GREMLIN Database
FdsD - NADH-dependant formate dehydrogenase delta subunit FdsD
PFAM: PF11390 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 61 (60)
Sequences: 7577 (4649)
Seq/√Len: 600.2
META: 0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
28_D32_K3.1101.00
19_R59_E2.6041.00
11_A54_D2.2921.00
14_A54_D2.2461.00
19_R23_V2.1561.00
6_A57_V2.0551.00
8_Q11_A1.9841.00
1_K4_R1.9601.00
45_H50_G1.7701.00
10_A57_V1.7211.00
16_Q21_E1.6001.00
11_A14_A1.4791.00
40_R44_A1.4681.00
26_I56_L1.4621.00
4_R8_Q1.4481.00
6_A30_I1.4381.00
41_Q44_A1.4111.00
36_P40_R1.3871.00
21_E25_G1.3231.00
26_I57_V1.3191.00
44_A47_A1.2741.00
1_K8_Q1.2681.00
12_F15_S1.2501.00
27_A31_R1.2441.00
4_R11_A1.2151.00
42_I61_V1.1491.00
42_I53_L1.1121.00
17_P21_E1.0881.00
24_A28_D1.0831.00
44_A48_A1.0761.00
23_V26_I1.0641.00
45_H52_G1.0201.00
39_R43_L1.0181.00
22_A56_L0.9841.00
5_M8_Q0.9821.00
46_L58_R0.9781.00
25_G28_D0.9671.00
54_D57_V0.9301.00
43_L61_V0.9251.00
20_E24_A0.9211.00
24_A27_A0.8931.00
16_Q25_G0.8751.00
12_F25_G0.8471.00
13_F22_A0.8321.00
19_R55_P0.8151.00
21_E24_A0.7961.00
5_M38_M0.7821.00
36_P39_R0.7781.00
14_A19_R0.7711.00
23_V59_E0.7681.00
43_L47_A0.7521.00
13_F25_G0.7381.00
17_P22_A0.7261.00
10_A54_D0.7231.00
14_A56_L0.7221.00
49_G52_G0.7161.00
3_V7_N0.6791.00
45_H53_L0.6711.00
12_F16_Q0.6571.00
19_R22_A0.6531.00
45_H49_G0.6501.00
42_I60_A0.6471.00
45_H51_A0.6451.00
48_A51_A0.6301.00
28_D31_R0.6211.00
31_R43_L0.6211.00
13_F16_Q0.6211.00
55_P59_E0.6101.00
42_I46_L0.6071.00
46_L53_L0.6061.00
45_H48_A0.5831.00
17_P25_G0.5751.00
50_G58_R0.5711.00
9_I30_I0.5701.00
31_R39_R0.5701.00
2_L45_H0.5691.00
20_E23_V0.5530.99
15_S25_G0.5470.99
47_A50_G0.5420.99
42_I57_V0.5410.99
22_A26_I0.5370.99
16_Q22_A0.5310.99
2_L5_M0.5230.99
10_A26_I0.5160.99
41_Q45_H0.5120.99
35_D40_R0.5090.99
24_A32_K0.5080.99
48_A52_G0.5060.99
3_V51_A0.5040.99
51_A58_R0.5000.99
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  
2vn4A 1 0.918 34.5 0.852 Contact Map
1gaiA 1 0.9016 29.2 0.857 Contact Map
2i5kA 5 0.623 24.9 0.863 Contact Map
2fbaA 1 0.9672 18.5 0.871 Contact Map
4r7pA 4 0.6557 12 0.881 Contact Map
4wodA 1 0.9836 11.9 0.881 Contact Map
3ju5A 2 0.9016 11.7 0.882 Contact Map
4nzgA 4 0.8689 10.3 0.884 Contact Map
4ae8A 2 0.623 9 0.887 Contact Map
3wfsC 1 0.9672 8.8 0.888 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.

Page generated in 0.0043 seconds.