GREMLIN Database
NIDO - Nidogen-like
PFAM: PF06119 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 85 (78)
Sequences: 2521 (1899)
Seq/√Len: 215.0
META: 0.704

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
39_R60_G3.7121.00
23_Q27_Q3.6091.00
20_N78_R3.1961.00
46_D52_T3.0001.00
39_R55_E2.5901.00
32_D35_S2.3521.00
12_G15_D2.1991.00
37_P62_N2.0251.00
40_A56_L1.9511.00
3_T22_D1.9481.00
46_D51_G1.8601.00
11_R17_D1.8381.00
26_I68_T1.7511.00
71_S74_G1.6121.00
55_E60_G1.5991.00
67_L71_S1.5891.00
30_T37_P1.5591.00
21_Y40_A1.5281.00
2_N28_W1.4371.00
42_F54_F1.3761.00
44_A52_T1.3461.00
47_G51_G1.3251.00
66_L69_N1.2911.00
75_V78_R1.2311.00
30_T33_G1.2181.00
17_D83_V1.2161.00
36_T60_G1.2031.00
29_T63_G1.2001.00
71_S81_F1.1981.00
17_D84_R1.1781.00
11_R15_D1.1461.00
66_L70_S1.1351.00
8_L18_I1.1131.00
10_D15_D1.1051.00
42_F81_F1.0611.00
69_N79_W1.0581.00
70_S79_W1.0451.00
61_T64_A1.0431.00
33_G36_T1.0321.00
30_T34_G1.0111.00
3_T23_Q1.0041.00
18_I80_V1.0041.00
66_L71_S0.9531.00
61_T65_L0.9290.99
11_R14_G0.8840.99
6_L19_F0.8660.99
66_L72_N0.8610.99
18_I83_V0.8580.99
29_T37_P0.8580.99
3_T7_V0.8540.99
33_G37_P0.8440.99
11_R84_R0.8320.99
3_T6_L0.8170.99
58_G63_G0.8150.99
23_Q26_I0.8090.98
46_D53_F0.8080.98
6_L32_D0.8050.98
73_S80_V0.8040.98
71_S79_W0.7880.98
19_F81_F0.7620.98
7_V20_N0.7120.97
9_I18_I0.7100.97
28_W38_A0.7020.96
68_T76_P0.6890.96
9_I78_R0.6860.96
15_D84_R0.6790.96
54_F57_P0.6770.96
29_T64_A0.6740.95
29_T65_L0.6740.95
31_G38_A0.6680.95
63_G69_N0.6630.95
10_D14_G0.6620.95
67_L79_W0.6590.95
7_V18_I0.6460.94
70_S76_P0.6450.94
72_N79_W0.6370.94
67_L76_P0.6370.94
23_Q68_T0.6350.94
2_N38_A0.6340.94
69_N74_G0.6340.94
20_N80_V0.6260.93
30_T38_A0.6250.93
16_F83_V0.6220.93
39_R83_V0.6180.93
78_R81_F0.6170.93
43_S46_D0.6010.92
14_G82_R0.6000.92
22_D26_I0.5980.92
14_G17_D0.5950.91
14_G84_R0.5880.91
73_S79_W0.5790.90
47_G52_T0.5780.90
54_F81_F0.5760.90
37_P64_A0.5730.90
47_G82_R0.5730.90
40_A67_L0.5650.89
6_L18_I0.5620.89
43_S53_F0.5570.89
68_T71_S0.5510.88
44_A53_F0.5480.88
55_E59_S0.5450.87
9_I20_N0.5420.87
42_F84_R0.5390.87
15_D19_F0.5380.87
73_S78_R0.5370.87
19_F31_G0.5340.86
68_T72_N0.5280.86
37_P61_T0.5260.86
56_L79_W0.5240.85
16_F41_G0.5220.85
70_S73_S0.5150.84
13_A23_Q0.5130.84
39_R42_F0.5110.84
6_L10_D0.5070.83
9_I16_F0.5050.83
73_S76_P0.5020.83
22_D27_Q0.5000.83
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  
3lsoA 1 0.9176 2.4 0.916 Contact Map
2bu3A 1 0.8941 2.2 0.917 Contact Map
4a1xC 1 0.1059 1.9 0.92 Contact Map
4u36A 3 0.7412 1.5 0.924 Contact Map
1lrwB 1 0.7529 1.2 0.929 Contact Map
1w6sB 1 0.7529 1.2 0.929 Contact Map
4dvyP 1 0.8588 1 0.932 Contact Map
1upiA 2 0.2118 0.9 0.933 Contact Map
1kwiA 1 0.4706 0.9 0.935 Contact Map
3vrpA 1 0.7647 0.9 0.935 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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