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ID: 1507305840 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 123 (114)
Sequences: 5370 (3595.9)
Seq/Len: 47.105
Nf(neff/√len): 336.8

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 47.105).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
81_N94_Q3.9881.00
11_L48_L3.7191.00
39_A47_G3.1551.00
12_R16_F2.4301.00
51_L76_L2.2771.00
115_T118_R2.2041.00
44_I83_L2.1761.00
15_P41_G2.0261.00
76_L101_L1.9861.00
118_R122_A1.9621.00
47_G50_R1.9091.00
43_E46_E1.8901.00
55_L101_L1.8421.00
58_K72_E1.8161.00
49_Q53_Q1.7931.00
54_T75_E1.7791.00
55_L76_L1.7671.00
14_I87_R1.7581.00
91_G95_R1.7541.00
88_E92_R1.6991.00
12_R44_I1.6601.00
75_E79_S1.6561.00
15_P40_I1.6421.00
84_H91_G1.6391.00
73_A98_F1.5441.00
10_Y13_H1.5151.00
43_E47_G1.4971.00
118_R121_V1.4591.00
77_F94_Q1.4241.00
84_H92_R1.4040.99
80_L94_Q1.3810.99
72_E105_A1.3780.99
7_W87_R1.3540.99
53_Q57_E1.3310.99
80_L97_F1.3260.99
7_W13_H1.2890.99
89_G92_R1.2550.99
84_H88_E1.2430.98
77_F119_M1.2330.98
117_E121_V1.2290.98
72_E101_L1.2100.98
116_K120_M1.2080.98
77_F81_N1.1920.98
45_Q49_Q1.1740.98
50_R53_Q1.1700.97
94_Q98_F1.1640.97
48_L52_D1.1570.97
73_A101_L1.1440.97
100_N104_A1.1360.97
79_S82_Q1.1310.97
18_F38_F1.1210.97
101_L105_A1.1160.96
73_A102_A1.1100.96
16_F38_F1.0970.96
112_S115_T1.0720.95
36_N82_Q1.0690.95
80_L93_T1.0610.95
7_W10_Y1.0490.94
101_L104_A1.0370.94
81_N91_G1.0300.94
111_F114_I1.0190.93
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4npsA10.918799.90.092Contact Map
4n67A1199.90.093Contact Map
4m16A1199.90.099Contact Map
4py3A10099.90.104Contact Map
2jk8A2199.90.114Contact Map
3zc7A10.87899.90.118Contact Map
3shgA10.87899.90.119Contact Map
4u04A20.845599.90.155Contact Map
4rglA10.861899.90.167Contact Map
3cucA20.894399.90.175Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

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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