GREMLIN Database
DUF3408 - Protein of unknown function (DUF3408)
PFAM: PF11888 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 136 (126)
Sequences: 1411 (993)
Seq/√Len: 88.5
META: 0.782

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
74_F120_H4.1991.00
89_S115_D3.2511.00
120_H125_Y2.8391.00
120_H124_E2.5371.00
98_R102_V2.5041.00
89_S92_T2.2451.00
35_E39_E2.0951.00
5_E8_R2.0491.00
24_E27_P2.0441.00
21_P24_E2.0041.00
27_P33_E1.9581.00
31_E39_E1.9471.00
8_R11_M1.9051.00
70_Y121_H1.7901.00
47_P51_T1.7661.00
34_E37_E1.7421.00
22_E25_E1.7401.00
94_E106_R1.7081.00
93_H122_L1.6311.00
83_R87_Y1.5771.00
59_S63_R1.5671.00
59_S62_R1.5611.00
114_I126_K1.5411.00
28_A31_E1.5281.00
42_E46_E1.4891.00
84_K111_S1.4781.00
6_L10_M1.4640.99
33_E38_E1.4430.99
30_E33_E1.4320.99
85_P93_H1.4240.99
97_D112_G1.4170.99
58_E62_R1.3550.99
25_E36_E1.3480.99
43_E46_E1.3170.99
39_E44_E1.3080.99
86_V114_I1.3010.99
70_Y113_Y1.2880.99
91_E95_R1.2800.99
130_N134_N1.2640.98
87_Y93_H1.2500.98
78_P112_G1.2460.98
106_R115_D1.2360.98
90_R111_S1.2340.98
5_E11_M1.2220.98
23_E26_T1.2170.98
27_P30_E1.1930.98
9_E12_A1.1840.98
122_L126_K1.1840.98
25_E30_E1.1730.97
26_T30_E1.1700.97
108_V114_I1.1540.97
57_R60_S1.1500.97
24_E31_E1.1280.97
92_T115_D1.1260.97
92_T119_R1.0940.96
82_D90_R1.0880.96
26_T42_E1.0870.96
38_E41_E1.0840.96
126_K129_I1.0780.96
9_E13_G1.0610.95
32_E41_E1.0480.95
37_E40_E1.0460.95
26_T39_E1.0410.95
6_L9_E1.0230.94
32_E45_P1.0210.94
28_A32_E1.0150.94
84_K110_V1.0140.94
58_E61_K1.0060.94
35_E38_E1.0030.94
33_E36_E1.0030.94
42_E45_P0.9990.94
36_E40_E0.9930.93
113_Y117_I0.9930.93
108_V115_D0.9910.93
90_R110_V0.9820.93
28_A42_E0.9560.92
85_P100_V0.9560.92
36_E39_E0.9510.92
31_E34_E0.9420.91
107_K111_S0.9330.91
86_V93_H0.9310.91
84_K95_R0.9300.91
93_H115_D0.9230.91
92_T122_L0.9210.91
35_E45_P0.9160.90
130_N133_Y0.9140.90
119_R123_E0.9120.90
113_Y118_L0.9050.90
70_Y99_I0.8800.88
24_E28_A0.8780.88
32_E37_E0.8750.88
29_P43_E0.8690.88
57_R61_K0.8620.87
27_P39_E0.8540.87
36_E41_E0.8480.86
45_P52_K0.8460.86
84_K93_H0.8410.86
7_L14_G0.8350.86
39_E45_P0.8310.85
27_P38_E0.8310.85
40_E46_E0.8260.85
32_E46_E0.8210.85
80_I89_S0.8190.85
6_L13_G0.8110.84
108_V119_R0.8090.84
34_E45_P0.7890.82
90_R94_E0.7890.82
115_D119_R0.7870.82
89_S93_H0.7840.82
23_E29_P0.7810.82
33_E45_P0.7800.82
49_P52_K0.7750.81
21_P34_E0.7690.81
24_E39_E0.7620.80
25_E28_A0.7600.80
33_E39_E0.7540.79
30_E37_E0.7510.79
89_S122_L0.7480.79
34_E38_E0.7380.78
35_E41_E0.7350.78
37_E44_E0.7240.77
39_E43_E0.7220.76
23_E30_E0.7180.76
88_I95_R0.6940.73
24_E37_E0.6860.73
25_E33_E0.6710.71
30_E40_E0.6670.70
48_E51_T0.6650.70
7_L11_M0.6640.70
44_E47_P0.6630.70
5_E9_E0.6630.70
6_L11_M0.6600.70
40_E43_E0.6570.69
45_P48_E0.6560.69
30_E34_E0.6530.69
23_E37_E0.6480.68
22_E31_E0.6450.68
7_L10_M0.6380.67
26_T29_P0.6370.67
8_R12_A0.6340.67
71_R111_S0.6320.66
99_I122_L0.6300.66
29_P32_E0.6250.65
93_H97_D0.6250.65
21_P26_T0.6220.65
73_T120_H0.6200.65
78_P92_T0.6190.65
44_E53_E0.6160.64
20_K23_E0.6130.64
28_A38_E0.6120.64
37_E47_P0.6100.64
38_E43_E0.6060.63
46_E51_T0.6030.63
5_E12_A0.6020.63
21_P29_P0.6010.62
26_T44_E0.5990.62
49_P53_E0.5980.62
34_E39_E0.5980.62
85_P111_S0.5890.61
26_T36_E0.5870.61
77_P109_S0.5810.60
103_I132_L0.5810.60
50_E54_V0.5780.59
24_E29_P0.5780.59
28_A35_E0.5660.58
132_L135_K0.5660.58
33_E51_T0.5600.57
39_E46_E0.5590.57
33_E37_E0.5540.56
21_P30_E0.5490.56
31_E44_E0.5440.55
84_K89_S0.5430.55
30_E38_E0.5360.54
75_L129_I0.5320.53
36_E44_E0.5310.53
25_E29_P0.5310.53
22_E34_E0.5300.53
36_E43_E0.5270.53
26_T32_E0.5250.52
98_R106_R0.5240.52
33_E40_E0.5230.52
84_K130_N0.5230.52
97_D106_R0.5230.52
100_V106_R0.5210.52
32_E38_E0.5130.51
74_F96_L0.5130.51
46_E49_P0.5100.50
26_T43_E0.5040.50
22_E33_E0.5000.49
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  
1p94A 2 0.5588 72.6 0.875 Contact Map
2cpgA 2 0.3309 71.9 0.876 Contact Map
2kelA 2 0.3382 68.5 0.878 Contact Map
1bazA 4 0.3676 65.6 0.881 Contact Map
3omyA 2 0.3529 56.9 0.887 Contact Map
1dp3A 1 0.3676 56.2 0.888 Contact Map
2mdvA 2 0.2794 54.8 0.888 Contact Map
2k9iA 2 0.4044 54.1 0.889 Contact Map
4hv0A 1 0.3456 52.7 0.89 Contact Map
4qpoA 4 0.3529 50.9 0.891 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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