YFGD - ECOLI - GREMLIN Contacts

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YFGD - Uncharacterized protein YfgD

UniProt:	P76569	Sequences: MTKQVKIYHNPRCSKSRETLNLLKENGVEPEVVLYLETPADAATLRDLLKILGMNSARELMRQKEDLYKELNLADSSLSEEALIQAMVDNPKLMERPIVVANGKARIGRPPEQVLEIVG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14200
Length:	119 (113)
Sequences:	3220 (2024)
Seq/√Len:	190.4

ECOLI - YFGD ARSC YFFB
BACSU - MGSR SPX YUSI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_L	37_E	3.980	1.00
42_A	85_Q	3.113	1.00
24_K	30_P	2.785	1.00
47_D	51_I	2.406	1.00
79_S	82_A	2.370	1.00
87_M	94_M	2.318	1.00
41_D	44_T	2.264	1.00
49_L	84_I	2.211	1.00
66_D	70_E	2.146	1.00
85_Q	89_D	1.882	1.00
57_A	80_E	1.881	1.00
7_I	99_V	1.825	1.00
21_N	25_E	1.794	1.00
113_Q	116_E	1.762	1.00
42_A	84_I	1.730	1.00
9_H	32_V	1.717	1.00
67_L	90_N	1.696	1.00
46_R	81_E	1.694	1.00
42_A	46_R	1.691	1.00
51_I	105_A	1.677	1.00
48_L	100_V	1.660	1.00
24_K	29_E	1.631	1.00
33_V	44_T	1.603	1.00
56_S	59_E	1.493	1.00
6_K	31_E	1.490	1.00
101_A	104_K	1.479	1.00
78_L	86_A	1.475	1.00
49_L	57_A	1.466	1.00
15_K	18_E	1.441	1.00
40_A	94_M	1.429	1.00
7_I	20_L	1.415	1.00
56_S	80_E	1.391	1.00
33_V	38_T	1.328	1.00
72_N	75_D	1.314	1.00
20_L	32_V	1.299	1.00
9_H	16_S	1.288	1.00
67_L	70_E	1.264	1.00
67_L	92_K	1.257	1.00
52_L	60_L	1.247	1.00
60_L	98_I	1.244	1.00
11_P	34_L	1.242	1.00
67_L	71_L	1.237	1.00
8_Y	48_L	1.230	1.00
46_R	84_I	1.215	1.00
71_L	90_N	1.200	1.00
39_P	94_M	1.176	1.00
54_M	60_L	1.161	1.00
18_E	21_N	1.158	1.00
63_Q	69_K	1.155	1.00
61_M	83_L	1.142	1.00
42_A	88_V	1.138	1.00
49_L	60_L	1.125	1.00
9_H	20_L	1.117	1.00
19_T	114_V	1.097	1.00
6_K	33_V	1.069	1.00
22_L	115_L	1.068	1.00
101_A	117_I	1.053	1.00
20_L	24_K	1.045	1.00
52_L	98_I	1.037	1.00
42_A	81_E	1.034	1.00
106_R	116_E	1.031	1.00
46_R	80_E	1.023	1.00
64_K	95_E	1.016	1.00
51_I	103_G	0.999	0.99
106_R	113_Q	0.998	0.99
58_R	68_Y	0.991	0.99
45_L	84_I	0.981	0.99
8_Y	33_V	0.973	0.99
44_T	47_D	0.959	0.99
58_R	75_D	0.956	0.99
5_V	28_V	0.952	0.99
8_Y	100_V	0.926	0.99
22_L	26_N	0.919	0.99
54_M	59_E	0.918	0.99
36_L	92_K	0.915	0.99
48_L	98_I	0.906	0.99
18_E	111_P	0.879	0.99
63_Q	95_E	0.870	0.99
66_D	69_K	0.866	0.99
112_E	115_L	0.847	0.98
78_L	83_L	0.845	0.98
21_N	24_K	0.836	0.98
22_L	111_P	0.831	0.98
8_Y	44_T	0.829	0.98
99_V	114_V	0.827	0.98
106_R	117_I	0.823	0.98
