GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0844

ID: 1404751851 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 145 (143)
Sequences: 204 (186.3)
Seq/Len: 1.427
Nf(neff/√len): 15.6

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: 1.427).

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_E2.8681.00
47_I86_K2.0670.98
31_A40_I2.0340.98
43_L104_N1.9310.97
39_K91_G1.8670.96
40_I43_L1.8260.96
98_Y101_S1.8240.96
58_I111_E1.6850.92
22_E130_H1.6350.91
22_E126_I1.6070.90
48_Y56_Q1.5950.89
6_H44_S1.5890.89
44_S54_L1.5070.86
23_V123_R1.4480.82
133_K136_R1.4230.81
56_Q95_S1.3790.78
126_I130_H1.3480.76
59_S71_L1.3440.75
30_D138_L1.3090.72
10_I141_V1.3060.72
46_L86_K1.2550.68
56_Q135_R1.2510.67
61_I112_I1.2480.67
96_Q119_V1.2450.67
87_G101_S1.2440.67
22_E51_P1.2410.67
27_I53_I1.2400.67
59_S105_A1.2310.66
3_H6_H1.2270.65
83_G118_K1.2260.65
68_G119_V1.2240.65
87_G98_Y1.2160.64
35_K39_K1.2030.63
12_A142_K1.1860.61
20_E123_R1.1720.60
5_H74_R1.1680.60
60_H63_A1.1580.59
34_Q107_I1.1500.58
78_S95_S1.1490.58
23_V95_S1.1380.57
9_L13_E1.1360.56
27_I84_R1.1170.55
119_V126_I1.1140.54
127_M138_L1.1030.53
46_L100_I1.0980.53
71_L81_S1.0880.52
18_L126_I1.0710.50
38_E125_T1.0570.48
65_P116_A1.0560.48
18_L136_R1.0510.48
91_G105_A1.0500.48
15_L62_N1.0480.48
86_K101_S1.0470.47
23_V71_L1.0400.47
55_E129_E1.0370.46
3_H7_H1.0350.46
13_E45_K1.0320.46
78_S139_Q1.0310.46
33_I72_S1.0270.45
17_P77_N1.0240.45
21_E128_R1.0210.45
105_A116_A1.0190.45
50_N92_Y1.0180.45
53_I80_K1.0170.44
37_L40_I1.0130.44
9_L15_L1.0130.44
18_L33_I1.0120.44
68_G116_A1.0080.44
89_K99_K1.0060.43
120_S123_R1.0040.43
41_R52_E1.0000.43
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  
2lnmA10.406936.20.929Contact Map
2llwA10.489716.70.94Contact Map
2llvA10.489712.10.943Contact Map
2zbcA80.53190.946Contact Map
2f4mB10.41387.90.948Contact Map
3hwsA60.641470.949Contact Map
3k8pC10.4695.80.951Contact Map
2djwA100.52415.70.951Contact Map
2oeqA40.4695.70.951Contact Map
1u1jA10.64833.80.955Contact 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.

Page generated in 0.0314 seconds.