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2bl2

ID: 1499969598 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 145 (143)
Sequences: 1073 (613.5)
Seq/Len: 7.503
Nf(neff/√len): 51.3

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: 7.503).

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
65_I85_S3.1461.00
91_T134_G2.6571.00
85_S89_A2.5121.00
54_Q92_G2.2301.00
18_G22_G2.0401.00
25_M104_A1.9151.00
124_A128_E1.7531.00
60_V136_V1.7491.00
125_A129_T1.7441.00
32_A51_P1.7261.00
37_Q40_K1.6881.00
96_G100_G1.6521.00
136_V139_F1.5801.00
106_G124_A1.5321.00
54_Q95_S1.5150.99
60_V129_T1.5000.99
93_L96_G1.4830.99
12_T62_A1.4600.99
9_A13_I1.4260.99
51_P54_Q1.4200.99
57_Y128_E1.4110.99
135_F139_F1.4090.99
74_S77_Q1.4050.99
8_M84_A1.3760.99
15_S58_G1.3610.99
3_F78_G1.3080.98
47_L52_G1.3070.98
10_T14_F1.2710.98
64_L142_V1.2690.98
17_I93_L1.2250.97
11_A62_A1.1910.96
61_I88_I1.1870.96
29_A47_L1.1870.96
46_I144_N1.1850.96
13_I25_M1.1760.96
23_V52_G1.1760.96
63_F139_F1.1740.96
130_Y133_L1.1740.96
56_L60_V1.1630.95
4_A7_A1.1620.95
46_I121_I1.1450.95
21_K98_A1.1410.95
111_A114_P1.1370.95
14_F89_A1.1320.94
61_I138_S1.1250.94
48_Q91_T1.1190.94
2_V6_L1.1010.93
25_M97_I1.0930.93
68_N81_F1.0920.93
7_A85_S1.0900.93
50_L53_T1.0850.93
98_A127_V1.0830.93
68_N143_L1.0790.92
54_Q57_Y1.0660.92
61_I139_F1.0630.92
54_Q99_Q1.0550.91
30_A46_I1.0510.91
27_G32_A1.0470.91
22_G100_G1.0420.90
65_I142_V1.0410.90
61_I137_I1.0290.90
132_I136_V1.0240.89
87_P138_S1.0200.89
100_G104_A1.0160.89
11_A138_S1.0150.89
84_A141_L1.0150.89
8_M65_I1.0140.89
5_V8_M1.0050.88
47_L50_L1.0040.88
51_P99_Q1.0010.88
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  
3j9tY1001000.116Contact Map
2bl2A1011000.122Contact Map
4bemJ10.986299.90.267Contact Map
2xquA50.510399.10.602Contact Map
4v1gA3099.10.603Contact Map
1a91A10.510399.10.606Contact Map
1wu0A10.469990.614Contact Map
3zk1A220.5379990.618Contact Map
4bemA90.510398.90.63Contact Map
4cbkA130.441498.90.633Contact 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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