IDI - ECOLI - GREMLIN Contacts

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IDI - Isopentenyl-diphosphate Delta-isomerase

UniProt:	Q46822	Sequences: MQTEHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13072
Length:	182 (163)
Sequences:	2563 (1757)
Seq/√Len:	137.6

ECOLI - IDI YFCD
HALSA - IDI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_N	14_V	6.137	1.00
41_N	45_Q	5.613	1.00
53_L	60_G	4.680	1.00
50_R	138_D	3.936	1.00
42_A	126_T	3.677	1.00
85_R	91_E	3.378	1.00
50_R	137_M	2.879	1.00
142_C	147_V	2.808	1.00
37_S	80_V	2.681	1.00
75_S	78_D	2.363	1.00
66_V	84_C	2.348	1.00
53_L	137_M	2.171	1.00
23_A	27_A	2.169	1.00
143_D	146_D	2.169	1.00
150_G	158_F	2.083	1.00
13_G	33_L	1.994	1.00
9_L	33_L	1.978	1.00
5_H	18_T	1.957	1.00
45_Q	143_D	1.827	1.00
76_N	119_P	1.819	1.00
19_L	24_A	1.813	1.00
83_R	86_Y	1.789	1.00
60_G	137_M	1.780	1.00
19_L	23_A	1.763	1.00
47_L	139_Y	1.735	1.00
58_W	160_P	1.718	1.00
74_E	82_R	1.716	1.00
20_E	23_A	1.694	1.00
40_F	46_L	1.622	1.00
129_L	139_Y	1.608	1.00
79_A	82_R	1.506	1.00
42_A	124_R	1.480	1.00
25_H	69_H	1.453	1.00
62_W	140_Q	1.435	1.00
84_C	92_I	1.431	1.00
6_V	24_A	1.406	1.00
50_R	60_G	1.399	1.00
19_L	30_R	1.380	1.00
25_H	116_E	1.358	1.00
140_Q	150_G	1.345	1.00
47_L	141_W	1.338	1.00
131_I	136_V	1.324	1.00
39_L	123_A	1.280	1.00
90_V	125_T	1.267	1.00
88_L	139_Y	1.258	1.00
7_I	72_L	1.239	1.00
63_T	159_S	1.230	1.00
48_V	142_C	1.212	1.00
90_V	129_L	1.190	1.00
27_A	30_R	1.185	1.00
149_H	153_A	1.182	1.00
63_T	67_C	1.181	1.00
3_T	20_E	1.174	0.99
131_I	139_Y	1.156	0.99
81_I	91_E	1.146	0.99
49_T	63_T	1.134	0.99
46_L	147_V	1.134	0.99
25_H	32_H	1.130	0.99
147_V	162_M	1.129	0.99
69_H	116_E	1.127	0.99
39_L	90_V	1.098	0.99
103_R	117_V	1.069	0.99
76_N	121_F	1.062	0.99
46_L	65_S	1.053	0.99
37_S	84_C	1.047	0.99
64_N	67_C	1.047	0.99
4_E	82_R	1.045	0.99
5_H	20_E	1.037	0.99
31_L	103_R	1.027	0.99
62_W	138_D	1.022	0.99
105_R	113_V	1.010	0.98
100_P	120_V	1.008	0.98
45_Q	146_D	1.004	0.98
4_E	71_Q	1.003	0.98
90_V	127_S	0.998	0.98
86_Y	132_N	0.997	0.98
41_N	141_W	0.996	0.98
125_T	129_L	0.981	0.98
151_I	166_A	0.981	0.98
3_T	22_Y	0.970	0.98
18_T	72_L	0.960	0.98
61_V	159_S	0.948	0.98
36_S	64_N	0.944	0.98
105_R	115_N	0.923	0.97
92_I	123_A	0.916	0.97
140_Q	146_D	0.911	0.97
149_H	152_D	0.905	0.97
158_F	162_M	0.893	0.97
40_F	122_A	0.889	0.97
50_R	62_W	0.886	0.96
49_T	139_Y	0.876	0.96
21_K	83_R	0.873	0.96
39_L	84_C	0.864	0.96
6_V	32_H	0.863	0.96
40_F	124_R	0.861	0.96
81_I	85_R	0.857	0.96
56_K	112_I	0.854	0.96
142_C	150_G	0.851	0.96
146_D	149_H	0.845	0.95
154_T	157_A	0.840	0.95
36_S	116_E	0.832	0.95
35_F	79_A	0.828	0.95
11_A	103_R	0.828	0.95
6_V	69_H	0.827	0.95
148_L	152_D	0.819	0.94
8_L	30_R	0.819	0.94
13_G	76_N	0.817	0.94
7_I	73_G	0.803	0.94
136_V	139_Y	0.801	0.94
13_G	117_V	0.792	0.93
36_S	63_T	0.788	0.93
70_P	79_A	0.784	0.93
88_L	136_V	0.780	0.93
4_E	68_G	0.777	0.93
70_P	83_R	0.773	0.93
18_T	22_Y	0.772	0.93
155_P	158_F	0.769	0.92
36_S	118_C	0.764	0.92
104_Y	114_E	0.762	0.92
38_W	165_Q	0.762	0.92
125_T	128_A	0.759	0.92
101_D	119_P	0.757	0.92
32_H	69_H	0.756	0.92
21_K	56_K	0.756	0.92
6_V	71_Q	0.751	0.92
