GREMLIN Database
DUF4041 - Domain of unknown function (DUF4041)
PFAM: PF13250 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 56 (56)
Sequences: 3400 (2076)
Seq/√Len: 277.4
META: 0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
34_F53_L2.8451.00
7_F53_L2.8271.00
34_F38_N2.6911.00
3_M41_G2.5431.00
14_A26_M2.5231.00
27_E31_E2.0241.00
11_C30_I1.9851.00
25_T28_K1.8731.00
31_E53_L1.7901.00
5_R10_E1.7631.00
28_K32_K1.7011.00
41_G44_M1.5631.00
34_F50_P1.5551.00
6_A9_G1.5041.00
5_R36_A1.4531.00
32_K35_E1.3471.00
23_V27_E1.3471.00
24_G27_E1.2981.00
25_T29_R1.2821.00
9_G13_A1.2351.00
2_L41_G1.2121.00
17_K29_R1.1961.00
18_V26_M1.1771.00
31_E35_E1.1561.00
2_L6_A1.1351.00
24_G28_K1.0871.00
11_C56_K1.0701.00
35_E39_K1.0011.00
39_K42_K1.0001.00
13_A17_K0.9701.00
15_I18_V0.9531.00
32_K36_A0.9261.00
42_K45_N0.9211.00
31_E50_P0.8931.00
47_R50_P0.8931.00
8_N12_D0.8701.00
50_P54_D0.8551.00
3_M37_I0.8531.00
28_K31_E0.8491.00
51_E54_D0.8471.00
18_V22_N0.8100.99
14_A29_R0.8000.99
13_A26_M0.7740.99
18_V21_N0.7580.99
13_A16_A0.7460.99
51_E55_L0.7410.99
34_F48_I0.7340.99
52_Y55_L0.7150.99
22_N38_N0.7140.99
17_K26_M0.6940.98
8_N52_Y0.6790.98
22_N28_K0.6780.98
29_R39_K0.6700.98
41_G46_I0.6500.97
4_L9_G0.6450.97
31_E34_F0.6370.97
5_R40_L0.6300.97
11_C15_I0.6260.97
6_A37_I0.6220.97
48_I52_Y0.6180.96
42_K47_R0.6130.96
31_E54_D0.6000.96
5_R33_A0.5890.95
14_A17_K0.5690.94
41_G56_K0.5650.94
20_W23_V0.5580.94
22_N26_M0.5570.94
7_F34_F0.5490.93
3_M44_M0.5490.93
14_A33_A0.5470.93
30_I53_L0.5450.93
33_A40_L0.5440.93
1_K40_L0.5440.93
38_N47_R0.5440.93
35_E50_P0.5400.93
21_N26_M0.5390.93
36_A52_Y0.5290.92
14_A44_M0.5170.91
24_G45_N0.5160.91
20_W25_T0.5120.91
10_E29_R0.5070.90
26_M43_T0.5070.90
47_R51_E0.5050.90
3_M43_T0.5000.90
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  
2p3pA 1 1 5.6 0.869 Contact Map
2noxA 6 0.9107 5.6 0.869 Contact Map
3ombA 1 0.6964 5.5 0.869 Contact Map
4hkaA 4 0.9286 5.4 0.87 Contact Map
4pw8A 4 0.9286 5.4 0.87 Contact Map
2nw8A 4 0.9286 3.9 0.879 Contact Map
3a09A 1 0.6786 3.6 0.88 Contact Map
4k6jA 1 0.8571 3.3 0.883 Contact Map
4kmlA 1 0.8929 2.9 0.887 Contact Map
1larA 1 0.5 2.8 0.887 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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