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T0846

ID: 1404843043 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 146 (143)
Sequences: 265 (231)
Seq/Len: 1.853
Nf(neff/√len): 19.3

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: 1.853).

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_E2.5821.00
47_V86_A2.1690.99
31_H40_I1.8550.98
40_I43_L1.8330.97
39_E91_F1.7820.97
98_R101_A1.7680.97
43_L104_N1.6990.96
89_K93_I1.6870.95
44_S54_L1.6330.94
87_G101_A1.5470.92
23_F123_M1.5440.92
133_E136_R1.5370.91
89_K92_G1.5340.91
48_F56_N1.5270.91
3_H6_H1.4910.90
6_H44_S1.4010.85
48_F75_L1.3890.85
10_I141_V1.3520.82
22_E126_I1.3490.82
58_L111_A1.3220.80
56_N95_N1.3070.79
13_Q45_Q1.2470.75
9_F13_Q1.2120.72
22_E130_H1.2090.71
83_A118_A1.2050.71
27_V33_I1.1830.69
65_P102_E1.1830.69
44_S102_E1.1780.69
3_H7_H1.1740.68
14_K38_K1.1650.67
78_S95_N1.1600.67
88_S91_F1.1590.67
35_E39_E1.1580.67
24_I89_K1.1560.66
13_Q16_V1.1550.66
30_D138_A1.1540.66
65_P109_V1.1530.66
68_T119_V1.1480.66
53_Q80_E1.1470.66
19_S22_E1.1380.65
69_K115_Y1.1370.65
3_H14_K1.1280.64
60_Q63_E1.1190.63
86_A92_G1.1090.62
65_P111_A1.1090.62
126_I130_H1.1030.61
44_S94_K1.0980.61
46_I86_A1.0950.60
68_T116_A1.0940.60
21_N28_V1.0910.60
85_L101_A1.0890.60
91_F105_I1.0800.59
5_H8_H1.0790.59
84_K102_E1.0780.58
96_S122_S1.0770.58
87_G98_R1.0770.58
64_N81_S1.0760.58
23_F95_N1.0760.58
110_E116_A1.0610.57
50_N92_G1.0590.56
56_N135_K1.0510.56
54_L93_I1.0470.55
24_I61_I1.0460.55
58_L124_G1.0370.54
56_N81_S1.0360.54
106_S112_I1.0320.54
38_K125_N1.0290.53
90_T93_I1.0250.53
22_E51_Q1.0210.52
48_F82_F1.0200.52
47_V93_I1.0120.51
8_H143_L1.0110.51
96_S119_V1.0100.51
4_H11_S1.0040.50
18_L33_I1.0020.50
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: (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  
2lnmA10.41152.20.911Contact Map
2llwA10.486316.80.931Contact Map
3vejA20.274120.935Contact Map
2cqpA10.56169.30.939Contact Map
2zbcA80.52749.30.939Contact Map
2ywkA10.53429.20.939Contact Map
3hwsA60.6377.60.941Contact Map
2do4A10.56857.30.941Contact Map
3k8pC10.46587.30.941Contact Map
4n78F10.87676.70.942Contact 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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