HYCI - ECOLI - GREMLIN Contacts

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HYCI - Hydrogenase 3 maturation protease

UniProt:	P0AEV9	Sequences: MTDVLLCVGNSMMGDDGAGPLLAEKCAAAPKGNWVVIDGGSAPENDIVAIRELRPTRLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKEDIGEVIFLGIQPDIVGFYYPMTQPIKDAVETVYQRLEGWEGNGGFAQLAVEEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13396
Length:	156 (141)
Sequences:	1466 (1128)
Seq/√Len:	95.0

ECOLI - HYCI HYBD HYAD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
116_D	127_P	5.836	1.00
23_A	36_V	3.849	1.00
75_I	142_W	2.934	1.00
18_A	113_I	2.804	1.00
65_D	114_Q	2.803	1.00
21_L	24_E	2.701	1.00
61_V	139_L	2.554	1.00
57_R	107_E	2.514	1.00
75_I	111_L	2.268	1.00
29_A	140_E	2.218	1.00
22_L	61_V	2.129	1.00
14_G	117_I	2.101	1.00
115_P	118_V	2.091	1.00
68_L	72_E	2.040	1.00
69_N	72_E	1.991	1.00
56_T	106_G	1.973	1.00
7_C	23_A	1.957	1.00
67_G	114_Q	1.940	1.00
75_I	109_I	1.937	1.00
35_V	53_L	1.929	1.00
25_K	133_E	1.833	1.00
64_T	112_G	1.679	1.00
126_Q	130_D	1.660	1.00
25_K	29_A	1.657	1.00
25_K	28_A	1.644	1.00
128_I	131_A	1.627	1.00
22_L	132_V	1.626	1.00
111_L	135_V	1.617	1.00
138_R	141_G	1.616	1.00
74_R	114_Q	1.601	1.00
113_I	128_I	1.594	1.00
111_L	139_L	1.519	1.00
68_L	74_R	1.508	1.00
25_K	136_Y	1.506	1.00
126_Q	129_K	1.494	1.00
66_M	74_R	1.477	1.00
142_W	145_N	1.475	1.00
18_A	135_V	1.434	1.00
11_S	16_D	1.395	0.99
59_L	139_L	1.392	0.99
77_D	107_E	1.354	0.99
4_V	53_L	1.344	0.99
11_S	20_P	1.339	0.99
66_M	114_Q	1.333	0.99
60_I	108_V	1.324	0.99
93_P	96_Y	1.315	0.99
61_V	135_V	1.294	0.99
134_T	138_R	1.237	0.99
5_L	143_E	1.234	0.99
20_P	38_D	1.218	0.98
22_L	136_Y	1.217	0.98
133_E	137_Q	1.181	0.98
68_L	114_Q	1.177	0.98
57_R	109_I	1.176	0.98
24_E	38_D	1.175	0.98
131_A	135_V	1.164	0.98
113_I	135_V	1.154	0.98
59_L	142_W	1.085	0.97
21_L	123_P	1.082	0.97
64_T	74_R	1.081	0.97
11_S	24_E	1.075	0.96
58_L	108_V	1.072	0.96
16_D	103_E	1.056	0.96
141_G	144_G	1.055	0.96
77_D	80_D	1.051	0.96
131_A	134_T	1.042	0.96
23_A	61_V	1.033	0.96
60_I	94_L	1.031	0.96
18_A	128_I	1.030	0.96
59_L	111_L	1.018	0.95
44_E	100_Q	0.990	0.94
75_I	138_R	0.990	0.94
13_M	16_D	0.984	0.94
6_L	39_G	0.984	0.94
7_C	19_G	0.981	0.94
109_I	142_W	0.980	0.94
133_E	136_Y	0.977	0.94
4_V	58_L	0.968	0.94
10_N	17_G	0.959	0.93
43_P	93_P	0.942	0.93
3_D	57_R	0.941	0.93
134_T	137_Q	0.936	0.93
4_V	37_I	0.910	0.92
123_P	129_K	0.881	0.90
73_I	135_V	0.880	0.90
17_G	21_L	0.875	0.90
89_T	92_M	0.868	0.90
18_A	132_V	0.868	0.90
113_I	131_A	0.860	0.89
47_I	101_L	0.858	0.89
30_P	140_E	0.855	0.89
14_G	121_Y	0.844	0.88
112_G	115_P	0.843	0.88
17_G	20_P	0.837	0.88
111_L	142_W	0.828	0.87
137_Q	141_G	0.827	0.87
20_P	23_A	0.826	0.87
39_G	46_D	0.809	0.86
74_R	112_G	0.803	0.86
101_L	111_L	0.795	0.85
77_D	109_I	0.793	0.85
26_C	30_P	0.783	0.84
18_A	63_A	0.780	0.84
47_I	100_Q	0.776	0.84
23_A	38_D	0.775	0.83
73_I	134_T	0.772	0.83
