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T0800

ID: 1401732168 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 247 (242)
Sequences: 509 (490.3)
Seq/Len: 2.103
Nf(neff/√len): 31.5

Jackhmmer Results: (2014_04_16)
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: 2.103).

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
159_V182_V5.9251.00
138_T159_V5.5451.00
138_T182_V4.9541.00
137_G158_G4.4891.00
182_V203_V4.1961.00
182_V239_V4.0581.00
158_G181_G3.7531.00
159_V239_V3.4551.00
140_E184_E3.3011.00
159_V203_V3.2661.00
181_G238_G3.0461.00
140_E161_K3.0421.00
158_G238_G3.0271.00
120_W125_N3.0231.00
137_G181_G3.0061.00
60_V138_T2.9801.00
203_V239_V2.8621.00
161_K184_E2.8401.00
184_E241_A2.7181.00
97_G101_I2.7141.00
60_V159_V2.6881.00
161_K241_A2.5721.00
138_T203_V2.3991.00
94_D97_G2.2911.00
60_V182_V2.2871.00
138_T239_V2.2451.00
137_G238_G2.0940.99
181_G202_G2.0470.99
160_G183_G2.0290.99
201_K237_A1.9540.99
180_G237_A1.9500.99
202_G238_G1.9290.99
184_E205_A1.8660.98
140_E205_A1.7550.97
157_M180_G1.7360.97
180_G201_K1.7300.97
183_G204_G1.6850.96
70_E74_K1.6290.95
59_G158_G1.6000.95
161_K205_A1.5980.95
60_V239_V1.5880.94
158_G202_G1.5400.93
59_G137_G1.4810.91
204_G240_G1.4470.90
60_V203_V1.4150.88
68_N123_N1.4010.88
139_G160_G1.3680.86
205_A241_A1.3560.85
162_V185_A1.3100.83
140_E241_A1.2910.81
137_G202_G1.2520.78
153_L176_V1.2480.78
94_D101_I1.1990.74
59_G181_G1.1930.74
7_F13_V1.1840.73
13_V20_A1.1610.71
138_T181_G1.1550.70
117_R120_W1.1510.70
18_A23_N1.1470.69
115_N120_W1.1420.69
160_G204_G1.1330.68
118_N125_N1.1240.67
58_F61_G1.1180.67
136_L157_M1.1150.66
201_K204_G1.1070.65
156_G236_E1.0990.65
62_K161_K1.0860.63
157_M201_K1.0770.62
180_G185_A1.0670.61
179_E200_E1.0590.60
179_E236_E1.0560.60
61_G153_L1.0540.60
136_L141_F1.0410.58
94_D99_L1.0360.58
120_W129_P1.0340.58
157_M237_A1.0010.54
206_V240_G1.0000.54
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: (24May14)
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  
3lycA160.801699.10.676Contact Map
3jx8A60.8138990.698Contact Map
4opwA20.793598.80.714Contact Map
3petA20.781498.80.715Contact Map
3glaA20.364412.50.931Contact Map
4jg9A20.485812.10.932Contact Map
2xcmC20.36447.90.937Contact Map
1qleD10.09316.60.939Contact Map
1m56D20.093160.94Contact Map
4m5sA10.32395.90.941Contact 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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