GREMLIN Database
DUF3955 - Protein of unknown function (DUF3955)
PFAM: PF13127 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 59 (55)
Sequences: 926 (742)
Seq/√Len: 100.1
META: 0.676

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
12_G46_L2.8631.00
16_L42_G2.8591.00
27_D31_V2.8071.00
27_D33_H2.6931.00
9_L49_G2.3151.00
19_F24_S2.1951.00
22_I35_P2.1811.00
35_P38_L1.8491.00
24_S35_P1.7621.00
19_F35_P1.5191.00
41_L45_F1.5081.00
8_L48_L1.4571.00
11_L14_A1.3720.99
52_L56_S1.3480.99
5_G52_L1.3480.99
44_L47_L1.3470.99
8_L45_F1.3270.99
18_A22_I1.1440.98
49_G53_L1.1340.98
19_F34_E1.1180.98
23_G35_P1.1060.97
15_C45_F1.0780.97
12_G49_G1.0780.97
19_F39_I1.0400.96
30_G33_H1.0090.96
21_L37_F0.9900.95
22_I38_L0.9810.95
26_V30_G0.9780.95
51_I55_I0.9600.94
6_L41_L0.9150.93
5_G8_L0.9120.93
12_G42_G0.9100.93
11_L45_F0.8990.92
15_C37_F0.8840.91
24_S34_E0.8590.90
6_L9_L0.8460.90
19_F23_G0.8410.89
26_V31_V0.8320.89
12_G16_L0.8280.89
16_L20_N0.8250.88
17_I21_L0.7990.87
5_G9_L0.7960.87
10_L50_I0.7860.86
37_F40_P0.7840.86
28_E56_S0.7740.85
3_I48_L0.7600.84
30_G36_F0.7540.83
36_F39_I0.7470.83
5_G53_L0.7440.83
15_C41_L0.7390.82
12_G45_F0.7260.81
23_G39_I0.7260.81
19_F37_F0.7110.80
16_L43_Y0.6950.78
15_C38_L0.6940.78
3_I7_L0.6880.77
18_A38_L0.6840.77
10_L48_L0.6800.77
6_L10_L0.6750.76
40_P43_Y0.6670.75
19_F22_I0.6510.73
19_F26_V0.6430.73
48_L52_L0.6420.72
13_V46_L0.6350.72
46_L50_I0.6260.71
21_L26_V0.6180.70
18_A45_F0.6040.68
14_A41_L0.5980.67
7_L55_I0.5950.67
17_I55_I0.5780.64
18_A35_P0.5710.64
54_L57_L0.5510.61
10_L37_F0.5410.59
18_A37_F0.5350.59
16_L46_L0.5190.56
42_G49_G0.5150.56
11_L17_I0.5110.55
13_V43_Y0.5090.55
25_Y33_H0.5060.54
5_G36_F0.5030.54
3_I28_E0.5020.54
33_H42_G0.5000.54
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  
3mk7C 2 0.9831 2.8 0.884 Contact Map
2mfrA 1 0.7119 2.4 0.889 Contact Map
3ixzA 1 0.8475 2.1 0.893 Contact Map
2bs2C 2 0.7119 1.9 0.894 Contact Map
4p02A 1 0.9661 1.7 0.896 Contact Map
2zxeA 1 0.8475 1.7 0.898 Contact Map
4q4hA 1 0.9831 1.6 0.899 Contact Map
3j01B 1 0.8475 1.5 0.901 Contact Map
4d8pB 1 0 1.4 0.902 Contact Map
3hunA 1 0.2712 1.4 0.902 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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