44_G	124_R	0.750	0.91
77_E	80_V	0.747	0.91
154_T	158_F	0.745	0.91
25_H	114_E	0.744	0.91
148_L	166_A	0.743	0.91
50_R	53_L	0.733	0.91
8_L	19_L	0.730	0.90
102_F	165_Q	0.727	0.90
26_T	29_T	0.726	0.90
23_A	26_T	0.713	0.89
99_Y	122_A	0.710	0.89
37_S	123_A	0.705	0.89
68_G	83_R	0.705	0.89
15_P	72_L	0.704	0.89
10_N	16_T	0.698	0.88
25_H	36_S	0.697	0.88
58_W	112_I	0.692	0.88
31_L	115_N	0.691	0.88
41_N	124_R	0.691	0.88
55_K	135_E	0.687	0.87
24_A	30_R	0.685	0.87
44_G	144_L	0.683	0.87
144_L	148_L	0.682	0.87
8_L	17_G	0.678	0.87
36_S	67_C	0.678	0.87
57_A	112_I	0.677	0.87
38_W	162_M	0.668	0.86
41_N	44_G	0.665	0.86
32_H	116_E	0.664	0.86
76_N	80_V	0.662	0.85
24_A	69_H	0.658	0.85
4_E	83_R	0.657	0.85
40_F	99_Y	0.657	0.85
160_P	163_V	0.655	0.85
54_S	134_D	0.653	0.85
80_V	121_F	0.647	0.84
143_D	147_V	0.635	0.83
93_T	96_E	0.634	0.83
6_V	56_K	0.629	0.82
22_Y	26_T	0.627	0.82
34_A	69_H	0.626	0.82
77_E	121_F	0.623	0.82
36_S	114_E	0.623	0.82
81_I	96_E	0.622	0.82
85_R	92_I	0.620	0.82
65_S	88_L	0.619	0.81
4_E	21_K	0.618	0.81
34_A	67_C	0.615	0.81
118_C	165_Q	0.613	0.81
96_E	125_T	0.610	0.81
7_I	47_L	0.609	0.80
19_L	27_A	0.607	0.80
150_G	153_A	0.601	0.80
70_P	114_E	0.600	0.79
21_K	57_A	0.600	0.79
7_I	33_L	0.596	0.79
7_I	18_T	0.596	0.79
67_C	114_E	0.596	0.79
34_A	114_E	0.595	0.79
150_G	154_T	0.592	0.79
41_N	126_T	0.591	0.78
58_W	61_V	0.591	0.78
64_N	114_E	0.590	0.78
33_L	76_N	0.588	0.78
5_H	72_L	0.587	0.78
35_F	69_H	0.582	0.77
46_L	144_L	0.582	0.77
26_T	30_R	0.582	0.77
45_Q	141_W	0.579	0.77
98_I	101_D	0.579	0.77
5_H	130_Q	0.579	0.77
23_A	30_R	0.578	0.77
144_L	162_M	0.576	0.77
74_E	86_Y	0.574	0.76
36_S	69_H	0.573	0.76
77_E	81_I	0.571	0.76
114_E	161_W	0.567	0.76
8_L	24_A	0.567	0.76
66_V	88_L	0.566	0.75
21_K	71_Q	0.566	0.75
9_L	13_G	0.561	0.75
67_C	70_P	0.560	0.75
49_T	88_L	0.559	0.74
51_R	55_K	0.558	0.74
81_I	94_P	0.554	0.74
164_M	167_T	0.552	0.74
64_N	118_C	0.552	0.74
147_V	158_F	0.550	0.73
96_E	149_H	0.548	0.73
21_K	25_H	0.545	0.73
74_E	79_A	0.545	0.73
13_G	16_T	0.541	0.72
48_V	140_Q	0.541	0.72
13_G	103_R	0.540	0.72
101_D	117_V	0.536	0.71
21_K	82_R	0.532	0.71
7_I	13_G	0.531	0.71
92_I	95_P	0.531	0.71
13_G	119_P	0.531	0.71
36_S	161_W	0.530	0.71
160_P	164_M	0.529	0.70
81_I	93_T	0.527	0.70
57_A	64_N	0.526	0.70
25_H	34_A	0.526	0.70
77_E	148_L	0.525	0.70
74_E	78_D	0.525	0.70
21_K	26_T	0.522	0.69
58_W	118_C	0.522	0.69
65_S	69_H	0.521	0.69
150_G	157_A	0.521	0.69
35_F	80_V	0.520	0.69
4_E	59_P	0.518	0.69
145_A	148_L	0.512	0.68
37_S	88_L	0.509	0.68
13_G	101_D	0.508	0.67
91_E	127_S	0.503	0.67
57_A	69_H	0.503	0.67
95_P	123_A	0.500	0.66
81_I	92_I	0.500	0.66

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
2pnyA	1	0.989	100	0.333	Contact Map
2dhoA	1	0.989	100	0.334	Contact Map
1hztA	1	0.8352	100	0.4	Contact Map
3dupA	2	0.9835	100	0.449	Contact Map
1q27A	1	0.9176	100	0.51	Contact Map
2fkbA	1	0.8901	100	0.516	Contact Map
2xsqA	2	0.8516	99.9	0.62	Contact Map
3e57A	2	0.8407	99.8	0.643	Contact Map
3q91A	2	0.7253	99.8	0.655	Contact Map
1sjyA	2	0.8242	99.8	0.655	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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