GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0836

ID: 1404172776 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (166)
Sequences: 182 (87.8)
Seq/Len: 1.096
Nf(neff/√len): 6.8

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: 1.096).

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_A2.4510.99
62_F91_F2.2370.98
99_W143_T1.9250.95
50_G95_A1.9070.95
61_N188_L1.8710.94
95_A197_A1.8590.94
180_L183_R1.8000.92
91_F94_A1.7620.91
50_G197_A1.7380.90
132_F135_I1.6060.85
56_L91_F1.5900.84
95_A146_F1.5830.84
114_E175_A1.5190.80
115_A150_W1.5010.79
142_A146_F1.4940.79
50_G135_I1.4930.79
154_W180_L1.4670.77
154_W158_K1.4650.77
75_L78_A1.4260.74
178_A183_R1.3910.71
50_G142_A1.3900.71
47_V197_A1.3880.71
137_T142_A1.3820.71
135_I192_M1.3570.69
95_A135_I1.3440.68
62_F89_F1.3320.67
65_I119_G1.3280.66
95_A142_A1.3270.66
100_V104_L1.3260.66
156_N160_A1.3230.66
61_N65_I1.3170.65
39_Q137_T1.3140.65
64_Q67_V1.2930.63
47_V50_G1.2800.62
163_I168_A1.2660.61
156_N177_T1.2480.59
166_A173_K1.2380.58
45_L118_L1.2230.57
59_Y190_I1.2110.56
50_G195_T1.1990.55
112_L164_V1.1900.54
62_F158_K1.1860.53
61_N89_F1.1810.53
72_P89_F1.1600.51
179_M183_R1.1590.51
47_V193_L1.1520.50
127_G130_M1.1510.50
84_A161_L1.1460.50
49_F193_L1.1440.49
78_A83_I1.1420.49
51_I133_T1.1350.49
51_I104_L1.1320.48
45_L101_M1.1170.47
82_Y123_G1.1000.45
60_F88_L1.0890.44
62_F65_I1.0880.44
156_N174_A1.0830.44
73_A78_A1.0830.44
68_M80_S1.0820.44
114_E179_M1.0800.43
64_Q179_M1.0780.43
156_N175_A1.0740.43
56_L94_A1.0710.43
161_L178_A1.0670.42
69_P142_A1.0630.42
61_N186_T1.0580.41
147_F158_K1.0550.41
77_P110_G1.0520.41
56_L160_A1.0490.41
42_F108_N1.0460.40
106_A139_M1.0370.39
110_G123_G1.0260.38
132_F146_F1.0220.38
80_S83_I1.0210.38
154_W178_A1.0200.38
95_A176_K1.0190.38
118_L193_L1.0160.38
115_A169_D1.0140.37
135_I197_A1.0070.37
141_L146_F1.0070.37
50_G101_M1.0020.36
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  
1kqfC10.89224.50.974Contact Map
1j2rA40.30882.80.976Contact Map
3hd7A20.1522.30.978Contact Map
2hc9A10.313720.978Contact Map
3kzwA120.31371.40.98Contact Map
1c1yB10.26961.30.98Contact Map
3peiA10.33331.20.981Contact Map
2kluA10.31371.20.981Contact Map
4l35A10.71081.20.981Contact Map
3kr4A120.31861.10.981Contact 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.

Page generated in 0.0153 seconds.