YGGL - ECOLI - GREMLIN Contacts

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YGGL - Uncharacterized protein YggL

UniProt:	P38521	Sequences: MAKNRSRRLRKKMHIDEFQELGFSVAWRFPEGTSEEQIDKTVDDFINEVIEPNKLAFDGSGYLAWEGLICMQEIGKCTEEHQAIVRKWLEERKLDEVRTSELFDVWWD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12443
Length:	108 (104)
Sequences:	219 (127)
Seq/√Len:	12.4

ECOLI - YGGL

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_N	81_H	4.337	1.00
6_S	16_D	3.102	0.97
44_D	92_R	2.959	0.96
86_R	90_E	2.821	0.94
6_S	9_L	2.383	0.87
83_A	87_K	2.279	0.85
28_R	96_E	2.273	0.85
5_R	9_L	2.259	0.84
68_L	103_F	2.248	0.84
44_D	91_E	2.232	0.84
45_F	55_L	2.076	0.79
59_G	88_W	1.811	0.68
57_F	67_G	1.793	0.67
20_E	106_W	1.596	0.58
45_F	67_G	1.524	0.54
25_V	81_H	1.519	0.54
8_R	12_K	1.507	0.54
8_R	11_K	1.507	0.54
6_S	15_I	1.481	0.52
5_R	16_D	1.467	0.52
87_K	91_E	1.375	0.47
53_N	84_I	1.369	0.47
27_W	65_W	1.363	0.46
37_Q	40_K	1.346	0.45
45_F	57_F	1.343	0.45
58_D	88_W	1.340	0.45
15_I	87_K	1.332	0.45
7_R	78_T	1.311	0.44
56_A	103_F	1.292	0.43
68_L	105_V	1.277	0.42
45_F	85_V	1.269	0.41
23_F	99_T	1.249	0.40
7_R	18_F	1.237	0.40
26_A	98_R	1.220	0.39
30_P	95_D	1.176	0.37
70_C	89_L	1.163	0.36
87_K	98_R	1.161	0.36
27_W	74_I	1.130	0.35
10_R	16_D	1.126	0.35
77_C	102_L	1.124	0.35
89_L	107_W	1.080	0.33
48_E	93_K	1.072	0.32
5_R	22_G	1.069	0.32
72_Q	75_G	1.058	0.32
19_Q	106_W	1.050	0.31
3_K	95_D	1.033	0.30
66_E	97_V	1.024	0.30
43_D	50_I	1.024	0.30
58_D	62_Y	1.020	0.30
34_S	37_Q	1.014	0.30
63_L	94_L	1.007	0.29
42_V	50_I	1.007	0.29
14_H	73_E	1.003	0.29
20_E	75_G	1.002	0.29
14_H	74_I	0.992	0.29
24_S	107_W	0.990	0.29
26_A	90_E	0.981	0.28
14_H	106_W	0.979	0.28
87_K	90_E	0.966	0.28
71_M	94_L	0.952	0.27
33_T	84_I	0.949	0.27
29_F	37_Q	0.945	0.27
56_A	67_G	0.942	0.27
51_E	96_E	0.932	0.26
69_I	99_T	0.906	0.25
58_D	105_V	0.905	0.25
77_C	81_H	0.899	0.25
13_M	41_T	0.891	0.25
28_R	91_E	0.872	0.24
84_I	95_D	0.870	0.24
9_L	16_D	0.867	0.24
7_R	48_E	0.866	0.24
15_I	99_T	0.855	0.23
33_T	63_L	0.851	0.23
4_N	69_I	0.848	0.23
14_H	52_P	0.839	0.23
54_K	91_E	0.838	0.23
78_T	101_E	0.824	0.22
37_Q	93_K	0.815	0.22
5_R	15_I	0.813	0.22
43_D	46_I	0.804	0.22
73_E	81_H	0.799	0.21
69_I	80_E	0.795	0.21
40_K	52_P	0.794	0.21
42_V	79_E	0.791	0.21
24_S	58_D	0.789	0.21
14_H	94_L	0.786	0.21
21_L	106_W	0.778	0.21
41_T	74_I	0.774	0.21
40_K	83_A	0.772	0.20
40_K	79_E	0.770	0.20
6_S	72_Q	0.768	0.20
86_R	99_T	0.764	0.20
56_A	60_S	0.756	0.20
88_W	93_K	0.753	0.20
25_V	45_F	0.752	0.20
75_G	106_W	0.748	0.20
69_I	96_E	0.747	0.20
50_I	81_H	0.740	0.19
43_D	61_G	0.737	0.19
44_D	51_E	0.729	0.19
74_I	106_W	0.721	0.19
83_A	99_T	0.720	0.19
24_S	71_M	0.720	0.19
21_L	85_V	0.719	0.19
9_L	24_S	0.714	0.19
29_F	38_I	0.712	0.19
84_I	99_T	0.707	0.18
6_S	22_G	0.691	0.18
81_H	84_I	0.690	0.18
24_S	74_I	0.684	0.18
49_V	53_N	0.684	0.18
72_Q	77_C	0.683	0.18
8_R	13_M	0.680	0.18
13_M	45_F	0.674	0.17
46_I	54_K	0.668	0.17
39_D	98_R	0.666	0.17
49_V	105_V	0.664	0.17
33_T	93_K	0.659	0.17
14_H	76_K	0.647	0.17
55_L	69_I	0.645	0.17
87_K	95_D	0.644	0.17
80_E	97_V	0.632	0.16
74_I	105_V	0.629	0.16
10_R	17_E	0.627	0.16
29_F	39_D	0.622	0.16
27_W	45_F	0.618	0.16
6_S	75_G	0.616	0.16
52_P	106_W	0.614	0.16
42_V	82_Q	0.612	0.16
32_G	84_I	0.608	0.16
32_G	69_I	0.607	0.15
4_N	18_F	0.607	0.15
59_G	106_W	0.595	0.15
37_Q	64_A	0.594	0.15
7_R	21_L	0.589	0.15
65_W	74_I	0.581	0.15
36_E	87_K	0.565	0.14
13_M	76_K	0.563	0.14
46_I	96_E	0.562	0.14
25_V	59_G	0.559	0.14
22_G	68_L	0.550	0.14
61_G	94_L	0.544	0.14
21_L	86_R	0.541	0.14
27_W	68_L	0.540	0.14
14_H	24_S	0.531	0.14
29_F	35_E	0.523	0.13
53_N	80_E	0.522	0.13
31_E	100_S	0.521	0.13
68_L	107_W	0.518	0.13
4_N	13_M	0.517	0.13
24_S	41_T	0.513	0.13
37_Q	95_D	0.510	0.13
31_E	36_E	0.503	0.13
74_I	101_E	0.500	0.13
88_W	106_W	0.500	0.13

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
4jr2A	2	0.9167	44.5	0.923	Contact Map
1f1jA	3	0.8704	40.3	0.925	Contact Map
4jj7A	1	0.8796	39.8	0.925	Contact Map
1m72A	2	0.9074	38.3	0.926	Contact Map
2nn3C	2	0.8889	35.5	0.927	Contact Map
3sirA	2	0.8704	32.7	0.929	Contact Map
2j32A	3	0.8704	32.2	0.929	Contact Map
3od5A	1	0.9074	30.8	0.93	Contact Map
4likA	1	0.9537	27.5	0.931	Contact Map
4m9rA	2	0.8981	27.3	0.931	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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