HYBF - ECOLI - GREMLIN Contacts

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HYBF - Probable hydrogenase nickel incorporation protein HybF

UniProt:	P0A703	Sequences: MHELSLCQSAVEIIQRQAEQHDVKRVTAVWLEIGALSCVEESAVRFSFEIVCHGTVAQGCDLHIVYKPAQAWCWDCSQVVEIHQHDAQCPLCHGERLRVDTGDSLIVKSIEVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11804
Length:	113 (111)
Sequences:	1430 (1108)
Seq/√Len:	105.2

ECOLI - HYBF HYPA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_A	63_H	3.158	1.00
48_F	62_L	2.898	1.00
75_D	96_R	2.690	1.00
32_E	65_V	2.590	1.00
17_Q	20_Q	2.447	1.00
32_E	106_I	2.380	1.00
28_A	61_D	2.329	1.00
52_C	59_G	2.267	1.00
32_E	108_K	2.231	1.00
78_Q	91_L	2.073	1.00
54_G	58_Q	2.038	1.00
48_F	60_C	2.007	1.00
70_Q	79_V	1.975	1.00
70_Q	101_T	1.940	1.00
7_C	44_V	1.923	1.00
35_A	66_Y	1.907	1.00
30_W	109_S	1.888	1.00
72_W	79_V	1.872	1.00
14_I	26_V	1.819	1.00
72_W	77_S	1.694	1.00
74_W	98_R	1.622	1.00
18_A	23_V	1.621	1.00
18_A	56_V	1.613	1.00
72_W	98_R	1.545	1.00
25_R	59_G	1.501	1.00
9_S	13_I	1.461	1.00
43_A	46_F	1.448	1.00
13_I	107_V	1.446	1.00
6_L	39_V	1.422	1.00
71_A	97_L	1.412	1.00
30_W	63_H	1.376	1.00
74_W	96_R	1.337	0.99
43_A	47_S	1.298	0.99
8_Q	51_V	1.271	0.99
11_V	57_A	1.250	0.99
12_E	15_Q	1.194	0.99
10_A	31_L	1.189	0.99
30_W	65_V	1.180	0.99
71_A	82_I	1.172	0.99
79_V	100_D	1.172	0.99
33_I	44_V	1.170	0.99
6_L	38_C	1.163	0.98
15_Q	19_E	1.158	0.98
71_A	80_V	1.144	0.98
28_A	111_E	1.137	0.98
72_W	100_D	1.127	0.98
32_E	67_K	1.114	0.98
14_I	29_V	1.104	0.98
68_P	81_E	1.101	0.98
67_K	104_S	1.099	0.98
18_A	26_V	1.096	0.98
14_I	107_V	1.095	0.98
53_H	58_Q	1.084	0.98
80_V	90_P	1.050	0.97
17_Q	21_H	1.038	0.97
35_A	68_P	1.035	0.97
34_G	102_G	1.027	0.97
75_D	94_G	1.018	0.96
38_C	47_S	1.016	0.96
11_V	51_V	1.003	0.96
15_Q	56_V	0.994	0.96
10_A	107_V	0.980	0.96
45_R	49_E	0.978	0.96
14_I	23_V	0.978	0.96
101_T	104_S	0.959	0.95
55_T	58_Q	0.958	0.95
7_C	43_A	0.954	0.95
29_V	62_L	0.931	0.94
65_V	108_K	0.928	0.94
107_V	110_I	0.928	0.94
80_V	97_L	0.927	0.94
41_E	66_Y	0.920	0.94
9_S	12_E	0.905	0.93
70_Q	81_E	0.898	0.93
30_W	108_K	0.892	0.93
6_L	105_L	0.884	0.92
67_K	101_T	0.880	0.92
39_V	44_V	0.868	0.92
48_F	52_C	0.868	0.92
11_V	52_C	0.858	0.91
16_R	19_E	0.854	0.91
26_V	57_A	0.849	0.91
7_C	51_V	0.825	0.90
4_L	47_S	0.821	0.89