15_K	111_P	0.822	0.98
12_R	65_E	0.816	0.98
18_E	64_K	0.809	0.98
108_G	113_Q	0.805	0.98
58_R	83_L	0.787	0.97
82_A	85_Q	0.786	0.97
111_P	115_L	0.782	0.97
7_I	19_T	0.779	0.97
57_A	83_L	0.767	0.97
58_R	61_M	0.761	0.97
23_L	26_N	0.754	0.97
68_Y	73_L	0.750	0.96
98_I	107_I	0.742	0.96
12_R	17_R	0.736	0.96
22_L	109_R	0.732	0.96
49_L	53_G	0.726	0.96
61_M	87_M	0.719	0.95
71_L	93_L	0.717	0.95
26_N	115_L	0.707	0.95
49_L	80_E	0.670	0.93
31_E	38_T	0.663	0.93
61_M	68_Y	0.663	0.93
40_A	44_T	0.662	0.93
17_R	20_L	0.660	0.93
74_A	78_L	0.653	0.93
57_A	84_I	0.649	0.92
95_E	108_G	0.646	0.92
45_L	94_M	0.638	0.92
57_A	87_M	0.636	0.92
20_L	30_P	0.635	0.92
6_K	44_T	0.635	0.92
65_E	92_K	0.633	0.91
80_E	83_L	0.630	0.91
68_Y	74_A	0.629	0.91
25_E	28_V	0.621	0.91
63_Q	68_Y	0.621	0.91
78_L	82_A	0.620	0.91
10_N	36_L	0.616	0.90
43_A	46_R	0.615	0.90
61_M	80_E	0.614	0.90
51_I	100_V	0.613	0.90
46_R	50_K	0.613	0.90
5_V	99_V	0.609	0.90
7_I	32_V	0.605	0.89
56_S	83_L	0.605	0.89
8_Y	40_A	0.601	0.89
14_S	18_E	0.599	0.89
19_T	111_P	0.598	0.89
60_L	87_M	0.598	0.89
68_Y	83_L	0.587	0.88
19_T	113_Q	0.584	0.88
19_T	106_R	0.582	0.88
52_L	105_A	0.578	0.87
51_I	101_A	0.575	0.87
5_V	101_A	0.574	0.87
73_L	76_S	0.571	0.87
48_L	105_A	0.555	0.85
27_G	30_P	0.554	0.85
83_L	86_A	0.553	0.85
59_E	95_E	0.551	0.85
50_K	80_E	0.550	0.85
110_P	113_Q	0.550	0.85
113_Q	117_I	0.549	0.84
5_V	23_L	0.548	0.84
75_D	78_L	0.545	0.84
80_E	84_I	0.544	0.84
14_S	111_P	0.540	0.83
45_L	88_V	0.535	0.83
12_R	34_L	0.532	0.83
19_T	99_V	0.531	0.82
25_E	103_G	0.530	0.82
82_A	86_A	0.528	0.82
19_T	108_G	0.525	0.82
15_K	64_K	0.524	0.82
69_K	108_G	0.520	0.81
18_E	25_E	0.517	0.81
99_V	106_R	0.513	0.80
8_Y	98_I	0.512	0.80
65_E	69_K	0.511	0.80
28_V	101_A	0.505	0.79
63_Q	74_A	0.504	0.79
49_L	54_M	0.500	0.79
71_L	82_A	0.500	0.79
77_S	86_A	0.500	0.79

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
2mu0A	1	0.9832	100	0.282	Contact Map
1s3cA	2	0.9664	100	0.286	Contact Map
3f0iA	1	0.9664	100	0.3	Contact Map
3rdwA	1	0.9664	100	0.308	Contact Map
3gkxA	2	0.9664	100	0.312	Contact Map
1z3eA	1	0.9748	100	0.316	Contact Map
3fz4A	1	0.9664	100	0.32	Contact Map
2kokA	1	0.9664	100	0.325	Contact Map
3l78A	1	0.9664	100	0.327	Contact Map
1rw1A	1	0.9496	100	0.335	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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