GTRA - ECOLI - GREMLIN Contacts

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GTRA - Bactoprenol-linked glucose translocase homolog from prophage CPS-53

UniProt:	P77682	Sequences: MLKLFAKYTSIGVLNTLIHWVVFGVCIYVAHTNQALANFAGFVVAVSFSFFANAKFTFKASTTTMRYMLYVGFMGTLSATVGWAADRCALPPMITLVTFSAISLVCGFVYSKFIVFRDAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14131
Length:	120 (116)
Sequences:	155 (115)
Seq/√Len:	10.7

ECOLI - GTRA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_F	78_S	5.424	1.00
18_I	48_F	4.086	0.99
70_Y	106_C	2.682	0.89
32_T	37_A	2.670	0.89
47_S	78_S	2.383	0.83
47_S	62_T	2.078	0.73
14_L	21_V	2.026	0.71
48_F	52_A	1.942	0.68
73_F	110_Y	1.904	0.66
22_V	44_V	1.893	0.66
69_L	106_C	1.888	0.65
8_Y	16_T	1.863	0.64
110_Y	115_V	1.826	0.63
20_W	95_T	1.803	0.62
52_A	92_P	1.785	0.61
87_R	117_R	1.760	0.60
35_A	61_S	1.670	0.55
17_L	27_I	1.667	0.55
54_A	105_V	1.629	0.54
72_G	77_L	1.627	0.53
77_L	90_L	1.607	0.52
3_K	6_A	1.603	0.52
20_W	116_F	1.598	0.52
9_T	13_V	1.550	0.50
5_F	104_L	1.536	0.49
26_C	69_L	1.456	0.45
16_T	103_S	1.440	0.45
17_L	114_I	1.438	0.44
17_L	44_V	1.425	0.44
26_C	41_G	1.314	0.39
11_I	41_G	1.293	0.38
79_A	109_V	1.290	0.38
7_K	37_A	1.245	0.36
27_I	37_A	1.231	0.35
63_T	68_M	1.229	0.35
39_F	106_C	1.223	0.35
50_F	73_F	1.218	0.35
47_S	50_F	1.207	0.34
112_K	118_D	1.203	0.34
68_M	98_T	1.195	0.34
37_A	115_V	1.193	0.33
83_W	106_C	1.161	0.32
8_Y	103_S	1.159	0.32
27_I	113_F	1.157	0.32
102_I	106_C	1.155	0.32
85_A	88_C	1.148	0.32
12_G	16_T	1.142	0.31
72_G	113_F	1.136	0.31
8_Y	12_G	1.127	0.31
8_Y	15_N	1.123	0.31
2_L	6_A	1.118	0.30
18_I	39_F	1.111	0.30
21_V	69_L	1.110	0.30
47_S	51_F	1.092	0.29
2_L	85_A	1.039	0.27
46_V	57_T	1.036	0.27
69_L	76_T	1.033	0.27
36_L	79_A	1.023	0.27
31_H	78_S	1.023	0.27
31_H	41_G	1.020	0.27
15_N	103_S	1.019	0.27
90_L	98_T	1.015	0.26
36_L	101_A	1.002	0.26
43_V	62_T	0.999	0.26
11_I	52_A	0.997	0.26
59_K	93_M	0.979	0.25
41_G	62_T	0.953	0.24
6_A	85_A	0.949	0.24
60_A	78_S	0.949	0.24
72_G	76_T	0.932	0.23
35_A	65_M	0.911	0.23
55_K	88_C	0.896	0.22
74_M	117_R	0.894	0.22
32_T	94_I	0.890	0.22
18_I	50_F	0.881	0.22
55_K	92_P	0.869	0.21
47_S	56_F	0.866	0.21
63_T	109_V	0.864	0.21
22_V	28_Y	0.854	0.21
84_A	106_C	0.848	0.21
24_G	115_V	0.836	0.20
77_L	98_T	0.836	0.20
17_L	22_V	0.834	0.20
35_A	78_S	0.829	0.20
79_A	114_I	0.814	0.20
20_W	99_F	0.808	0.20
75_G	111_S	0.806	0.19
16_T	100_S	0.795	0.19
