GREMLIN Database
Col_cuticle_N - Nematode cuticle collagen N-terminal domain
PFAM: PF01484 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 50 (49)
Sequences: 1992 (1420)
Seq/√Len: 202.9
META: 0.325

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
24_Y39_F2.8901.00
24_Y28_V2.1641.00
29_Q33_Q2.0741.00
26_Q29_Q1.9331.00
34_D37_D1.9321.00
38_F42_R1.9251.00
47_W50_M1.8151.00
42_R46_A1.6531.00
7_S11_I1.6131.00
16_I19_P1.5751.00
5_A9_V1.5571.00
30_S33_Q1.4431.00
2_V38_F1.4341.00
37_D41_V1.3301.00
4_V35_E1.3041.00
23_N27_S1.1991.00
19_P28_V1.1851.00
41_V45_D1.1331.00
10_A14_C1.1211.00
21_L24_Y1.1091.00
32_V36_M1.1071.00
42_R45_D1.0961.00
32_V37_D1.0791.00
9_V45_D1.0451.00
30_S37_D1.0371.00
17_T25_I1.0361.00
25_I35_E1.0311.00
8_T15_L1.0161.00
40_K44_D1.0141.00
5_A8_T1.0021.00
14_C31_E0.9841.00
28_V32_V0.9811.00
11_I31_E0.9500.99
41_V44_D0.9440.99
28_V33_Q0.9290.99
22_Y25_I0.8920.99
17_T21_L0.8580.99
14_C45_D0.8560.99
33_Q37_D0.8480.99
27_S31_E0.8270.98
13_A17_T0.8210.98
2_V6_F0.8080.98
46_A49_E0.7880.98
8_T22_Y0.7800.98
28_V36_M0.7680.97
15_L38_F0.7620.97
20_M23_N0.7620.97
25_I40_K0.7470.97
26_Q30_S0.7400.97
26_Q33_Q0.7290.97
10_A40_K0.7130.96
2_V21_L0.7120.96
27_S30_S0.6920.95
28_V31_E0.6790.95
45_D50_M0.6780.95
14_C26_Q0.6700.94
12_L16_I0.6580.94
34_D47_W0.6480.93
17_T24_Y0.6320.93
27_S41_V0.6310.93
22_Y29_Q0.6270.92
18_L21_L0.6120.91
18_L44_D0.5950.90
20_M32_V0.5640.88
14_C42_R0.5530.87
39_F46_A0.5520.87
10_A19_P0.5510.86
32_V46_A0.5330.85
40_K43_A0.5250.84
39_F47_W0.5230.83
6_F21_L0.5100.82
32_V47_W0.5080.82
24_Y35_E0.5050.81
35_E48_K0.5000.81
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  
3mhsE 1 0.52 9 0.802 Contact Map
2clyA 1 0.58 7.4 0.81 Contact Map
4mt1A 3 0.56 6.5 0.814 Contact Map
3ne5A 3 0.6 4.7 0.826 Contact Map
4k0jA 3 0.56 4 0.832 Contact Map
3qprA 8 0.02 3.9 0.832 Contact Map
1bf5A 2 0.5 3.5 0.836 Contact Map
2ygkA 2 0.6 2.7 0.846 Contact Map
3rvyA 3 0.5 2.7 0.846 Contact Map
4k5yA 1 0.98 2.6 0.847 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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