42_S	45_R	0.807	0.89
38_C	41_E	0.797	0.88
45_R	61_D	0.797	0.88
7_C	48_F	0.786	0.87
7_C	10_A	0.785	0.87
49_E	52_C	0.776	0.87
88_Q	95_E	0.775	0.86
4_L	51_V	0.772	0.86
57_A	60_C	0.752	0.85
41_E	45_R	0.751	0.85
14_I	110_I	0.751	0.85
18_A	57_A	0.749	0.85
35_A	81_E	0.746	0.84
15_Q	57_A	0.734	0.83
94_G	97_L	0.721	0.82
47_S	50_I	0.709	0.81
8_Q	12_E	0.706	0.81
42_S	46_F	0.705	0.81
29_V	57_A	0.705	0.81
31_L	64_I	0.699	0.80
24_K	56_V	0.686	0.79
7_C	47_S	0.678	0.78
18_A	21_H	0.673	0.78
15_Q	55_T	0.669	0.77
82_I	97_L	0.669	0.77
7_C	62_L	0.662	0.77
69_A	99_V	0.655	0.76
14_I	18_A	0.644	0.75
45_R	64_I	0.643	0.74
67_K	108_K	0.642	0.74
4_L	43_A	0.636	0.74
11_V	15_Q	0.635	0.74
45_R	66_Y	0.632	0.73
35_A	69_A	0.624	0.72
16_R	20_Q	0.623	0.72
8_Q	57_A	0.620	0.72
37_S	43_A	0.618	0.72
23_V	110_I	0.612	0.71
7_C	37_S	0.608	0.70
10_A	14_I	0.605	0.70
14_I	56_V	0.603	0.70
47_S	52_C	0.595	0.69
38_C	43_A	0.588	0.68
13_I	17_Q	0.584	0.67
33_I	105_L	0.584	0.67
7_C	46_F	0.584	0.67
24_K	78_Q	0.583	0.67
6_L	44_V	0.579	0.67
5_S	38_C	0.574	0.66
69_A	87_A	0.573	0.66
27_T	111_E	0.567	0.65
36_L	69_A	0.566	0.65
82_I	87_A	0.564	0.65
5_S	8_Q	0.563	0.64
5_S	9_S	0.563	0.64
52_C	57_A	0.559	0.64
41_E	44_V	0.555	0.63
52_C	62_L	0.548	0.62
40_E	110_I	0.548	0.62
26_V	56_V	0.547	0.62
74_W	95_E	0.546	0.62
48_F	111_E	0.539	0.61
13_I	106_I	0.539	0.61
88_Q	93_H	0.533	0.60
46_F	51_V	0.533	0.60
82_I	103_D	0.531	0.60
48_F	57_A	0.531	0.60
74_W	94_G	0.528	0.60
11_V	55_T	0.523	0.59
40_E	105_L	0.523	0.59
52_C	55_T	0.521	0.59
35_A	101_T	0.520	0.58
19_E	22_D	0.520	0.58
50_I	53_H	0.517	0.58
5_S	37_S	0.512	0.57
20_Q	26_V	0.508	0.57
19_E	91_L	0.506	0.56
40_E	43_A	0.506	0.56
25_R	91_L	0.503	0.56
19_E	23_V	0.503	0.56
89_C	92_C	0.501	0.56
17_Q	57_A	0.500	0.55

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
5aunA	1	1	100	0.062	Contact Map
2kdxA	1	1	100	0.079	Contact Map
2k2dA	1	0.3982	99	0.67	Contact Map
4qiwP	1	0.3451	97.2	0.796	Contact Map
1lkoA	3	0.885	96.8	0.807	Contact Map
3pwfA	4	0.8319	96.6	0.811	Contact Map
2lcqA	1	0.9115	96.3	0.818	Contact Map
1yuzA	2	0.7965	96.2	0.819	Contact Map
4aybP	1	0.3451	94.6	0.838	Contact Map
3wwlA	1	0.3894	88.1	0.865	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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