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T0846

ID: 1404840905 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 146 (135)
Sequences: 170 (153.7)
Seq/Len: 1.259
Nf(neff/√len): 13.2

HHblits Results: (2013_03)
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: 1.259).

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
94_K102_E2.4671.00
47_V86_A2.4671.00
13_Q48_F1.9930.97
23_F123_M1.9590.97
44_S54_L1.7980.94
98_R101_A1.6840.91
43_L104_N1.6280.89
39_E91_F1.5140.83
48_F56_N1.4910.82
56_N95_N1.4530.80
61_I112_I1.3890.75
119_V126_I1.3870.75
40_I43_L1.3850.75
60_Q63_E1.3200.70
59_S71_I1.3070.69
110_E116_A1.3050.68
23_F95_N1.2990.68
78_S82_F1.2690.65
65_P116_A1.2670.65
103_K121_N1.2660.65
87_G101_A1.2430.63
27_V53_Q1.2370.62
34_Q107_K1.2190.61
133_E139_Q1.2050.59
37_E48_F1.2010.59
34_Q104_N1.1850.58
13_Q75_L1.1850.58
33_I121_N1.1690.56
24_I33_I1.1390.53
86_A101_A1.1270.52
12_P48_F1.1130.50
33_I72_S1.1120.50
58_L111_A1.1090.50
27_V110_E1.1040.50
22_E126_I1.0930.48
47_V123_M1.0900.48
47_V93_I1.0840.48
19_S22_E1.0750.47
63_E74_T1.0740.47
24_I84_K1.0600.45
12_P142_E1.0590.45
13_Q144_P1.0570.45
16_V136_R1.0560.45
83_A118_A1.0550.45
59_S115_Y1.0500.44
96_S119_V1.0490.44
41_R52_N1.0480.44
24_I89_K1.0480.44
15_I141_V1.0470.44
48_F52_N1.0460.44
26_K34_Q1.0420.43
22_E51_Q1.0410.43
57_Q135_K1.0370.43
40_I135_K1.0340.43
26_K136_R1.0310.42
50_N92_G1.0270.42
16_V45_Q1.0240.42
39_E86_A1.0170.41
49_G68_T1.0140.41
31_H40_I1.0120.41
68_T116_A1.0090.40
35_E39_E1.0070.40
43_L133_E1.0070.40
78_S139_Q1.0050.40
33_I37_E1.0040.40
98_R143_L1.0040.40
105_I124_G1.0030.40
37_E40_I1.0010.40
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: (05Jul14)
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  
2lnmA10.404139.60.931Contact Map
2llvA10.486330.70.935Contact Map
2llwA10.486324.90.938Contact Map
2zbcA80.527413.20.945Contact Map
3hwsA60.637100.948Contact Map
2djwA100.52057.20.951Contact Map
2oeqA40.465860.953Contact Map
4o4fA10.94525.20.954Contact Map
2lmdA10.46585.20.954Contact Map
2f4mB10.4114.70.955Contact 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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