4_L	10_S	0.794	0.19
37_A	88_C	0.790	0.19
108_F	111_S	0.789	0.19
17_L	105_V	0.786	0.19
102_I	114_I	0.781	0.19
60_A	106_C	0.778	0.19
2_L	10_S	0.768	0.18
103_S	111_S	0.767	0.18
46_V	73_F	0.766	0.18
35_A	70_Y	0.763	0.18
52_A	94_I	0.760	0.18
33_N	39_F	0.752	0.18
13_V	109_V	0.750	0.18
26_C	31_H	0.748	0.18
15_N	19_H	0.740	0.18
25_V	39_F	0.726	0.17
69_L	101_A	0.720	0.17
11_I	90_L	0.717	0.17
46_V	110_Y	0.713	0.17
84_A	118_D	0.712	0.17
63_T	66_R	0.712	0.17
7_K	46_V	0.709	0.17
63_T	73_F	0.707	0.17
88_C	112_K	0.701	0.17
52_A	102_I	0.701	0.17
100_S	103_S	0.700	0.16
6_A	9_T	0.699	0.16
21_V	41_G	0.693	0.16
28_Y	32_T	0.691	0.16
20_W	115_V	0.680	0.16
62_T	72_G	0.679	0.16
10_S	46_V	0.678	0.16
11_I	111_S	0.677	0.16
28_Y	77_L	0.672	0.16
34_Q	95_T	0.671	0.16
54_A	73_F	0.663	0.16
43_V	80_T	0.661	0.16
9_T	70_Y	0.655	0.15
27_I	71_V	0.655	0.15
43_V	71_V	0.644	0.15
81_V	84_A	0.643	0.15
21_V	117_R	0.637	0.15
106_C	117_R	0.634	0.15
70_Y	73_F	0.630	0.15
18_I	105_V	0.623	0.15
63_T	96_L	0.617	0.14
61_S	64_T	0.615	0.14
58_F	107_G	0.611	0.14
14_L	35_A	0.611	0.14
7_K	72_G	0.611	0.14
35_A	52_A	0.607	0.14
13_V	98_T	0.604	0.14
99_F	105_V	0.603	0.14
88_C	91_P	0.603	0.14
56_F	89_A	0.602	0.14
81_V	98_T	0.595	0.14
3_K	91_P	0.594	0.14
46_V	70_Y	0.591	0.14
93_M	112_K	0.585	0.14
12_G	42_F	0.577	0.14
12_G	20_W	0.571	0.13
40_A	62_T	0.567	0.13
91_P	118_D	0.562	0.13
85_A	92_P	0.558	0.13
15_N	54_A	0.555	0.13
69_L	72_G	0.554	0.13
56_F	72_G	0.548	0.13
16_T	19_H	0.543	0.13
81_V	106_C	0.541	0.13
10_S	73_F	0.540	0.13
2_L	109_V	0.539	0.13
3_K	43_V	0.538	0.13
40_A	113_F	0.536	0.13
47_S	77_L	0.535	0.13
99_F	116_F	0.534	0.13
30_A	35_A	0.534	0.13
11_I	105_V	0.531	0.13
6_A	71_V	0.527	0.12
43_V	106_C	0.519	0.12
44_V	89_A	0.516	0.12
92_P	117_R	0.513	0.12
47_S	115_V	0.512	0.12
32_T	41_G	0.512	0.12
98_T	113_F	0.505	0.12
40_A	80_T	0.505	0.12
89_A	114_I	0.500	0.12

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
2zy9A	2	0.7	33.6	0.936	Contact Map
4q65A	1	0.825	12.5	0.948	Contact Map
4oh3A	2	0.875	11.7	0.948	Contact Map
2gfpA	2	0.7833	10.3	0.95	Contact Map
3wdoA	1	0.85	8	0.952	Contact Map
1p7bA	3	0.9833	7.4	0.953	Contact Map
4ikvA	1	0.9583	6.2	0.954	Contact Map
4lp8A	4	0.9833	4.7	0.957	Contact Map
4ldsA	2	0.75	4.7	0.957	Contact Map
3syaA	3	1	4.5	0.957	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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