PGPGW - PFAM28P - GREMLIN Contacts

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PGPGW - Putative transmembrane protein (PGPGW)

PFAM:	PF09656	Sequences: RIVVAVVGFTLLLLGIAMLVLPGPGILVIPLGLAILATEFAWARRLLDRARRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (52)
Sequences:	10549 (6064)
Seq/√Len:	840.9
META:	0.948

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_M	23_G	2.661	1.00
17_A	21_L	2.500	1.00
5_A	40_F	2.386	1.00
5_A	9_F	2.167	1.00
11_L	35_I	2.046	1.00
25_G	30_P	1.983	1.00
18_M	28_V	1.969	1.00
4_V	39_E	1.677	1.00
26_I	30_P	1.660	1.00
47_L	51_R	1.614	1.00
9_F	40_F	1.504	1.00
19_L	25_G	1.459	1.00
44_R	48_D	1.447	1.00
14_L	18_M	1.434	1.00
12_L	32_G	1.415	1.00
34_A	38_T	1.367	1.00
41_A	45_R	1.273	1.00
18_M	21_L	1.239	1.00
15_G	29_I	1.160	1.00
11_L	28_V	1.126	1.00
4_V	35_I	1.108	1.00
15_G	19_L	1.037	1.00
12_L	29_I	1.032	1.00
4_V	38_T	1.024	1.00
46_L	49_R	1.012	1.00
49_R	52_R	0.993	1.00
37_A	47_L	0.990	1.00
9_F	36_L	0.986	1.00
11_L	31_L	0.979	1.00
19_L	29_I	0.974	1.00
19_L	26_I	0.968	1.00
24_P	27_L	0.921	1.00
25_G	28_V	0.917	1.00
3_V	7_V	0.909	1.00
27_L	30_P	0.868	1.00
45_R	49_R	0.858	1.00
20_V	28_V	0.855	1.00
16_I	20_V	0.852	1.00
34_A	47_L	0.826	1.00
41_A	46_L	0.787	1.00
3_V	6_V	0.786	1.00
41_A	44_R	0.786	1.00
48_D	51_R	0.771	1.00
9_F	13_L	0.770	1.00
7_V	35_I	0.735	1.00
8_G	32_G	0.730	1.00
2_I	6_V	0.728	1.00
23_G	28_V	0.728	1.00
33_L	50_A	0.723	1.00
17_A	20_V	0.715	1.00
13_L	17_A	0.712	1.00
19_L	27_L	0.708	1.00
42_W	46_L	0.705	1.00
38_T	41_A	0.703	1.00
5_A	39_E	0.697	1.00
20_V	25_G	0.697	1.00
34_A	37_A	0.692	1.00
48_D	52_R	0.691	1.00
15_G	18_M	0.680	1.00
47_L	50_A	0.679	1.00
16_I	19_L	0.663	1.00
12_L	36_L	0.659	1.00
38_T	44_R	0.651	1.00
2_I	5_A	0.639	1.00
12_L	21_L	0.622	1.00
6_V	10_T	0.620	1.00
11_L	32_G	0.619	1.00
10_T	14_L	0.611	1.00
32_G	36_L	0.600	1.00
45_R	48_D	0.597	1.00
24_P	28_V	0.580	1.00
14_L	28_V	0.576	1.00
7_V	10_T	0.574	1.00
37_A	44_R	0.531	1.00
33_L	46_L	0.519	1.00
10_T	41_A	0.513	1.00
27_L	31_L	0.510	1.00
43_A	46_L	0.500	1.00

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
1ciyA	1	0.9057	3.3	0.852	Contact Map
2qc3A	1	0.6981	3.2	0.853	Contact Map
3qe7A	2	0.9811	3.1	0.854	Contact Map
1ji6A	1	0.9057	3	0.856	Contact Map
4o6mA	2	1	2.9	0.857	Contact Map
2j4tA	1	0.1887	2.9	0.858	Contact Map
2cuyA	2	0.6981	2.7	0.86	Contact Map
2mpnA	2	1	2.4	0.862	Contact Map
2qjyA	2	0.3585	2.1	0.868	Contact Map
4mndA	2	0.8868	1.9	0.871	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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