YWBC - BACSU - GREMLIN Contacts

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YWBC - Uncharacterized protein YwbC

UniProt:	P39586	Sequences: MAKRIDHTGIMVRDINASITFYEEVLGMKLKDRITHTNGVIELAFLGFEDGPETEIELIQGYSSELPAEGKVHHIALLTDDIAAEYTKAEKMNAKFIDEEITTLPNGYRYFYIEGPDGEWIEFFQR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	126 (117)
Sequences:	2840 (1429)
Seq/√Len:	132.1

ECOLI - LGUL YAER
BACSU - YWBC YWKD YURT YETH YQJC
HALSA - Q9HQK8
SULSO - Q97W20

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_T	24_E	5.610	1.00
87_T	91_K	4.454	1.00
81_D	84_A	2.904	1.00
95_K	114_E	2.587	1.00
15_I	44_A	2.548	1.00
30_L	33_R	2.463	1.00
14_D	17_A	2.216	1.00
23_E	29_K	2.084	1.00
89_A	94_A	2.044	1.00
88_K	92_M	1.899	1.00
40_V	63_S	1.834	1.00
13_R	64_S	1.821	1.00
31_K	47_G	1.729	1.00
114_E	120_W	1.703	1.00
25_V	92_M	1.693	1.00
35_T	42_E	1.690	1.00
29_K	49_E	1.679	1.00
28_M	48_F	1.671	1.00
112_Y	122_E	1.523	1.00
30_L	44_A	1.508	1.00
28_M	77_L	1.502	1.00
67_P	70_G	1.486	1.00
97_I	114_E	1.484	1.00
87_T	90_E	1.441	1.00
19_I	46_L	1.424	1.00
18_S	58_L	1.406	1.00
8_T	54_T	1.401	1.00
31_K	55_E	1.393	1.00
6_D	78_L	1.335	1.00
12_V	15_I	1.331	1.00
84_A	88_K	1.318	1.00
85_E	88_K	1.313	1.00
16_N	20_T	1.298	1.00
35_T	62_Y	1.282	1.00
42_E	62_Y	1.242	1.00
18_S	22_Y	1.227	1.00
74_H	122_E	1.216	1.00
25_V	89_A	1.216	1.00
33_R	42_E	1.215	1.00
36_H	41_I	1.209	1.00
13_R	66_L	1.201	0.99
13_R	65_E	1.188	0.99
17_A	20_T	1.187	0.99
110_Y	124_F	1.184	0.99
26_L	113_I	1.174	0.99
20_T	25_V	1.168	0.99
3_K	85_E	1.148	0.99
33_R	44_A	1.137	0.99
40_V	62_Y	1.128	0.99
24_E	92_M	1.124	0.99
17_A	117_D	1.122	0.99
48_F	77_L	1.099	0.99
97_I	120_W	1.081	0.99
86_Y	90_E	1.067	0.99
68_A	71_K	1.067	0.99
18_S	117_D	1.060	0.99
86_Y	111_F	1.057	0.99
64_S	71_K	1.054	0.99
13_R	17_A	1.047	0.99
77_L	121_I	1.043	0.99
89_A	123_F	1.012	0.98
83_A	87_T	1.010	0.98
6_D	124_F	0.992	0.98
7_H	76_A	0.990	0.98
20_T	23_E	0.988	0.98
114_E	118_G	0.980	0.98
15_I	60_Q	0.973	0.98
7_H	57_E	0.960	0.98
37_T	62_Y	0.953	0.97
26_L	123_F	0.952	0.97
75_I	121_I	0.950	0.97
89_A	111_F	0.948	0.97
36_H	39_G	0.935	0.97
22_Y	115_G	0.927	0.97
8_T	75_I	0.926	0.97
49_E	52_P	0.909	0.97
48_F	52_P	0.899	0.96
74_H	112_Y	0.898	0.96
42_E	60_Q	0.896	0.96
9_G	59_I	0.881	0.96
37_T	40_V	0.880	0.96
19_I	23_E	0.873	0.96
4_R	53_E	0.871	0.96
4_R	78_L	0.859	0.95
44_A	60_Q	0.854	0.95
39_G	106_N	0.853	0.95
39_G	62_Y	0.842	0.95
11_M	119_E	0.810	0.93
