LEUD - SULSO - GREMLIN Contacts

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LEUD - 3-isopropylmalate dehydratase small subunit

UniProt:	Q97VY3	Sequences: MIIEGPVIKFGDKIDTDIIIPARYLKYTDPQYLAQHVMEPLDPEFYKKASKGVIIVAGKVFGMGSSREQAAIALKAAGVKAVVAESFARIFYRNAINNGLPVITLPNSTKEIDENSYVKIDVETGEILVGNKVLKGKGITGMALEILQAGGIMEYLKKMQTVNRN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	165 (146)
Sequences:	6768 (3300)
Seq/√Len:	273.1

ECOLI - LEUD YBHJ ACON1
BACSU - LEUD ACON
HALSA - Q9HMF1
SULSO - LEUD Q97Z42

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_E	132_K	3.765	1.00
59_K	85_E	2.804	1.00
57_A	84_A	2.661	1.00
60_V	63_M	2.633	1.00
121_D	124_T	2.477	1.00
15_D	18_I	2.385	1.00
74_L	100_L	2.201	1.00
36_H	39_E	2.194	1.00
81_A	120_I	2.141	1.00
18_I	41_L	2.106	1.00
126_E	133_V	2.095	1.00
85_E	110_K	2.083	1.00
5_G	53_V	2.012	1.00
32_Y	35_Q	1.999	1.00
95_A	102_V	1.953	1.00
42_D	45_F	1.936	1.00
8_I	42_D	1.928	1.00
108_S	111_E	1.902	1.00
12_D	59_K	1.902	1.00
24_Y	39_E	1.819	1.00
54_I	81_A	1.726	1.00
13_K	60_V	1.722	1.00
12_D	58_G	1.721	1.00
95_A	100_L	1.698	1.00
119_K	128_L	1.690	1.00
12_D	85_E	1.635	1.00
47_K	50_S	1.613	1.00
71_A	88_A	1.560	1.00
104_T	137_K	1.535	1.00
6_P	117_Y	1.517	1.00
96_I	102_V	1.492	1.00
23_R	40_P	1.461	1.00
43_P	47_K	1.457	1.00
141_G	145_E	1.453	1.00
37_V	73_A	1.415	1.00
145_E	149_A	1.409	1.00
142_M	146_I	1.401	1.00
91_F	95_A	1.398	1.00
144_L	148_Q	1.342	1.00
113_D	116_S	1.337	1.00
61_F	91_F	1.335	1.00
37_V	77_A	1.330	1.00
126_E	135_K	1.323	1.00
140_T	143_A	1.319	1.00
145_E	148_Q	1.271	1.00
54_I	83_V	1.271	1.00
71_A	100_L	1.255	1.00
5_G	54_I	1.250	1.00
44_E	47_K	1.227	1.00
105_L	109_T	1.169	1.00
25_L	29_D	1.151	1.00
85_E	108_S	1.139	1.00
116_S	129_V	1.137	1.00
75_K	80_K	1.134	1.00
55_I	79_V	1.134	1.00
10_F	58_G	1.131	1.00
96_I	143_A	1.131	1.00
92_Y	143_A	1.129	1.00
85_E	109_T	1.128	1.00
53_V	79_V	1.127	1.00
122_V	125_G	1.118	1.00
138_G	147_L	1.114	1.00
6_P	115_N	1.114	1.00
56_V	109_T	1.112	1.00
24_Y	36_H	1.102	1.00
123_E	148_Q	1.101	1.00
10_F	14_I	1.094	1.00
43_P	46_Y	1.092	1.00
128_L	133_V	1.089	1.00
23_R	39_E	1.087	1.00
75_K	100_L	1.079	1.00
125_G	144_L	1.078	1.00
48_K	51_K	1.073	1.00
34_A	76_A	1.053	1.00
47_K	51_K	1.051	1.00
27_Y	33_L	1.042	1.00
45_F	49_A	1.041	1.00
25_L	69_Q	1.041	1.00
113_D	130_G	1.038	1.00
138_G	144_L	1.036	1.00
20_I	73_A	1.018	1.00
27_Y	32_Y	1.015	1.00
27_Y	36_H	1.011	1.00
42_D	48_K	1.011	1.00
124_T	130_G	1.001	1.00
31_Q	76_A	0.988	1.00
59_K	107_N	0.986	1.00
122_V	127_I	0.983	1.00
75_K	98_N	0.982	1.00
54_I	118_V	0.971	1.00
53_V	80_K	0.971	1.00
92_Y	96_I	0.963	1.00
141_G	144_L	0.957	1.00
107_N	110_K	0.955	1.00
20_I	37_V	0.954	1.00
96_I	139_I	0.943	1.00
105_L	108_S	0.942	1.00
123_E	144_L	0.932	1.00
22_A	66_S	0.915	1.00
22_A	40_P	0.905	1.00
101_P	147_L	0.905	1.00
71_A	98_N	0.897	1.00
38_M	41_L	0.895	1.00
58_G	110_K	0.890	1.00
111_E	134_L	0.890	1.00
121_D	126_E	0.879	1.00
9_K	109_T	0.876	1.00
46_Y	49_A	0.875	1.00
