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T0842

ID: 1404412742 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 146 (140)
Sequences: 204 (187.7)
Seq/Len: 1.457
Nf(neff/√len): 15.9

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: 1.457).

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
95_K103_E2.8041.00
48_V87_A2.0880.99
32_P41_V2.0770.98
41_V44_W2.0070.98
44_W105_G2.0050.98
40_E92_C1.9420.97
134_E137_R1.6650.92
99_R102_A1.6240.91
49_Y57_E1.6060.90
23_E127_I1.5980.90
11_A142_S1.5520.88
59_M112_A1.4860.85
57_E96_T1.4700.84
45_C55_L1.4490.83
60_Q72_L1.4190.81
24_I124_Q1.3940.79
47_I87_A1.3500.76
23_E52_S1.3320.75
60_Q106_F1.3090.73
84_H119_A1.3080.73
23_E131_P1.3000.72
127_I131_P1.2790.71
7_H45_C1.2680.70
128_K139_G1.2670.70
62_V113_L1.2510.68
57_E136_R1.2480.68
79_N96_T1.2450.68
10_V14_S1.2330.67
31_N139_G1.2210.65
28_M85_K1.1970.63
21_R124_Q1.1940.63
69_G120_V1.1890.62
36_A40_E1.1860.62
35_Q108_H1.1720.61
42_M53_D1.1680.60
72_L82_S1.1660.60
97_N120_V1.1360.57
28_M54_V1.1350.57
44_W134_E1.1320.57
62_V120_V1.1280.56
14_S46_K1.1200.56
24_I72_L1.1180.55
38_Q41_V1.1170.55
89_R92_C1.0970.53
87_A102_A1.0930.53
73_S110_C1.0920.53
61_E64_Q1.0910.53
106_F117_T1.0880.52
41_V60_Q1.0820.52
66_P110_C1.0800.51
55_L61_E1.0790.51
120_V127_I1.0770.51
4_H7_H1.0760.51
24_I96_T1.0760.51
51_N93_G1.0760.51
121_T124_Q1.0650.50
10_V142_S1.0630.50
75_Q132_Q1.0600.49
48_V94_L1.0500.48
34_V123_A1.0470.48
22_E129_H1.0400.47
27_R137_R1.0390.47
56_K130_V1.0390.47
19_L127_I1.0380.47
69_G117_T1.0350.47
19_L137_R1.0310.46
10_V16_I1.0250.46
52_S64_Q1.0200.45
54_V81_T1.0160.45
17_P22_E1.0140.45
16_I142_S1.0060.44
12_M46_K1.0050.44
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  
2lnmA10.404127.30.933Contact Map
3hwsA60.643815.20.94Contact Map
2llvA10.486313.10.942Contact Map
2zbcA80.527412.80.942Contact Map
2djwA100.520510.30.945Contact Map
2llwA10.48639.80.945Contact Map
4o4fA10.94528.30.947Contact Map
2f4mB10.41180.947Contact Map
4l8iA20.3636.60.949Contact Map
1um8A10.63016.30.95Contact 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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