56_I	75_I	0.803	0.93
109_R	125_Q	0.802	0.93
43_L	59_I	0.797	0.93
41_I	104_L	0.796	0.93
41_I	61_G	0.792	0.93
111_F	123_F	0.784	0.92
72_V	75_I	0.778	0.92
32_D	55_E	0.767	0.92
30_L	42_E	0.766	0.91
9_G	61_G	0.766	0.91
84_A	87_T	0.760	0.91
105_P	109_R	0.758	0.91
50_D	55_E	0.748	0.90
36_H	40_V	0.741	0.90
10_I	22_Y	0.735	0.90
12_V	20_T	0.734	0.90
41_I	59_I	0.721	0.89
16_N	33_R	0.720	0.89
34_I	43_L	0.712	0.88
6_D	55_E	0.710	0.88
7_H	74_H	0.708	0.88
9_G	73_H	0.704	0.88
11_M	61_G	0.701	0.87
4_R	50_D	0.699	0.87
5_I	75_I	0.690	0.87
79_T	85_E	0.690	0.87
35_T	60_Q	0.685	0.86
24_E	88_K	0.685	0.86
47_G	55_E	0.682	0.86
14_D	60_Q	0.681	0.86
88_K	91_K	0.680	0.86
86_Y	95_K	0.674	0.85
20_T	92_M	0.674	0.85
88_K	95_K	0.673	0.85
115_G	119_E	0.673	0.85
23_E	46_L	0.672	0.85
5_I	10_I	0.669	0.85
10_I	75_I	0.653	0.83
43_L	57_E	0.639	0.82
104_L	107_G	0.637	0.82
45_F	57_E	0.633	0.82
25_V	94_A	0.628	0.81
98_D	111_F	0.624	0.81
29_K	50_D	0.623	0.81
96_F	114_E	0.622	0.80
18_S	115_G	0.612	0.79
18_S	116_P	0.606	0.79
4_R	7_H	0.603	0.78
83_A	109_R	0.602	0.78
46_L	56_I	0.596	0.78
11_M	72_V	0.592	0.77
41_I	106_N	0.590	0.77
76_A	112_Y	0.589	0.77
4_R	55_E	0.588	0.77
70_G	73_H	0.581	0.76
94_A	113_I	0.575	0.75
33_R	62_Y	0.572	0.75
69_E	118_G	0.565	0.74
57_E	61_G	0.565	0.74
61_G	67_P	0.560	0.73
78_L	82_I	0.559	0.73
76_A	122_E	0.554	0.72
19_I	30_L	0.554	0.72
107_G	112_Y	0.554	0.72
105_P	125_Q	0.552	0.72
26_L	77_L	0.548	0.71
21_F	113_I	0.544	0.71
34_I	39_G	0.544	0.71
25_V	113_I	0.532	0.69
82_I	109_R	0.531	0.69
78_L	124_F	0.530	0.69
67_P	71_K	0.529	0.69
90_E	93_N	0.528	0.69
61_G	72_V	0.527	0.69
69_E	72_V	0.527	0.69
59_I	67_P	0.521	0.68
5_I	48_F	0.518	0.67
50_D	53_E	0.517	0.67
35_T	40_V	0.517	0.67
68_A	118_G	0.517	0.67
31_K	53_E	0.517	0.67
64_S	67_P	0.513	0.66
90_E	98_D	0.511	0.66
97_I	105_P	0.507	0.66
82_I	106_N	0.505	0.65
90_E	95_K	0.502	0.65
36_H	43_L	0.502	0.65
6_D	54_T	0.500	0.65

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
1ss4A	4	0.9762	99.9	0.398	Contact Map
3hdpA	2	0.9603	99.8	0.408	Contact Map
1f9zA	2	0.9762	99.8	0.411	Contact Map
3w0tA	2	0.9841	99.8	0.411	Contact Map
4mtsA	2	0.9762	99.8	0.416	Contact Map
2c21A	2	0.9444	99.8	0.421	Contact Map
1jc4A	2	1	99.8	0.424	Contact Map
3rmuA	4	0.9683	99.8	0.426	Contact Map
3l7tA	2	0.9524	99.8	0.431	Contact Map
3gm5A	2	0.9524	99.8	0.433	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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