35_V	49_A	0.764	0.83
3_D	143_E	0.762	0.82
26_C	140_E	0.762	0.82
70_P	114_Q	0.746	0.81
78_P	110_F	0.741	0.81
51_R	104_D	0.741	0.81
130_D	134_T	0.735	0.80
88_T	113_I	0.735	0.80
66_M	115_P	0.734	0.80
24_E	27_A	0.734	0.80
26_C	61_V	0.729	0.80
17_G	38_D	0.721	0.79
78_P	102_K	0.703	0.77
22_L	139_L	0.703	0.77
132_V	135_V	0.691	0.76
39_G	49_A	0.690	0.76
70_P	130_D	0.683	0.75
44_E	93_P	0.682	0.75
11_S	38_D	0.680	0.75
20_P	115_P	0.675	0.74
8_V	48_V	0.674	0.74
14_G	122_Y	0.673	0.74
14_G	119_G	0.668	0.73
37_I	49_A	0.667	0.73
29_A	133_E	0.665	0.73
64_T	81_I	0.661	0.73
86_M	91_N	0.660	0.72
14_G	123_P	0.659	0.72
14_G	125_T	0.658	0.72
66_M	72_E	0.656	0.72
89_T	120_F	0.648	0.71
127_P	130_D	0.642	0.70
12_M	122_Y	0.630	0.69
127_P	131_A	0.629	0.69
31_K	64_T	0.629	0.69
11_S	40_G	0.624	0.68
18_A	138_R	0.616	0.67
73_I	138_R	0.615	0.67
16_D	115_P	0.615	0.67
58_L	106_G	0.614	0.67
73_I	111_L	0.612	0.67
73_I	113_I	0.605	0.66
5_L	26_C	0.602	0.65
17_G	124_M	0.598	0.65
107_E	144_G	0.597	0.65
13_M	45_N	0.593	0.64
116_D	126_Q	0.592	0.64
20_P	74_R	0.591	0.64
38_D	41_S	0.589	0.64
97_L	114_Q	0.589	0.64
64_T	76_I	0.588	0.64
45_N	88_T	0.588	0.64
43_P	46_D	0.587	0.64
21_L	124_M	0.584	0.63
3_D	34_W	0.582	0.63
130_D	133_E	0.581	0.63
94_L	112_G	0.579	0.62
62_D	90_H	0.579	0.62
16_D	39_G	0.578	0.62
127_P	145_N	0.577	0.62
22_L	102_K	0.576	0.62
126_Q	134_T	0.572	0.62
117_I	125_T	0.572	0.62
5_L	34_W	0.571	0.61
50_I	81_I	0.567	0.61
50_I	108_V	0.562	0.60
72_E	134_T	0.559	0.60
28_A	143_E	0.558	0.60
13_M	20_P	0.553	0.59
28_A	83_E	0.550	0.59
16_D	20_P	0.548	0.58
134_T	141_G	0.547	0.58
86_M	112_G	0.545	0.58
3_D	33_N	0.543	0.58
25_K	129_K	0.543	0.58
75_I	135_V	0.542	0.57
7_C	13_M	0.537	0.57
13_M	89_T	0.536	0.57
18_A	22_L	0.536	0.57
129_K	132_V	0.535	0.57
69_N	127_P	0.535	0.57
71_G	131_A	0.533	0.56
87_M	96_Y	0.532	0.56
61_V	128_I	0.530	0.56
23_A	27_A	0.529	0.56
95_N	110_F	0.523	0.55
12_M	92_M	0.519	0.54
111_L	115_P	0.519	0.54
57_R	108_V	0.519	0.54
137_Q	145_N	0.517	0.54
27_A	129_K	0.517	0.54
50_I	58_L	0.516	0.54
14_G	17_G	0.515	0.54
74_R	110_F	0.513	0.53
130_D	137_Q	0.513	0.53
46_D	105_I	0.512	0.53
27_A	36_V	0.512	0.53
32_G	130_D	0.511	0.53
93_P	100_Q	0.510	0.53
8_V	92_M	0.507	0.53
20_P	97_L	0.505	0.52
14_G	115_P	0.503	0.52
41_S	45_N	0.503	0.52
16_D	90_H	0.502	0.52
16_D	38_D	0.501	0.52
5_L	36_V	0.500	0.52

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
1cfzA	1	0.9872	100	0.156	Contact Map
2e85A	2	0.9872	100	0.172	Contact Map
3pu6A	1	0.8654	100	0.218	Contact Map
1c8bA	3	0.8013	98	0.797	Contact Map
3b1fA	2	0.891	84.5	0.892	Contact Map
4wjiA	2	0.9167	81.1	0.896	Contact Map
3l9wA	2	0.8974	77.1	0.9	Contact Map
3hp4A	1	0.8333	76.6	0.9	Contact Map
3k1yA	4	0.9103	73.6	0.903	Contact Map
2q9uA	3	0.9103	69.7	0.906	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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