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3zja

ID: 1500381439 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 114 (114)
Sequences: 2544 (1986.6)
Seq/Len: 22.316
Nf(neff/√len): 186.1

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: 22.316).

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
34_E100_A2.6761.00
39_T98_H2.4271.00
8_A109_L2.1771.00
32_A62_E2.1581.00
64_P67_G2.0921.00
92_S108_K2.0581.00
37_S98_H2.0501.00
38_V45_V1.9381.00
34_E60_R1.9301.00
32_A65_A1.8971.00
46_T57_E1.8501.00
98_H104_P1.8261.00
88_K91_Q1.8221.00
6_D26_T1.8201.00
95_V109_L1.8061.00
35_L99_F1.7741.00
4_S26_T1.7501.00
26_T68_Q1.7481.00
55_M79_M1.7291.00
5_V8_A1.6971.00
41_E94_A1.6821.00
94_A106_A1.6771.00
21_G109_L1.6601.00
5_V23_L1.6541.00
94_A108_K1.6511.00
24_T70_V1.5991.00
4_S28_E1.5711.00
33_D102_S1.5551.00
47_V61_I1.5321.00
23_L71_F1.5221.00
46_T81_E1.5111.00
10_I93_V1.4911.00
13_P52_D1.4891.00
50_T53_G1.4701.00
61_I69_L1.4681.00
38_V97_L1.4521.00
23_L78_L1.4401.00
61_I71_F1.4161.00
35_L97_L1.4000.99
49_E56_K1.3970.99
33_D101_H1.3850.99
43_G82_K1.3830.99
21_G95_V1.3300.99
69_L76_N1.3290.99
87_P111_V1.2570.99
21_G80_F1.2540.99
10_I19_A1.2370.98
33_D100_A1.2360.98
33_D103_D1.2310.98
44_E81_E1.1860.98
43_G84_K1.1690.97
34_E62_E1.1580.97
24_T68_Q1.1520.97
8_A23_L1.1510.97
9_Y73_S1.1400.97
10_I21_G1.1340.97
7_A24_T1.1150.96
85_Q91_Q1.0880.96
58_V76_N1.0880.96
96_E106_A1.0720.95
96_E104_P1.0550.95
39_T104_P1.0460.94
40_S80_F1.0350.94
49_E76_N1.0300.94
6_D24_T1.0210.93
21_G78_L1.0200.93
92_S110_P1.0200.93
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  
3zjaA11100-0.059Contact Map
1x9lA1199.9-0.026Contact Map
2k6wA10.973799.90.012Contact Map
4phzA30.859657.40.85Contact Map
1yewA30.868455.70.852Contact Map
2x3cA10.815854.50.853Contact Map
3isyA10.868446.70.859Contact Map
1ufgA10.894729.70.874Contact Map
2lllA10.894724.90.879Contact Map
1ifrA10.8684240.88Contact 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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