YNDB - BACSU - GREMLIN Contacts

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YNDB - Uncharacterized protein YndB

UniProt:	O31806	Sequences: MAQNNENALPDITKSITLEAPIQKVWETVSTSEGIAKWFMPNDFQLKEGQEFHLQSPFGPSPCKVLAVQAPTELSFEWDTEGWVVTFQLEDLGEKTGFTLIHSGWKEPNEVIGKANEKSSVVRGKMDGGWTGIVNERLRKAVEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	144 (122)
Sequences:	3631 (2696)
Seq/√Len:	244.0

BACSU - YNDB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_Q	72_T	3.179	1.00
22_I	91_D	2.925	1.00
27_E	31_T	2.804	1.00
17_T	92_L	2.632	1.00
67_A	73_E	2.363	1.00
92_L	97_G	2.293	1.00
23_Q	71_P	2.226	1.00
88_Q	101_I	2.130	1.00
46_L	68_V	2.083	1.00
90_E	99_T	2.038	1.00
26_W	68_V	2.034	1.00
15_S	99_T	1.976	1.00
15_S	97_G	1.945	1.00
17_T	97_G	1.908	1.00
29_V	89_L	1.870	1.00
29_V	87_F	1.860	1.00
90_E	97_G	1.809	1.00
19_E	95_K	1.806	1.00
26_W	71_P	1.795	1.00
34_G	141_A	1.744	1.00
73_E	86_T	1.712	1.00
67_A	75_S	1.667	1.00
27_E	34_G	1.663	1.00
73_E	88_Q	1.654	1.00
89_L	96_T	1.653	1.00
30_S	46_L	1.645	1.00
55_Q	60_P	1.618	1.00
13_T	99_T	1.610	1.00
13_T	101_I	1.579	1.00
22_I	72_T	1.557	1.00
17_T	95_K	1.520	1.00
51_E	64_K	1.519	1.00
31_T	34_G	1.445	1.00
25_V	96_T	1.415	1.00
48_E	68_V	1.351	1.00
24_K	34_G	1.337	1.00
20_A	25_V	1.316	1.00
43_D	53_H	1.315	1.00
33_E	36_A	1.279	1.00
25_V	89_L	1.270	1.00
91_D	94_E	1.266	1.00
18_L	98_F	1.246	1.00
65_V	68_V	1.239	1.00
45_Q	50_Q	1.210	1.00
66_L	77_E	1.206	1.00
18_L	139_R	1.178	1.00
21_P	24_K	1.161	1.00
86_T	103_S	1.153	1.00
75_S	86_T	1.141	1.00
92_L	95_K	1.139	1.00
55_Q	58_F	1.136	1.00
37_K	141_A	1.125	1.00
35_I	44_F	1.117	1.00
52_F	63_C	1.113	1.00
20_A	96_T	1.101	1.00
47_K	50_Q	1.100	1.00
34_G	37_K	1.081	1.00
16_I	135_N	1.076	1.00
11_D	101_I	1.055	1.00
23_Q	91_D	1.053	1.00
28_T	34_G	1.050	1.00
27_E	70_A	1.029	1.00
28_T	142_V	1.027	1.00
88_Q	99_T	1.022	1.00
76_F	85_V	0.988	1.00
66_L	75_S	0.982	1.00
40_M	56_S	0.981	1.00
32_S	36_A	0.980	1.00
39_F	56_S	0.972	1.00
53_H	62_P	0.964	1.00
22_I	26_W	0.939	1.00
135_N	139_R	0.936	1.00
23_Q	27_E	0.932	1.00
78_W	85_V	0.930	1.00
23_Q	70_A	0.923	1.00
102_H	126_M	0.902	1.00
9_L	107_E	0.898	1.00
87_F	98_F	0.894	1.00
69_Q	73_E	0.889	1.00
51_E	62_P	0.884	1.00
11_D	103_S	0.877	0.99
53_H	81_E	0.871	0.99
45_Q	48_E	0.870	0.99
98_F	134_V	0.854	0.99
85_V	102_H	0.853	0.99
104_G	121_V	0.853	0.99
28_T	138_L	0.848	0.99
100_L	130_W	0.837	0.99
64_K	77_E	0.831	0.99
16_I	139_R	0.831	0.99
42_N	45_Q	0.821	0.99
137_R	140_K	0.805	0.99
22_I	71_P	0.799	0.99
22_I	89_L	0.799	0.99
