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ID: 1513357830 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 69 (69)
Sequences: 405 (224.4)
Seq/Len: 5.870
Nf(neff/√len): 27.0

HHblits Results: (2016_02)
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: 5.870).

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
30_A37_I2.7231.00
11_C23_R1.7561.00
43_T57_Q1.7471.00
40_Q44_W1.6981.00
65_F68_K1.6721.00
47_V62_L1.6441.00
34_L44_W1.4600.99
59_I62_L1.4140.98
29_I61_L1.4050.98
34_L40_Q1.3840.98
34_L37_I1.3830.98
16_E19_L1.3440.97
1_S5_E1.3320.97
45_L50_S1.3100.97
7_Y10_I1.2920.97
33_V54_P1.2860.96
28_D31_R1.2240.95
46_G51_P1.2160.95
31_R35_E1.2050.94
27_F44_W1.2010.94
8_V32_N1.1890.94
60_K64_V1.1870.94
9_A12_R1.1770.93
46_G66_Y1.1660.93
56_V64_V1.1330.91
27_F40_Q1.1280.91
15_S18_K1.1250.91
16_E24_K1.1130.91
37_I44_W1.1040.90
8_V50_S1.0790.89
47_V61_L1.0750.88
15_S19_L1.0660.88
49_F60_K1.0230.85
1_S6_V1.0220.85
25_P30_A1.0200.85
63_L67_V1.0190.84
14_I18_K1.0160.84
33_V52_L1.0060.83
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: (06Aug15)
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  
2wscI10.376820.913Contact Map
4xk8I201.50.919Contact Map
2yevA20.98551.40.919Contact Map
4fzhA401.30.922Contact Map
4bkfC201.10.926Contact Map
2gsmA20.98551.10.926Contact Map
1rzhH10.333310.927Contact Map
4u4hA10.449310.928Contact Map
3wu2I20.40580.90.929Contact Map
1p4qA10.47830.90.929Contact 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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