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T0836

ID: 1404155991 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (159)
Sequences: 170 (83.7)
Seq/Len: 1.069
Nf(neff/√len): 6.6

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: 1.069).

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
49_F97_A2.4360.99
99_W143_T2.0680.97
62_F91_F1.9490.95
91_F94_A1.8490.93
180_L183_R1.8120.92
95_A197_A1.7920.92
132_F135_I1.7410.90
50_G95_A1.7250.90
61_N188_L1.6760.88
154_W158_K1.6640.87
95_A146_F1.6560.87
121_A132_F1.6390.86
156_N160_A1.5760.83
100_V104_L1.5550.82
178_A183_R1.5460.81
56_L91_F1.4970.78
142_A146_F1.4890.78
166_A173_K1.4880.78
50_G135_I1.4680.76
50_G197_A1.4600.76
61_N65_I1.4520.75
95_A135_I1.4440.75
137_T142_A1.3820.70
72_P89_F1.3790.70
95_A142_A1.3750.69
154_W180_L1.3440.67
156_N177_T1.3330.66
39_Q137_T1.3120.64
47_V197_A1.3060.64
64_Q179_M1.2990.63
154_W178_A1.2880.62
59_Y190_I1.2860.62
62_F89_F1.2740.61
47_V193_L1.2690.60
76_K91_F1.2460.58
50_G142_A1.2250.56
156_N174_A1.2050.54
118_L193_L1.1890.53
50_G195_T1.1850.53
115_A150_W1.1810.52
37_Y44_W1.1800.52
114_E175_A1.1740.52
173_K177_T1.1600.50
160_A183_R1.1540.50
163_I168_A1.1530.50
84_A161_L1.1470.49
118_L195_T1.1340.48
62_F65_I1.1330.48
56_L94_A1.1260.47
51_I133_T1.1170.46
50_G101_M1.1150.46
65_I119_G1.1130.46
45_L151_V1.1080.45
39_Q159_I1.1050.45
75_L78_A1.0940.44
74_E92_R1.0840.43
49_F193_L1.0840.43
47_V50_G1.0790.43
141_L146_F1.0780.43
47_V79_V1.0680.42
61_N186_T1.0650.41
97_A142_A1.0520.40
79_V193_L1.0440.39
60_F88_L1.0400.39
79_V144_V1.0380.39
44_W172_A1.0300.38
51_I91_F1.0280.38
71_I141_L1.0260.38
116_F178_A1.0260.38
160_A174_A1.0260.38
64_Q103_V1.0240.38
174_A188_L1.0230.38
156_N175_A1.0230.38
75_L80_S1.0180.37
114_E179_M1.0170.37
64_Q183_R1.0140.37
135_I142_A1.0050.36
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: (28Jun14)
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  
2hc9A10.29412.80.977Contact Map
1kqfC10.88732.50.977Contact Map
3hd7A20.1522.30.977Contact Map
1j2rA40.308820.978Contact Map
3kzwA120.31371.70.979Contact Map
3peiA10.33331.60.979Contact Map
1c1yB10.25981.30.98Contact Map
3j01B10.56861.30.98Contact Map
2kluA10.31371.30.981Contact Map
1ji6A10.4021.30.981Contact 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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