102_H	130_W	0.790	0.99
46_L	65_V	0.783	0.99
102_H	105_W	0.780	0.99
72_T	88_Q	0.776	0.99
53_H	60_P	0.775	0.99
76_F	87_F	0.774	0.99
14_K	131_T	0.770	0.99
18_L	25_V	0.759	0.99
48_E	67_A	0.749	0.98
85_V	100_L	0.749	0.98
43_D	51_E	0.745	0.98
30_S	74_L	0.742	0.98
85_V	130_W	0.737	0.98
63_C	77_E	0.737	0.98
56_S	61_S	0.737	0.98
29_V	76_F	0.734	0.98
122_V	127_D	0.734	0.98
78_W	102_H	0.733	0.98
18_L	142_V	0.727	0.98
29_V	98_F	0.723	0.98
21_P	25_V	0.713	0.98
128_G	132_G	0.705	0.98
12_I	102_H	0.696	0.97
14_K	130_W	0.682	0.97
121_V	124_G	0.677	0.97
60_P	81_E	0.675	0.97
131_T	135_N	0.665	0.97
49_G	64_K	0.661	0.96
26_W	65_V	0.660	0.96
52_F	102_H	0.658	0.96
80_T	126_M	0.654	0.96
132_G	137_R	0.654	0.96
105_W	126_M	0.651	0.96
26_W	74_L	0.639	0.96
29_V	65_V	0.637	0.96
40_M	137_R	0.633	0.95
100_L	134_V	0.633	0.95
17_T	94_E	0.632	0.95
22_I	96_T	0.628	0.95
39_F	54_L	0.625	0.95
122_V	126_M	0.624	0.95
127_D	131_T	0.622	0.95
41_P	56_S	0.622	0.95
64_K	79_D	0.618	0.95
61_S	80_T	0.617	0.95
130_W	134_V	0.617	0.95
82_G	128_G	0.615	0.95
24_K	28_T	0.613	0.95
78_W	124_G	0.609	0.94
29_V	74_L	0.608	0.94
52_F	65_V	0.608	0.94
24_K	27_E	0.602	0.94
26_W	30_S	0.601	0.94
62_P	81_E	0.597	0.94
40_M	133_I	0.589	0.93
28_T	141_A	0.577	0.93
22_I	95_K	0.577	0.93
10_P	123_R	0.574	0.93
39_F	133_I	0.572	0.92
61_S	78_W	0.562	0.92
39_F	78_W	0.561	0.92
80_T	84_V	0.560	0.92
50_Q	65_V	0.556	0.91
35_I	39_F	0.555	0.91
126_M	130_W	0.552	0.91
68_V	76_F	0.549	0.91
45_Q	65_V	0.547	0.91
18_L	134_V	0.546	0.91
56_S	60_P	0.543	0.90
72_T	90_E	0.543	0.90
35_I	38_W	0.541	0.90
123_R	128_G	0.540	0.90
50_Q	63_C	0.540	0.90
21_P	96_T	0.538	0.90
89_L	98_F	0.538	0.90
35_I	54_L	0.537	0.90
86_T	101_I	0.533	0.90
120_S	123_R	0.531	0.89
68_V	74_L	0.528	0.89
26_W	129_G	0.526	0.89
78_W	100_L	0.526	0.89
56_S	132_G	0.511	0.87
78_W	126_M	0.509	0.87
107_E	123_R	0.509	0.87
43_D	50_Q	0.507	0.87
56_S	78_W	0.502	0.87
30_S	34_G	0.502	0.87
30_S	68_V	0.502	0.87
124_G	128_G	0.500	0.86

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
2lioA	1	0.8403	99.9	0.32	Contact Map
2kewA	1	0.9931	99.9	0.322	Contact Map
1xfsA	2	0.9167	99.9	0.329	Contact Map
2k5gA	1	0.9097	99.9	0.334	Contact Map
2l9pA	1	0.9236	99.9	0.337	Contact Map
3uidA	1	0.9306	99.9	0.342	Contact Map
1xn5A	1	0.9514	99.9	0.344	Contact Map
2ldkA	1	0.9375	99.9	0.351	Contact Map
2lf2A	1	0.9375	99.9	0.354	Contact Map
2l8oA	1	0.8403	99.9	0.356	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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