YGIW - ECOLI - GREMLIN Contacts

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YGIW - Protein YgiW

UniProt:	P0ADU5	Sequences: MKKFAAVIAVMALCSAPVMAAEQGGFSGPSATQSQAGGFQGPNGSVTTVESAKSLRDDTWVTLRGNIVERISDDLYVFKDASGTINVDIDHKRWNGVTVTPKDTVEIQGEVDKDWNSVEIDVKQIRKVNP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13025
Length:	130 (125)
Sequences:	321 (250)
Seq/√Len:	22.4

ECOLI - YGIW YDEI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_R	106_E	4.671	1.00
111_V	120_I	3.122	1.00
107_I	120_I	2.531	0.98
66_N	104_T	2.454	0.98
90_D	121_D	2.365	0.97
103_D	127_K	2.327	0.97
4_F	8_I	2.273	0.97
87_V	107_I	2.267	0.97
76_Y	89_I	2.241	0.96
38_G	41_G	2.159	0.95
106_E	126_R	2.152	0.95
68_V	79_K	2.057	0.94
114_D	118_V	2.055	0.94
81_A	107_I	1.971	0.93
69_E	77_V	1.906	0.91
75_L	86_N	1.901	0.91
49_V	78_F	1.813	0.89
55_L	59_T	1.796	0.89
52_A	107_I	1.773	0.88
61_V	120_I	1.733	0.87
47_T	51_S	1.708	0.86
70_R	73_D	1.668	0.84
112_D	122_V	1.556	0.80
57_D	112_D	1.488	0.77
107_I	125_I	1.463	0.76
10_V	14_C	1.397	0.72
74_D	90_D	1.396	0.72
16_A	20_A	1.393	0.72
97_V	105_V	1.387	0.71
77_V	84_T	1.347	0.69
14_C	17_P	1.342	0.69
10_V	82_S	1.330	0.68
88_D	121_D	1.309	0.67
89_I	99_V	1.309	0.67
99_V	105_V	1.301	0.66
39_F	94_W	1.294	0.66
69_E	119_E	1.285	0.65
53_K	70_R	1.281	0.65
55_L	111_V	1.281	0.65
97_V	126_R	1.277	0.65
76_Y	105_V	1.273	0.65
68_V	77_V	1.222	0.61
108_Q	124_Q	1.197	0.60
49_V	82_S	1.189	0.59
8_I	12_A	1.187	0.59
114_D	117_S	1.183	0.59
67_I	87_V	1.164	0.58
10_V	13_L	1.163	0.58
67_I	125_I	1.154	0.57
72_S	123_K	1.136	0.56
48_T	52_A	1.123	0.55
39_F	113_K	1.118	0.55
66_N	102_K	1.117	0.54
70_R	74_D	1.108	0.54
37_G	127_K	1.103	0.54
92_K	110_E	1.087	0.52
49_V	57_D	1.080	0.52
49_V	52_A	1.073	0.51
72_S	105_V	1.067	0.51
55_L	79_K	1.064	0.51
58_D	121_D	1.063	0.51
18_V	23_Q	1.044	0.49
63_L	85_I	1.042	0.49
11_M	88_D	1.038	0.49
7_V	12_A	1.036	0.49
38_G	101_P	1.029	0.48
53_K	66_N	1.028	0.48
38_G	113_K	1.013	0.47
36_A	92_K	1.010	0.47
56_R	75_L	1.009	0.47
94_W	103_D	1.005	0.47
67_I	105_V	0.991	0.46
68_V	127_K	0.976	0.45
24_G	84_T	0.976	0.45
50_E	54_S	0.967	0.44
94_W	125_I	0.946	0.43
66_N	79_K	0.938	0.42
75_L	88_D	0.931	0.42
85_I	120_I	0.897	0.40
50_E	53_K	0.892	0.39
59_T	111_V	0.891	0.39
87_V	125_I	0.891	0.39
28_G	67_I	0.889	0.39
90_D	110_E	0.878	0.38
52_A	59_T	0.872	0.38
46_V	79_K	0.863	0.37
68_V	88_D	0.862	0.37
105_V	119_E	0.858	0.37
60_W	71_I	0.846	0.36
69_E	91_H	0.831	0.35
111_V	114_D	0.827	0.35
32_T	47_T	0.824	0.35
95_N	127_K	0.820	0.35
92_K	123_K	0.816	0.34
88_D	118_V	0.813	0.34
79_K	111_V	0.805	0.34
