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4_1hfypdb

ID: 1516869569 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 120 (114)
Sequences: 581 (339.4)
Seq/Len: 5.096
Nf(neff/√len): 31.8

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: 5.096).

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
82_D88_D3.5861.00
82_D87_D2.6961.00
75_I80_F2.4431.00
30_A52_L2.2021.00
50_Y81_L2.1581.00
33_T49_E1.8031.00
79_K82_D1.7921.00
8_V85_L1.7911.00
25_E29_T1.6800.99
37_D40_A1.6710.99
30_A36_Y1.6380.99
107_H111_C1.6090.99
50_Y57_N1.5800.99
21_V101_I1.5800.99
31_F35_G1.4940.99
73_C77_C1.4920.98
18_Y52_L1.4840.98
49_E56_N1.4730.98
72_I98_K1.4640.98
47_S56_N1.4620.98
22_S96_L1.4540.98
94_K98_K1.4530.98
95_I104_W1.4320.98
45_N58_K1.4070.98
96_L101_I1.3960.97
33_T47_S1.3770.97
32_H36_Y1.3520.97
19_G22_S1.3400.96
9_F30_A1.3360.96
12_L27_V1.3250.96
11_K89_I1.3190.96
41_I48_T1.3160.96
75_I88_D1.3040.96
60_W103_Y1.2620.95
8_V30_A1.2040.93
83_D86_T1.1840.92
26_W47_S1.1740.91
13_K20_G1.1660.91
99_V103_Y1.1570.91
90_V97_D1.1250.89
42_V49_E1.1240.89
55_I95_I1.1240.89
25_E107_H1.1220.89
75_I87_D1.1150.88
71_N76_S1.1030.88
30_A85_L1.0990.87
14_D114_K1.0990.87
107_H113_E1.0930.87
33_T56_N1.0910.87
100_G104_W1.0910.87
75_I79_K1.0610.85
61_C77_C1.0470.84
93_K96_L1.0450.83
32_H106_A1.0440.83
5_K8_V1.0290.82
47_S54_Q1.0280.82
76_S79_K1.0270.82
89_I93_K1.0270.82
14_D68_H1.0220.82
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  
1b9oA111000.128Contact Map
1yroA211000.132Contact Map
1hmlA111000.143Contact Map
4yf2A30.99171000.167Contact Map
2z2fA10.99171000.17Contact Map
2nwdX10.99171000.172Contact Map
2gv0A10.99171000.183Contact Map
1lmqA10.99171000.186Contact Map
1qqyA10.98331000.2Contact Map
1jugA10.99171000.21Contact 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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