GREMLIN Database
NifW - Nitrogen fixation protein NifW
PFAM: PF03206 Sequences:
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_D78_T3.4171.00
4_E17_F2.6141.00
82_F85_F2.5571.00
15_L27_V2.5101.00
65_E69_Q2.3631.00
74_S79_E2.3551.00
9_S13_D2.3421.00
45_E59_R2.3071.00
69_Q73_T2.2801.00
24_P28_N2.2501.00
77_L85_F2.1791.00
80_K85_F2.1541.00
41_Y70_D2.1531.00
13_D16_D2.1471.00
10_S13_D2.0391.00
19_G57_R1.8751.00
52_D55_A1.8601.00
16_D22_Y1.8481.00
8_L17_F1.7211.00
20_V65_E1.6441.00
87_D90_P1.6061.00
15_L20_V1.5761.00
40_Q86_Q1.5721.00
41_Y74_S1.5411.00
91_A94_P1.4950.99
30_N76_P1.4860.99
2_L56_L1.4660.99
83_K87_D1.4420.99
7_E36_K1.4090.99
61_R65_E1.4080.99
58_A62_A1.4030.99
41_Y66_R1.3780.99
74_S81_V1.3550.99
30_N38_F1.3020.98
94_P97_S1.2630.98
25_A28_N1.2310.98
45_E63_L1.2130.98
86_Q89_E1.1950.97
81_V85_F1.1850.97
85_F89_E1.1810.97
26_V72_V1.1040.96
91_A97_S1.0820.95
5_L14_F1.0810.95
21_P51_L1.0790.95
27_V34_I1.0740.95
57_R65_E1.0680.95
36_K39_H1.0620.95
42_L49_E1.0610.95
72_V81_V1.0580.95
29_V35_L1.0260.94
11_A35_L1.0160.93
47_L51_L1.0080.93
37_R70_D0.9950.93
8_L14_F0.9850.92
70_D74_S0.9770.92
55_A58_A0.9560.91
66_R69_Q0.9080.89
37_R81_V0.8770.87
17_F57_R0.8670.86
37_R41_Y0.8540.86
34_I68_Y0.8440.85
59_R62_A0.8120.83
43_A54_E0.7990.82
92_F96_D0.7900.81
77_L82_F0.7880.81
66_R73_T0.7830.80
50_P59_R0.7810.80
45_E62_A0.7660.79
38_F85_F0.7640.79
54_E58_A0.7420.76
37_R67_A0.7360.76
36_K85_F0.7290.75
50_P56_L0.7270.75
73_T76_P0.7260.75
26_V32_L0.7250.75
57_R61_R0.7220.75
42_L60_Y0.7210.74
24_P43_A0.7190.74
8_L63_L0.7180.74
29_V71_F0.7080.73
15_L64_L0.7040.73
70_D79_E0.6860.71
91_A98_L0.6800.70
55_A73_T0.6800.70
16_D49_E0.6770.70
30_N80_K0.6670.69
32_L71_F0.6590.68
12_E31_R0.6580.68
37_R79_E0.6570.67
5_L9_S0.6550.67
43_A57_R0.6530.67
55_A69_Q0.6510.67
38_F80_K0.6400.65
14_F68_Y0.6310.64
43_A63_L0.6270.64
35_L38_F0.6270.64
46_D56_L0.6260.64
41_Y79_E0.6220.63
17_F90_P0.6190.63
14_F18_F0.6130.62
47_L50_P0.6110.62
32_L67_A0.6100.62
15_L18_F0.6080.61
70_D81_V0.6020.61
32_L35_L0.6020.61
41_Y67_A0.6010.61
42_L65_E0.6000.60
9_S36_K0.5950.60
53_E57_R0.5890.59
18_F38_F0.5880.59
18_F22_Y0.5750.57
55_A59_R0.5750.57
20_V61_R0.5720.57
5_L8_L0.5710.57
21_P58_A0.5700.57
62_A65_E0.5640.56
87_D91_A0.5630.56
33_H71_F0.5600.55
30_N35_L0.5600.55
73_T79_E0.5580.55
45_E61_R0.5550.55
44_K83_K0.5550.55
46_D69_Q0.5550.55
55_A66_R0.5540.54
18_F39_H0.5480.54
30_N85_F0.5460.53
74_S84_V0.5410.53
47_L54_E0.5370.52
16_D19_G0.5340.52
19_G47_L0.5320.52
85_F88_A0.5310.51
7_E75_D0.5310.51
4_E8_L0.5300.51
45_E49_E0.5290.51
85_F90_P0.5270.51
56_L60_Y0.5210.50
78_T81_V0.5200.50
12_E72_V0.5180.50
44_K51_L0.5170.50
37_R94_P0.5160.49
88_A92_F0.5110.49
47_L56_L0.5100.49
10_S15_L0.5090.48
49_E56_L0.5040.48
18_F57_R0.5030.48
27_V85_F0.5000.47
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

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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