YVDS - BACSU - GREMLIN Contacts

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YVDS - Uncharacterized membrane protein YvdS

UniProt:	O32262	Sequences: MNWVLVFIAGLLEVVWASSLKHADSLLDWIIIFILIAVSFILLIRSYQKIPMAAAYTVFVGIGTVGTYLTGIVLGESFSAAQMFFLALLLAGILGMKLFTKESKSQPGGEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	111 (99)
Sequences:	4311 (2976)
Seq/√Len:	299.1

ECOLI - MDTJ SUGE MDTI EMRE
BACSU - YVDS YKKC YVAE YVDR YKKD EBRB EBRA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_F	95_G	3.040	1.00
12_L	38_V	2.676	1.00
45_R	48_Q	2.643	1.00
72_I	78_F	2.441	1.00
5_L	45_R	2.401	1.00
19_S	31_I	2.365	1.00
2_N	49_K	2.293	1.00
15_V	35_L	2.117	1.00
10_G	62_I	2.074	1.00
68_Y	86_L	2.071	1.00
47_Y	55_A	1.821	1.00
88_L	92_G	1.815	1.00
50_I	55_A	1.740	1.00
16_W	35_L	1.645	1.00
33_F	37_A	1.592	1.00
23_A	26_L	1.590	1.00
87_A	91_A	1.547	1.00
15_V	31_I	1.502	1.00
88_L	91_A	1.496	1.00
41_I	45_R	1.467	1.00
80_A	84_F	1.465	1.00
18_S	22_H	1.455	1.00
36_I	40_F	1.417	1.00
16_W	36_I	1.407	1.00
47_Y	52_M	1.402	1.00
18_S	70_T	1.363	1.00
20_L	32_I	1.362	1.00
89_L	92_G	1.346	1.00
83_M	87_A	1.343	1.00
85_F	92_G	1.331	1.00
24_D	28_D	1.319	1.00
85_F	99_F	1.290	1.00
5_L	42_L	1.288	1.00
64_T	68_Y	1.281	1.00
22_H	74_L	1.274	1.00
14_V	66_G	1.269	1.00
12_L	35_L	1.243	1.00
94_L	98_L	1.228	1.00
43_L	55_A	1.206	1.00
46_S	55_A	1.200	1.00
85_F	89_L	1.193	1.00
3_W	58_V	1.165	1.00
79_S	82_Q	1.155	1.00
81_A	99_F	1.140	1.00
86_L	96_M	1.140	1.00
15_V	19_S	1.138	1.00
71_G	76_E	1.060	1.00
78_F	83_M	1.035	1.00
77_S	82_Q	1.030	1.00
78_F	82_Q	1.024	1.00
23_A	28_D	1.023	1.00
53_A	57_T	1.018	1.00
37_A	41_I	1.014	1.00
57_T	60_V	0.996	1.00
70_T	74_L	0.976	1.00
81_A	84_F	0.976	1.00
89_L	93_I	0.972	1.00
7_F	62_I	0.962	1.00
4_V	8_I	0.957	1.00
91_A	95_G	0.938	1.00
82_Q	96_M	0.911	1.00
7_F	10_G	0.898	1.00
69_L	73_V	0.892	1.00
30_I	34_I	0.887	1.00
54_A	82_Q	0.884	1.00
21_K	25_S	0.880	1.00
85_F	88_L	0.876	1.00
52_M	67_T	0.876	1.00
19_S	22_H	0.872	1.00
65_V	86_L	0.866	1.00
19_S	32_I	0.861	1.00
80_A	83_M	0.859	1.00
76_E	82_Q	0.854	1.00
90_L	94_L	0.839	1.00
65_V	90_L	0.829	1.00
64_T	90_L	0.824	1.00
9_A	42_L	0.823	1.00
8_I	42_L	0.822	1.00
2_N	50_I	0.819	1.00
14_V	70_T	0.816	1.00
10_G	39_S	0.807	1.00
77_S	80_A	0.805	1.00
61_G	93_I	0.797	1.00
17_A	67_T	0.787	0.99
81_A	85_F	0.771	0.99
19_S	35_L	0.763	0.99
71_G	74_L	0.756	0.99
18_S	74_L	0.753	0.99
58_V	62_I	0.753	0.99
16_W	32_I	0.750	0.99
27_L	48_Q	0.741	0.99
25_S	28_D	0.724	0.99
51_P	54_A	0.715	0.99
54_A	57_T	0.711	0.99
88_L	95_G	0.710	0.99
52_M	74_L	0.707	0.99
84_F	88_L	0.698	0.99
24_D	27_L	0.696	0.99
20_L	59_F	0.691	0.99
11_L	66_G	0.686	0.99
6_V	55_A	0.684	0.99
60_V	71_G	0.677	0.98
30_I	33_F	0.672	0.98
45_R	49_K	0.667	0.98
72_I	83_M	0.666	0.98
62_I	66_G	0.661	0.98
34_I	38_V	0.653	0.98
2_N	5_L	0.651	0.98
31_I	35_L	0.649	0.98
71_G	82_Q	0.646	0.98
19_S	23_A	0.645	0.98
36_I	60_V	0.639	0.98
13_E	39_S	0.637	0.98
95_G	99_F	0.636	0.98
23_A	27_L	0.634	0.98
61_G	64_T	0.630	0.97
21_K	24_D	0.611	0.97
57_T	96_M	0.610	0.97
18_S	71_G	0.609	0.97
9_A	43_L	0.609	0.97
40_F	47_Y	0.590	0.96
25_S	44_I	0.590	0.96
72_I	77_S	0.589	0.96
20_L	39_S	0.585	0.96
34_I	37_A	0.584	0.96
5_L	46_S	0.584	0.96
6_V	46_S	0.583	0.96
19_S	33_F	0.575	0.96
11_L	15_V	0.574	0.96
60_V	97_K	0.569	0.95
6_V	50_I	0.562	0.95
36_I	52_M	0.559	0.95
66_G	70_T	0.557	0.95
4_V	45_R	0.555	0.95
40_F	44_I	0.553	0.95
10_G	93_I	0.548	0.94
57_T	86_L	0.532	0.94
16_W	64_T	0.532	0.94
12_L	32_I	0.531	0.93
97_K	100_T	0.529	0.93
68_Y	96_M	0.529	0.93
84_F	87_A	0.524	0.93
85_F	91_A	0.513	0.92
76_E	79_S	0.512	0.92
32_I	35_L	0.503	0.92
23_A	32_I	0.502	0.91
18_S	52_M	0.502	0.91
72_I	76_E	0.500	0.91

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
3b5dA	2	0.8829	99.9	0.418	Contact Map
2i68A	2	0.6937	99.8	0.446	Contact Map
4dx5A	3	0.982	18.8	0.921	Contact Map
1pw4A	1	0.991	18.4	0.921	Contact Map
3w9iA	3	0.964	10.7	0.929	Contact Map
4k0jA	3	0.9279	8.1	0.933	Contact Map
4o9uB	2	0.7387	6.8	0.935	Contact Map
1l1yA	1	0.0991	6.7	0.935	Contact Map
3effK	4	0.7928	6.3	0.936	Contact Map
4w6vA	1	0.9189	6.1	0.937	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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