GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0824

ID: 1403209699 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 110 (106)
Sequences: 197 (166.9)
Seq/Len: 1.858
Nf(neff/√len): 16.2

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: 1.858).

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
24_D78_R4.7361.00
59_D86_R2.3881.00
34_C63_W2.1120.99
68_C105_I1.9610.99
92_V107_F1.9160.98
21_H76_S1.8310.97
67_M96_L1.7950.97
63_W107_F1.7670.97
80_V84_D1.5680.92
18_T80_V1.5630.92
72_G75_A1.5590.92
12_A23_S1.5270.91
67_M92_V1.5210.91
15_Y87_G1.4750.89
34_C65_M1.4700.89
45_R66_A1.3900.85
49_L60_R1.3800.84
11_P34_C1.3240.81
21_H88_A1.2770.77
18_T88_A1.2460.75
18_T84_D1.2340.74
34_C68_C1.2330.74
21_H85_N1.2330.74
94_N109_V1.2150.72
59_D90_S1.2080.71
7_V42_D1.2070.71
25_A63_W1.1760.68
10_F91_W1.1250.63
25_A85_N1.1210.63
19_G25_A1.1110.62
47_E50_K1.1110.62
12_A19_G1.1100.62
60_R65_M1.1080.62
10_F68_C1.0990.61
48_S103_T1.0970.61
98_G109_V1.0970.61
8_L20_A1.0960.60
49_L52_I1.0960.60
82_S99_Y1.0940.60
34_C91_W1.0840.59
106_L109_V1.0790.59
76_S80_V1.0710.58
49_L59_D1.0700.58
58_F79_Y1.0510.56
85_N88_A1.0510.56
16_P55_K1.0490.55
25_A29_G1.0480.55
16_P84_D1.0450.55
60_R79_Y1.0440.55
19_G23_S1.0280.53
65_M96_L1.0160.52
18_T65_M1.0100.51
59_D85_N1.0070.51
26_I106_L1.0020.50
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: (14Jun14)
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  
2cmyB10.190912.60.93Contact Map
3cb4D60.99095.20.942Contact Map
2plxB10.236450.942Contact Map
3bdlA10.20914.60.943Contact Map
3j3bT10.39094.40.943Contact Map
4a17P10.39094.30.944Contact Map
3u5eT10.39094.30.944Contact Map
3iz5U10.44.20.944Contact Map
3zf7U10.390940.945Contact Map
1vq8Q10.39093.40.947Contact 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 0.0383 seconds.