YTPI - BACSU - GREMLIN Contacts

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YTPI - Uncharacterized membrane protein YtpI

UniProt:	O34922	Sequences: MLVLVFLIGLSACFYVYYKVKGVRAKPSLAKEICSAKSSMALGSLVLFYGLNQMILFHSVLTLVIGGIFIVIGAGSAWAGYKAFRHYNPLHAKEAERDHA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	100 (96)
Sequences:	120 (94)
Seq/√Len:	9.6

BACSU - YTPI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_G	69_F	3.529	0.97
61_L	65_I	3.355	0.96
44_S	48_F	2.882	0.90
84_F	89_P	2.850	0.90
18_Y	34_C	2.731	0.87
63_L	67_G	2.266	0.75
9_G	17_Y	2.260	0.75
4_L	10_L	2.138	0.71
83_A	87_Y	2.082	0.69
53_Q	57_F	2.039	0.67
65_I	68_I	2.011	0.66
36_A	83_A	1.915	0.62
4_L	48_F	1.813	0.57
18_Y	59_S	1.790	0.56
8_I	52_N	1.677	0.51
47_L	65_I	1.635	0.49
62_T	66_G	1.570	0.47
20_V	23_V	1.560	0.46
39_S	76_S	1.548	0.46
77_A	86_H	1.526	0.45
3_V	71_V	1.489	0.43
4_L	11_S	1.484	0.43
56_L	72_I	1.450	0.41
15_Y	23_V	1.450	0.41
36_A	46_V	1.337	0.36
8_I	38_S	1.334	0.36
12_A	64_V	1.328	0.36
11_S	17_Y	1.328	0.36
29_L	87_Y	1.265	0.33
17_Y	91_H	1.200	0.31
19_K	39_S	1.200	0.31
12_A	72_I	1.193	0.31
37_K	84_F	1.185	0.30
59_S	75_G	1.153	0.29
77_A	81_Y	1.135	0.28
63_L	66_G	1.130	0.28
44_S	96_E	1.114	0.28
20_V	67_G	1.096	0.27
54_M	69_F	1.058	0.26
48_F	61_L	1.054	0.26
82_K	90_L	1.050	0.25
46_V	78_W	1.046	0.25
49_Y	55_I	1.041	0.25
47_L	61_L	1.037	0.25
2_L	55_I	1.025	0.25
53_Q	56_L	1.011	0.24
75_G	79_A	1.009	0.24
38_S	76_S	1.004	0.24
93_K	96_E	0.993	0.24
72_I	76_S	0.991	0.24
33_I	95_A	0.991	0.24
10_L	68_I	0.977	0.23
4_L	88_N	0.976	0.23
69_F	85_R	0.970	0.23
56_L	62_T	0.970	0.23
16_V	20_V	0.957	0.22
10_L	26_K	0.948	0.22
2_L	13_C	0.944	0.22
50_G	85_R	0.937	0.22
23_V	91_H	0.927	0.22
3_V	26_K	0.911	0.21
37_K	45_L	0.892	0.20
16_V	85_R	0.882	0.20
25_A	31_K	0.878	0.20
22_G	38_S	0.868	0.20
51_L	72_I	0.866	0.20
87_Y	90_L	0.864	0.20
16_V	29_L	0.860	0.20
18_Y	44_S	0.850	0.19
37_K	40_M	0.849	0.19
7_L	47_L	0.842	0.19
2_L	86_H	0.838	0.19
30_A	89_P	0.828	0.19
17_Y	29_L	0.826	0.19
9_G	78_W	0.818	0.18
29_L	61_L	0.815	0.18
57_F	62_T	0.812	0.18
20_V	85_R	0.812	0.18
74_A	85_R	0.807	0.18
44_S	47_L	0.795	0.18
57_F	72_I	0.785	0.18
21_K	31_K	0.772	0.17
7_L	71_V	0.765	0.17
72_I	75_G	0.755	0.17
54_M	67_G	0.751	0.17
24_R	42_L	0.742	0.16
20_V	59_S	0.723	0.16
38_S	46_V	0.711	0.16
38_S	55_I	0.707	0.16
68_I	88_N	0.705	0.16
26_K	67_G	0.702	0.15
12_A	16_V	0.700	0.15
33_I	91_H	0.697	0.15
11_S	83_A	0.689	0.15
7_L	24_R	0.686	0.15
29_L	76_S	0.686	0.15
9_G	96_E	0.682	0.15
20_V	90_L	0.675	0.15
29_L	90_L	0.673	0.15
47_L	77_A	0.672	0.15
40_M	70_I	0.663	0.15
14_F	92_A	0.653	0.14
32_E	82_K	0.648	0.14
67_G	74_A	0.646	0.14
29_L	86_H	0.635	0.14
91_H	95_A	0.630	0.14
39_S	79_A	0.630	0.14
17_Y	84_F	0.629	0.14
66_G	82_K	0.625	0.14
35_S	63_L	0.617	0.14
54_M	59_S	0.616	0.14
33_I	84_F	0.615	0.14
12_A	51_L	0.611	0.13
25_A	66_G	0.608	0.13
24_R	50_G	0.608	0.13
5_V	52_N	0.592	0.13
7_L	48_F	0.581	0.13
15_Y	53_Q	0.571	0.13
76_S	80_G	0.562	0.12
3_V	87_Y	0.557	0.12
16_V	38_S	0.547	0.12
12_A	33_I	0.545	0.12
29_L	33_I	0.541	0.12
84_F	88_N	0.540	0.12
4_L	67_G	0.537	0.12
61_L	64_V	0.534	0.12
13_C	20_V	0.530	0.12
35_S	76_S	0.530	0.12
54_M	70_I	0.530	0.12
44_S	77_A	0.529	0.12
25_A	71_V	0.528	0.12
36_A	87_Y	0.525	0.12
39_S	57_F	0.523	0.12
35_S	94_E	0.522	0.12
2_L	49_Y	0.519	0.12
86_H	92_A	0.516	0.12
45_L	72_I	0.511	0.11
33_I	94_E	0.511	0.11
33_I	85_R	0.508	0.11
80_G	91_H	0.506	0.11
65_I	82_K	0.505	0.11
23_V	93_K	0.505	0.11
7_L	65_I	0.503	0.11
38_S	80_G	0.500	0.11

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
3l1lA	2	0.85	46.2	0.916	Contact Map
2xq2A	2	0.79	18.1	0.931	Contact Map
4k5yA	1	0.85	14.1	0.935	Contact Map
4kjrA	3	0.76	13.6	0.935	Contact Map
4o6yA	2	0.81	12.7	0.936	Contact Map
4djkA	2	0.8	11.9	0.937	Contact Map
3giaA	1	0.86	9.9	0.939	Contact Map
4kppA	1	0.9	9.2	0.94	Contact Map
2r9rB	3	0.81	9	0.94	Contact Map
3b9wA	3	0.98	8.9	0.94	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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