YUGU - BACSU - GREMLIN Contacts

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YUGU - UPF0047 protein YugU

UniProt:	O05243	Sequences: MLKTLQIKTTKRDEMIDITREVEAFLQETGITSGAALIYCPHTTAGITINENADPDVKKDMLRRFDEVYPWEHELDRHMEGNTAAHMKSSTVGASQHVIVENGRLILGTWQGIYFCEFDGPRTRTCYIKMMG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	132 (126)
Sequences:	2722 (1759)
Seq/√Len:	156.7

ECOLI - YJBQ
BACSU - YUGU
SULSO - Q97VS8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_V	113_I	2.935	1.00
46_G	118_F	2.793	1.00
101_E	106_I	2.763	1.00
36_A	128_I	2.700	1.00
4_T	125_T	2.565	1.00
31_I	130_M	2.190	1.00
48_T	90_S	2.183	1.00
5_L	128_I	2.179	1.00
21_E	24_A	2.168	1.00
40_C	45_A	2.149	1.00
63_R	76_D	2.148	1.00
6_Q	123_T	2.120	1.00
59_K	76_D	2.118	1.00
41_P	125_T	2.056	1.00
25_F	128_I	2.039	1.00
38_I	128_I	2.021	1.00
23_E	104_R	1.866	1.00
71_W	84_A	1.853	1.00
10_T	14_E	1.813	1.00
32_T	102_N	1.790	1.00
37_L	97_H	1.720	1.00
33_S	101_E	1.640	1.00
17_D	112_G	1.575	1.00
64_R	87_M	1.571	1.00
65_F	92_V	1.567	1.00
56_D	79_M	1.543	1.00
52_N	112_G	1.536	1.00
6_Q	125_T	1.472	1.00
35_A	97_H	1.467	1.00
24_A	28_E	1.406	1.00
64_R	68_V	1.368	1.00
31_I	100_V	1.336	1.00
37_L	129_K	1.333	1.00
75_L	78_H	1.324	1.00
67_E	73_H	1.322	1.00
46_G	92_V	1.316	1.00
89_S	94_A	1.296	1.00
29_T	130_M	1.294	1.00
15_M	116_C	1.288	1.00
56_D	76_D	1.281	1.00
61_M	90_S	1.267	1.00
62_L	66_D	1.254	1.00
100_V	130_M	1.242	1.00
8_K	123_T	1.229	1.00
22_V	36_A	1.220	1.00
26_L	130_M	1.217	1.00
49_I	98_V	1.200	1.00
39_Y	49_I	1.200	1.00
36_A	105_L	1.198	1.00
4_T	41_P	1.194	1.00
69_Y	91_T	1.185	1.00
23_E	105_L	1.174	1.00
82_N	119_D	1.154	1.00
41_P	127_Y	1.150	1.00
8_K	21_E	1.129	1.00
59_K	63_R	1.110	1.00
5_L	126_C	1.106	1.00
99_I	129_K	1.066	0.99
56_D	59_K	1.059	0.99
13_D	62_L	1.056	0.99
15_M	65_F	1.054	0.99
25_F	130_M	1.029	0.99
41_P	106_I	1.020	0.99
18_I	126_C	1.020	0.99
66_D	71_W	1.017	0.99
13_D	66_D	1.016	0.99
98_V	113_I	1.009	0.99
64_R	67_E	1.006	0.99
74_E	78_H	1.000	0.99
26_L	100_V	0.993	0.99
63_R	67_E	0.981	0.99
18_I	22_V	0.957	0.99
71_W	120_G	0.951	0.98
20_R	24_A	0.944	0.98
45_A	115_F	0.933	0.98
23_E	27_Q	0.920	0.98
26_L	29_T	0.920	0.98
40_C	89_S	0.916	0.98
65_F	116_C	0.910	0.98
64_R	69_Y	0.906	0.98
35_A	131_M	0.903	0.98
92_V	118_F	0.902	0.98
13_D	71_W	0.896	0.98
69_Y	75_L	0.893	0.98
26_L	105_L	0.881	0.98
27_Q	104_R	0.876	0.97
106_I	127_Y	0.865	0.97
48_T	116_C	0.859	0.97
54_D	57_V	0.850	0.97
27_Q	30_G	0.848	0.97
44_T	119_D	0.842	0.97
69_Y	87_M	0.839	0.97
7_I	16_I	0.834	0.97
48_T	93_G	0.823	0.96
40_C	115_F	0.815	0.96
