NifW - PFAM28P - GREMLIN Contacts

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NifW - Nitrogen fixation protein NifW

PFAM:	PF03206	Sequences: TLEELEELSSAEDFLDFFGVPYDPAVVNVNRLHILKRFHQYLAKEDLLEPLDEEALRARYRALLERAYQDFVTSDPLTEKVFKVFQDAEPAFVPLDSL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	98 (97)
Sequences:	1273 (831)
Seq/√Len:	84.3
META:	0.75

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_D	78_T	3.417	1.00
4_E	17_F	2.614	1.00
82_F	85_F	2.557	1.00
15_L	27_V	2.510	1.00
65_E	69_Q	2.363	1.00
74_S	79_E	2.355	1.00
9_S	13_D	2.342	1.00
45_E	59_R	2.307	1.00
69_Q	73_T	2.280	1.00
24_P	28_N	2.250	1.00
77_L	85_F	2.179	1.00
80_K	85_F	2.154	1.00
41_Y	70_D	2.153	1.00
13_D	16_D	2.147	1.00
10_S	13_D	2.039	1.00
19_G	57_R	1.875	1.00
52_D	55_A	1.860	1.00
16_D	22_Y	1.848	1.00
8_L	17_F	1.721	1.00
20_V	65_E	1.644	1.00
87_D	90_P	1.606	1.00
15_L	20_V	1.576	1.00
40_Q	86_Q	1.572	1.00
41_Y	74_S	1.541	1.00
91_A	94_P	1.495	0.99
30_N	76_P	1.486	0.99
2_L	56_L	1.466	0.99
83_K	87_D	1.442	0.99
7_E	36_K	1.409	0.99
61_R	65_E	1.408	0.99
58_A	62_A	1.403	0.99
41_Y	66_R	1.378	0.99
74_S	81_V	1.355	0.99
30_N	38_F	1.302	0.98
94_P	97_S	1.263	0.98
25_A	28_N	1.231	0.98
45_E	63_L	1.213	0.98
86_Q	89_E	1.195	0.97
81_V	85_F	1.185	0.97
85_F	89_E	1.181	0.97
26_V	72_V	1.104	0.96
91_A	97_S	1.082	0.95
5_L	14_F	1.081	0.95
21_P	51_L	1.079	0.95
27_V	34_I	1.074	0.95
57_R	65_E	1.068	0.95
36_K	39_H	1.062	0.95
42_L	49_E	1.061	0.95
72_V	81_V	1.058	0.95
29_V	35_L	1.026	0.94
11_A	35_L	1.016	0.93
47_L	51_L	1.008	0.93
37_R	70_D	0.995	0.93
8_L	14_F	0.985	0.92
70_D	74_S	0.977	0.92
55_A	58_A	0.956	0.91
66_R	69_Q	0.908	0.89
37_R	81_V	0.877	0.87
17_F	57_R	0.867	0.86
37_R	41_Y	0.854	0.86
34_I	68_Y	0.844	0.85
59_R	62_A	0.812	0.83
43_A	54_E	0.799	0.82
92_F	96_D	0.790	0.81
77_L	82_F	0.788	0.81
66_R	73_T	0.783	0.80
50_P	59_R	0.781	0.80
45_E	62_A	0.766	0.79
38_F	85_F	0.764	0.79
54_E	58_A	0.742	0.76
37_R	67_A	0.736	0.76
36_K	85_F	0.729	0.75
50_P	56_L	0.727	0.75
73_T	76_P	0.726	0.75
26_V	32_L	0.725	0.75
57_R	61_R	0.722	0.75
42_L	60_Y	0.721	0.74
24_P	43_A	0.719	0.74
8_L	63_L	0.718	0.74
29_V	71_F	0.708	0.73
15_L	64_L	0.704	0.73
70_D	79_E	0.686	0.71
91_A	98_L	0.680	0.70
55_A	73_T	0.680	0.70
16_D	49_E	0.677	0.70
30_N	80_K	0.667	0.69
32_L	71_F	0.659	0.68
12_E	31_R	0.658	0.68
37_R	79_E	0.657	0.67
5_L	9_S	0.655	0.67
43_A	57_R	0.653	0.67
55_A	69_Q	0.651	0.67
38_F	80_K	0.640	0.65
14_F	68_Y	0.631	0.64
43_A	63_L	0.627	0.64
35_L	38_F	0.627	0.64
46_D	56_L	0.626	0.64
41_Y	79_E	0.622	0.63
17_F	90_P	0.619	0.63
14_F	18_F	0.613	0.62
47_L	50_P	0.611	0.62
32_L	67_A	0.610	0.62
15_L	18_F	0.608	0.61
70_D	81_V	0.602	0.61
32_L	35_L	0.602	0.61
41_Y	67_A	0.601	0.61
42_L	65_E	0.600	0.60
9_S	36_K	0.595	0.60
53_E	57_R	0.589	0.59
18_F	38_F	0.588	0.59
18_F	22_Y	0.575	0.57
55_A	59_R	0.575	0.57
20_V	61_R	0.572	0.57
5_L	8_L	0.571	0.57
21_P	58_A	0.570	0.57
62_A	65_E	0.564	0.56
87_D	91_A	0.563	0.56
33_H	71_F	0.560	0.55
30_N	35_L	0.560	0.55
73_T	79_E	0.558	0.55
45_E	61_R	0.555	0.55
44_K	83_K	0.555	0.55
46_D	69_Q	0.555	0.55
55_A	66_R	0.554	0.54
18_F	39_H	0.548	0.54
30_N	85_F	0.546	0.53
74_S	84_V	0.541	0.53
47_L	54_E	0.537	0.52
16_D	19_G	0.534	0.52
19_G	47_L	0.532	0.52
85_F	88_A	0.531	0.51
7_E	75_D	0.531	0.51
4_E	8_L	0.530	0.51
45_E	49_E	0.529	0.51
85_F	90_P	0.527	0.51
56_L	60_Y	0.521	0.50
78_T	81_V	0.520	0.50
12_E	72_V	0.518	0.50
44_K	51_L	0.517	0.50
37_R	94_P	0.516	0.49
88_A	92_F	0.511	0.49
47_L	56_L	0.510	0.49
10_S	15_L	0.509	0.48
49_E	56_L	0.504	0.48
18_F	57_R	0.503	0.48
27_V	85_F	0.500	0.47

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
3zxuA	1	0.7653	29	0.91	Contact Map
4kzsA	1	0.8469	25.6	0.912	Contact Map
3ag7A	1	0.7143	11.7	0.925	Contact Map
2qwoB	1	0.7041	10.9	0.926	Contact Map
4jimA	3	0.7653	10.3	0.927	Contact Map
1tuzA	1	0.8673	10.3	0.927	Contact Map
2zq5A	1	0.551	9	0.928	Contact Map
3h35A	3	0.3163	8.3	0.93	Contact Map
2d58A	1	0.4286	6.5	0.933	Contact Map
3j8eG	3	1	6.2	0.934	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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