83_V	109_T	0.874	1.00
92_Y	104_T	0.870	1.00
139_I	144_L	0.858	1.00
103_I	136_G	0.858	1.00
123_E	127_I	0.858	1.00
146_I	150_G	0.848	1.00
56_V	83_V	0.832	1.00
44_E	48_K	0.820	0.99
83_V	105_L	0.810	0.99
129_V	132_K	0.804	0.99
101_P	122_V	0.802	0.99
120_I	127_I	0.801	0.99
29_D	36_H	0.797	0.99
7_V	56_V	0.796	0.99
116_S	130_G	0.788	0.99
69_Q	72_I	0.787	0.99
61_F	74_L	0.776	0.99
11_G	41_L	0.775	0.99
85_E	107_N	0.774	0.99
35_Q	39_E	0.760	0.99
33_L	73_A	0.756	0.99
9_K	110_K	0.728	0.99
132_K	135_K	0.728	0.99
96_I	146_I	0.726	0.99
119_K	131_N	0.716	0.99
30_P	72_I	0.714	0.98
106_P	135_K	0.714	0.98
15_D	25_L	0.710	0.98
118_V	129_V	0.698	0.98
56_V	105_L	0.693	0.98
8_I	46_Y	0.687	0.98
7_V	118_V	0.685	0.98
14_I	57_A	0.678	0.98
11_G	14_I	0.676	0.98
123_E	126_E	0.668	0.98
132_K	137_K	0.668	0.98
13_K	63_M	0.667	0.98
45_F	48_K	0.667	0.98
33_L	72_I	0.664	0.98
129_V	134_L	0.661	0.97
121_D	131_N	0.659	0.97
7_V	112_I	0.654	0.97
23_R	26_K	0.654	0.97
26_K	69_Q	0.652	0.97
5_G	52_G	0.650	0.97
65_S	94_N	0.648	0.97
37_V	74_L	0.643	0.97
72_I	98_N	0.643	0.97
8_I	49_A	0.642	0.97
139_I	142_M	0.641	0.97
83_V	103_I	0.641	0.97
22_A	69_Q	0.640	0.97
61_F	95_A	0.630	0.97
92_Y	102_V	0.628	0.97
9_K	56_V	0.628	0.97
55_I	74_L	0.623	0.96
19_I	38_M	0.623	0.96
10_F	57_A	0.619	0.96
71_A	95_A	0.617	0.96
20_I	33_L	0.606	0.96
146_I	149_A	0.604	0.96
8_I	53_V	0.604	0.96
28_T	69_Q	0.603	0.96
57_A	82_V	0.603	0.96
124_T	133_V	0.602	0.96
138_G	143_A	0.596	0.95
56_V	112_I	0.594	0.95
70_A	94_N	0.593	0.95
120_I	134_L	0.592	0.95
33_L	79_V	0.587	0.95
22_A	39_E	0.586	0.95
80_K	101_P	0.582	0.95
109_T	112_I	0.581	0.95
124_T	128_L	0.578	0.95
118_V	127_I	0.578	0.95
131_N	135_K	0.578	0.95
33_L	36_H	0.574	0.94
114_E	122_V	0.573	0.94
6_P	53_V	0.572	0.94
106_P	117_Y	0.570	0.94
108_S	134_L	0.569	0.94
143_A	146_I	0.568	0.94
69_Q	88_A	0.566	0.94
26_K	76_A	0.565	0.94
106_P	133_V	0.563	0.94
35_Q	38_M	0.560	0.94
33_L	69_Q	0.554	0.93
9_K	113_D	0.553	0.93
108_S	112_I	0.551	0.93
27_Y	38_M	0.551	0.93
68_E	88_A	0.544	0.93
20_I	82_V	0.541	0.92
6_P	51_K	0.538	0.92
83_V	136_G	0.533	0.92
124_T	127_I	0.533	0.92
67_R	90_I	0.532	0.92
121_D	125_G	0.531	0.92
72_I	76_A	0.530	0.92
93_R	96_I	0.529	0.92
125_G	141_G	0.529	0.92
122_V	126_E	0.527	0.91
116_S	131_N	0.525	0.91
83_V	134_L	0.516	0.91
139_I	147_L	0.516	0.91
117_Y	135_K	0.515	0.91
16_T	67_R	0.514	0.90
29_D	76_A	0.508	0.90
66_S	90_I	0.508	0.90
30_P	76_A	0.507	0.90
59_K	86_S	0.504	0.90
120_I	123_E	0.500	0.89

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
3vbaA	2	1	100	0.125	Contact Map
2pkpA	2	0.9879	100	0.13	Contact Map
1v7lA	6	0.9879	100	0.143	Contact Map
3q3wA	1	0.9394	100	0.215	Contact Map
2hcuA	1	0.9091	100	0.23	Contact Map
1l5jA	1	0.9879	100	0.235	Contact Map
3h5jA	1	0.9152	100	0.235	Contact Map
2b3yA	1	0.9455	100	0.308	Contact Map
1c96A	1	0.9818	100	0.322	Contact Map
3t05A	3	0.6182	70.1	0.933	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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