38_I	96_Q	0.815	0.96
49_I	94_A	0.814	0.96
80_E	83_T	0.809	0.96
47_I	96_Q	0.802	0.96
70_P	73_H	0.798	0.96
64_R	73_H	0.796	0.96
20_R	23_E	0.792	0.95
36_A	130_M	0.789	0.95
33_S	129_K	0.785	0.95
24_A	27_Q	0.779	0.95
58_K	62_L	0.778	0.95
25_F	29_T	0.773	0.95
33_S	102_N	0.766	0.94
40_C	47_I	0.762	0.94
36_A	100_V	0.761	0.94
52_N	114_Y	0.758	0.94
10_T	21_E	0.758	0.94
66_D	88_K	0.753	0.94
15_M	114_Y	0.747	0.94
4_T	106_I	0.740	0.93
32_T	103_G	0.732	0.93
39_Y	98_V	0.730	0.93
46_G	96_Q	0.728	0.93
44_T	82_N	0.724	0.93
39_Y	99_I	0.724	0.93
49_I	107_L	0.721	0.93
5_L	25_F	0.719	0.92
51_E	110_W	0.716	0.92
37_L	99_I	0.713	0.92
39_Y	95_S	0.705	0.92
99_I	127_Y	0.704	0.92
13_D	84_A	0.701	0.91
43_T	80_E	0.687	0.91
4_T	101_E	0.685	0.90
71_W	75_L	0.684	0.90
22_V	38_I	0.681	0.90
25_F	28_E	0.678	0.90
35_A	129_K	0.678	0.90
98_V	105_L	0.668	0.89
21_E	25_F	0.655	0.88
14_E	117_E	0.654	0.88
63_R	73_H	0.640	0.87
46_G	116_C	0.640	0.87
71_W	88_K	0.639	0.87
119_D	122_R	0.639	0.87
64_R	75_L	0.638	0.87
52_N	58_K	0.636	0.87
23_E	26_L	0.627	0.86
15_M	61_M	0.625	0.86
42_H	50_N	0.622	0.86
83_T	87_M	0.620	0.86
20_R	104_R	0.608	0.84
75_L	87_M	0.601	0.84
51_E	57_V	0.599	0.84
9_T	16_I	0.598	0.83
7_I	21_E	0.598	0.83
22_V	25_F	0.595	0.83
83_T	119_D	0.592	0.83
78_H	88_K	0.584	0.82
73_H	87_M	0.581	0.82
11_K	14_E	0.580	0.82
98_V	107_L	0.574	0.81
61_M	87_M	0.573	0.81
49_I	114_Y	0.572	0.81
57_V	81_G	0.570	0.80
33_S	130_M	0.570	0.80
25_F	36_A	0.552	0.78
57_V	80_E	0.548	0.78
15_M	48_T	0.541	0.77
37_L	95_S	0.538	0.77
31_I	34_G	0.538	0.77
42_H	86_H	0.535	0.76
50_N	114_Y	0.534	0.76
33_S	100_V	0.533	0.76
15_M	50_N	0.532	0.76
33_S	131_M	0.530	0.76
101_E	129_K	0.530	0.76
65_F	70_P	0.529	0.75
9_T	122_R	0.528	0.75
54_D	110_W	0.528	0.75
61_M	114_Y	0.527	0.75
50_N	61_M	0.526	0.75
51_E	124_R	0.525	0.75
90_S	93_G	0.524	0.75
89_S	92_V	0.518	0.74
45_A	81_G	0.516	0.74
20_R	27_Q	0.515	0.73
17_D	20_R	0.510	0.73
88_K	117_E	0.507	0.72
63_R	74_E	0.506	0.72
88_K	116_C	0.505	0.72
20_R	32_T	0.502	0.72
106_I	129_K	0.501	0.71
58_K	69_Y	0.500	0.71

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
2p6hA	3	0.9924	100	0.066	Contact Map
1vphA	4	0.9924	100	0.078	Contact Map
2p6cA	3	0.9924	100	0.078	Contact Map
1vmfA	3	0.9924	100	0.081	Contact Map
1vmhA	3	0.9773	100	0.084	Contact Map
1ve0A	3	0.9773	100	0.084	Contact Map
1vmjA	4	0.9924	100	0.086	Contact Map
2cu5A	3	0.9545	100	0.107	Contact Map
4lubA	2	0.6667	20.1	0.941	Contact Map
2qmwA	2	0.7121	15.6	0.944	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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