G	38_P	0.517	1.00
25_A	32_G	0.513	1.00
35_E	39_Q	0.502	0.99
3_V	7_I	0.501	0.99
1_R	25_A	0.501	0.99
47_D	52_T	0.501	0.99
18_I	22_V	0.501	0.99
8_G	16_T	0.500	0.99

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
3j1rA	5	0.325	86.2	0.712	Contact Map
2wnxA	2	0.575	26.5	0.813	Contact Map
2xbtA	1	0.6	19.5	0.824	Contact Map
1g43A	1	0.55	10.8	0.843	Contact Map
4b9pA	1	0.5625	9.4	0.847	Contact Map
1h2sB	2	0.3	6.9	0.857	Contact Map
3zqxA	1	0.5125	6.9	0.857	Contact Map
3zucA	1	0.55	6.6	0.858	Contact Map
4b9cA	1	0.575	6.2	0.86	Contact Map
4b9fA	1	0.5	5.9	0.861	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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