12_A	17_P	0.804	0.34
79_K	84_T	0.801	0.33
56_R	118_V	0.798	0.33
55_L	64_R	0.797	0.33
37_G	40_Q	0.794	0.33
101_P	113_K	0.791	0.33
110_E	123_K	0.779	0.32
63_L	83_G	0.773	0.32
34_S	107_I	0.773	0.32
95_N	98_T	0.768	0.31
15_S	18_V	0.767	0.31
74_D	91_H	0.751	0.30
37_G	98_T	0.748	0.30
9_A	106_E	0.747	0.30
113_K	117_S	0.740	0.30
41_G	61_V	0.738	0.30
76_Y	87_V	0.734	0.29
28_G	31_A	0.731	0.29
93_R	122_V	0.728	0.29
69_E	103_D	0.723	0.29
65_G	80_D	0.720	0.29
14_C	19_M	0.719	0.29
14_C	18_V	0.717	0.29
72_S	76_Y	0.717	0.29
42_P	72_S	0.715	0.28
75_L	115_W	0.710	0.28
64_R	104_T	0.709	0.28
50_E	71_I	0.708	0.28
116_N	120_I	0.707	0.28
27_S	97_V	0.706	0.28
52_A	111_V	0.706	0.28
20_A	126_R	0.700	0.28
26_F	29_P	0.699	0.28
61_V	76_Y	0.684	0.27
8_I	15_S	0.676	0.26
114_D	119_E	0.676	0.26
11_M	14_C	0.664	0.26
36_A	125_I	0.654	0.25
41_G	76_Y	0.647	0.25
12_A	36_A	0.646	0.25
36_A	39_F	0.635	0.24
47_T	94_W	0.633	0.24
46_V	62_T	0.632	0.24
74_D	110_E	0.631	0.24
9_A	84_T	0.628	0.24
71_I	77_V	0.624	0.24
64_R	119_E	0.617	0.23
6_A	9_A	0.615	0.23
19_M	45_S	0.614	0.23
102_K	114_D	0.608	0.23
4_F	73_D	0.606	0.23
40_Q	111_V	0.603	0.23
56_R	68_V	0.600	0.22
56_R	59_T	0.598	0.22
71_I	94_W	0.594	0.22
91_H	94_W	0.588	0.22
112_D	121_D	0.586	0.22
107_I	126_R	0.578	0.21
34_S	82_S	0.577	0.21
23_Q	75_L	0.576	0.21
93_R	110_E	0.575	0.21
5_A	19_M	0.575	0.21
63_L	122_V	0.572	0.21
97_V	103_D	0.565	0.21
4_F	10_V	0.565	0.21
62_T	106_E	0.556	0.20
29_P	37_G	0.554	0.20
46_V	107_I	0.554	0.20
35_Q	127_K	0.552	0.20
88_D	119_E	0.551	0.20
106_E	120_I	0.548	0.20
72_S	99_V	0.539	0.20
16_A	19_M	0.539	0.20
28_G	125_I	0.536	0.20
42_P	88_D	0.534	0.19
27_S	30_S	0.531	0.19
28_G	32_T	0.528	0.19
89_I	93_R	0.528	0.19
111_V	115_W	0.528	0.19
76_Y	93_R	0.521	0.19
52_A	55_L	0.521	0.19
6_A	30_S	0.518	0.19
6_A	124_Q	0.514	0.19
48_T	112_D	0.514	0.19
15_S	46_V	0.513	0.19
54_S	102_K	0.513	0.19
36_A	111_V	0.513	0.19
37_G	101_P	0.513	0.19
52_A	120_I	0.511	0.18
55_L	73_D	0.502	0.18
35_Q	72_S	0.500	0.18
96_G	99_V	0.500	0.18

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
1nnxA	1	0.7154	100	0.226	Contact Map
2pi2A	1	0.6769	96.9	0.846	Contact Map
4rmfA	2	0.6692	96.5	0.853	Contact Map
3nemA	2	0.6769	96.5	0.854	Contact Map
4gnxB	1	0.6462	96.5	0.854	Contact Map
1c0aA	1	0.6692	96.4	0.855	Contact Map
1x54A	2	0.6769	96.4	0.856	Contact Map
1wydA	2	0.6769	96.4	0.856	Contact Map
1n9wA	2	0.6231	96.3	0.856	Contact Map
2xgtA	2	0.6385	96.3	0.857	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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