GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0847

ID: 1404842590 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 176 (171)
Sequences: 261 (180.3)
Seq/Len: 1.526
Nf(neff/√len): 13.8

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: 1.526).

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
37_V64_C2.7671.00
55_A59_R2.6631.00
26_R51_D2.6621.00
91_N94_I1.8890.97
36_L121_S1.7770.95
118_F156_F1.5780.90
11_V146_S1.4760.85
118_F159_E1.4690.85
16_V20_N1.4360.83
107_G159_E1.4060.81
7_S139_H1.3930.80
59_R63_V1.3720.79
32_T36_L1.3650.79
66_L82_V1.3430.77
136_L140_V1.3410.77
82_V113_Q1.3390.77
67_L78_M1.3260.76
12_Y16_V1.3180.75
27_R169_P1.2980.73
65_V90_K1.2960.73
3_L6_K1.2750.72
157_D161_R1.2650.71
45_D135_W1.2540.70
48_I56_A1.2480.69
11_V83_Q1.2480.69
93_S96_S1.2390.68
53_L90_K1.2270.67
65_V99_G1.2240.67
3_L170_V1.2230.67
48_I70_G1.2220.67
29_I40_M1.2170.66
36_L94_I1.2040.65
112_G126_V1.1980.65
37_V62_F1.1920.64
23_D131_Y1.1700.62
45_D51_D1.1560.61
40_M43_F1.1550.60
20_N34_Q1.1450.59
115_R132_S1.1410.59
50_C53_L1.1390.59
18_H61_V1.1370.59
135_W140_V1.1190.57
31_R61_V1.1150.56
42_V71_G1.1130.56
33_S87_S1.1120.56
23_D173_L1.1120.56
37_V157_D1.1080.56
74_L88_H1.1070.56
160_F164_Y1.1040.55
91_N96_S1.1040.55
32_T94_I1.1030.55
38_I82_V1.1010.55
38_I54_E1.0970.55
75_F78_M1.0970.55
38_I65_V1.0950.54
60_G63_V1.0870.54
5_E112_G1.0850.53
10_T130_S1.0830.53
21_I29_I1.0800.53
55_A95_R1.0730.52
126_V170_V1.0710.52
45_D75_F1.0660.51
99_G150_G1.0650.51
22_R131_Y1.0630.51
26_R99_G1.0630.51
58_K136_L1.0600.51
130_S143_N1.0570.50
41_D51_D1.0510.50
33_S61_V1.0510.50
36_L86_D1.0500.50
36_L170_V1.0500.50
17_K29_I1.0480.50
77_E80_D1.0470.49
56_A121_S1.0470.49
99_G165_A1.0450.49
127_L153_V1.0440.49
5_E34_Q1.0400.49
137_C143_N1.0380.48
49_F63_V1.0310.48
12_Y152_A1.0280.47
82_V134_T1.0230.47
114_I121_S1.0200.47
3_L127_L1.0160.46
41_D44_T1.0160.46
22_R160_F1.0150.46
112_G159_E1.0140.46
34_Q62_F1.0120.46
116_E159_E1.0060.45
45_D160_F1.0050.45
131_Y138_G1.0040.45
29_I151_Q1.0030.45
45_D48_I1.0020.45
145_L166_S1.0010.45
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  
4gelA20.85899.90.587Contact Map
1byrA10.840999.90.601Contact Map
4ggjA10.795599.90.619Contact Map
3hsiA30.988699.80.631Contact Map
1v0wA10.920599.80.652Contact Map
2o8rA20.863699.80.668Contact Map
1xdpA20.903499.70.673Contact Map
2c1lA20.903499.70.681Contact Map
3qphA10.818297.70.855Contact Map
2f5tX10.721697.60.859Contact 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 0.0289 seconds.