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3zja

ID: 1501760547 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 114 (113)
Sequences: 687 (685)
Seq/Len: 6.080
Nf(neff/√len): 64.4

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: 6.080).

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 > 50% 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
5_V8_A2.3471.00
35_L99_F2.3291.00
55_M79_M2.1271.00
32_A65_A2.1161.00
34_E100_A2.0941.00
39_T98_H1.8501.00
64_P67_G1.8421.00
33_D101_H1.8321.00
38_V97_L1.8321.00
38_V47_V1.8301.00
23_L71_F1.8221.00
33_D102_S1.7851.00
23_L78_L1.7591.00
41_E94_A1.7561.00
46_T57_E1.7471.00
43_G82_K1.6871.00
32_A62_E1.6491.00
21_G109_L1.6351.00
37_S98_H1.5970.99
46_T81_E1.5830.99
10_I93_V1.5500.99
61_I69_L1.5150.99
6_D26_T1.4910.99
34_E60_R1.4590.99
24_T70_V1.4510.99
95_V109_L1.4380.99
38_V45_V1.4290.99
33_D103_D1.4050.98
50_T53_G1.3670.98
5_V23_L1.3240.97
21_G80_F1.3240.97
47_V61_I1.3110.97
69_L76_N1.3080.97
10_I21_G1.2910.97
48_H77_H1.2750.96
80_F95_V1.2660.96
55_M77_H1.2640.96
10_I19_A1.2600.96
8_A109_L1.2360.96
40_S80_F1.2220.95
25_I91_Q1.2150.95
63_V67_G1.1770.94
100_A103_D1.1570.93
48_H79_M1.1450.92
98_H104_P1.1360.92
22_F73_S1.1310.92
44_E81_E1.1150.91
20_A79_M1.1150.91
33_D100_A1.1140.91
94_A108_K1.1030.91
21_G95_V1.0890.90
87_P111_V1.0760.89
3_L25_I1.0680.89
21_G78_L1.0650.88
92_S108_K1.0600.88
8_A23_L1.0570.88
49_E56_K1.0440.87
9_Y110_P1.0390.87
26_T68_Q1.0270.86
19_A83_L1.0240.86
34_E62_E1.0220.85
2_E29_G1.0180.85
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  
3zjaA11100-0.03Contact Map
1x9lA1199.90.03Contact Map
2k6wA10.973799.90.069Contact Map
1yewA30.868475.90.832Contact Map
4phzA30.859674.30.835Contact Map
2x3cA10.798249.30.859Contact Map
3isyA10.868434.30.871Contact Map
3fsaA10.605329.50.876Contact Map
4ep8B10.824627.40.878Contact Map
1ufgA10.8772260.879Contact 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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