PhaG_MnhG_YufB - PFAM28P - GREMLIN Contacts

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PhaG_MnhG_YufB - Na+/H+ antiporter subunit

PFAM:	PF03334	Sequences: LLLLGAFFALVGAIGLLRLPDFYTRLHAATKADTLGAGLILLGLALYFFSLVSLKLLLIILFLLLTAPVAAHALARAAY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	79 (78)
Sequences:	19729 (11569)
Seq/√Len:	1309.9
META:	0.872

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_A	53_S	2.612	1.00
7_F	11_V	2.590	1.00
19_L	28_A	2.488	1.00
26_L	75_A	2.312	1.00
4_L	39_L	2.310	1.00
22_F	78_A	2.064	1.00
49_F	53_S	2.047	1.00
9_A	32_A	1.872	1.00
9_A	36_G	1.865	1.00
41_L	56_L	1.825	1.00
44_L	56_L	1.773	1.00
30_T	71_A	1.768	1.00
21_D	24_T	1.745	1.00
38_G	60_I	1.732	1.00
20_P	24_T	1.690	1.00
2_L	43_G	1.677	1.00
15_G	28_A	1.619	1.00
1_L	39_L	1.606	1.00
5_G	40_I	1.601	1.00
10_L	14_I	1.594	1.00
1_L	42_L	1.557	1.00
37_A	63_L	1.545	1.00
44_L	48_F	1.435	1.00
72_H	76_R	1.379	1.00
3_L	6_A	1.369	1.00
49_F	52_V	1.362	1.00
14_I	18_R	1.328	1.00
51_L	55_K	1.318	1.00
48_F	52_V	1.306	1.00
60_I	64_L	1.278	1.00
62_F	66_T	1.270	1.00
45_A	56_L	1.259	1.00
8_F	35_L	1.224	1.00
12_G	32_A	1.197	1.00
38_G	64_L	1.140	1.00
23_Y	78_A	1.101	1.00
6_A	10_L	1.101	1.00
50_S	53_S	1.089	1.00
42_L	46_L	1.053	1.00
41_L	60_I	1.023	1.00
3_L	7_F	0.986	1.00
8_F	31_K	0.983	1.00
48_F	53_S	0.955	1.00
40_I	44_L	0.947	1.00
45_A	57_L	0.947	1.00
16_L	29_A	0.894	1.00
1_L	46_L	0.870	1.00
34_T	68_P	0.868	1.00
34_T	64_L	0.868	1.00
5_G	43_G	0.853	1.00
73_A	77_A	0.850	1.00
42_L	45_A	0.843	1.00
63_L	67_A	0.827	1.00
17_L	20_P	0.819	1.00
6_A	13_A	0.819	1.00
9_A	13_A	0.805	1.00
5_G	36_G	0.803	1.00
31_K	35_L	0.795	1.00
51_L	54_L	0.794	1.00
12_G	31_K	0.792	1.00
54_L	57_L	0.786	1.00
35_L	39_L	0.785	1.00
38_G	42_L	0.782	1.00
66_T	70_A	0.765	1.00
67_A	71_A	0.760	1.00
70_A	74_L	0.752	1.00
9_A	40_I	0.746	1.00
6_A	9_A	0.714	1.00
45_A	49_F	0.712	1.00
53_S	57_L	0.697	1.00
65_L	69_V	0.695	1.00
30_T	33_D	0.689	1.00
27_H	58_L	0.683	1.00
50_S	54_L	0.679	1.00
21_D	25_R	0.679	1.00
40_I	47_Y	0.672	1.00
9_A	12_G	0.672	1.00
2_L	6_A	0.669	1.00
34_T	37_A	0.668	1.00
41_L	59_I	0.666	1.00
4_L	8_F	0.663	1.00
33_D	44_L	0.648	1.00
48_F	51_L	0.645	1.00
11_V	14_I	0.644	1.00
59_I	63_L	0.638	1.00
33_D	56_L	0.635	1.00
22_F	26_L	0.629	1.00
55_K	59_I	0.625	1.00
54_L	58_L	0.623	1.00
43_G	47_Y	0.620	1.00
62_F	65_L	0.620	1.00
10_L	13_A	0.615	1.00
8_F	36_G	0.613	1.00
57_L	61_L	0.606	1.00
70_A	76_R	0.598	1.00
33_D	67_A	0.597	1.00
37_A	59_I	0.581	1.00
45_A	48_F	0.577	1.00
38_G	41_L	0.569	1.00
2_L	5_G	0.560	1.00
34_T	67_A	0.558	1.00
24_T	27_H	0.557	1.00
32_A	37_A	0.551	1.00
29_A	33_D	0.548	1.00
56_L	59_I	0.547	1.00
13_A	32_A	0.545	1.00
11_V	31_K	0.544	1.00
62_F	68_P	0.537	1.00
26_L	71_A	0.524	1.00
18_R	28_A	0.524	1.00
31_K	38_G	0.519	1.00
39_L	42_L	0.512	1.00
49_F	54_L	0.510	1.00
49_F	55_K	0.503	1.00
9_A	37_A	0.502	1.00
61_L	68_P	0.500	1.00
14_I	17_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
3rkoM	1	0.9873	3.7	0.885	Contact Map
3rkoL	1	0.9241	3.2	0.889	Contact Map
4he8L	1	0.7975	2.1	0.9	Contact Map
3rkoN	1	0.9747	1.7	0.904	Contact Map
4p02B	1	0.2911	1.7	0.905	Contact Map
4he8M	1	0.8354	1.5	0.907	Contact Map
2i68A	2	0.7215	1.3	0.91	Contact Map
4hkrA	3	0.7595	1.2	0.912	Contact Map
2bg9E	1	0.3418	1.2	0.912	Contact Map
1oedA	1	0.3544	1.1	0.915	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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