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SCO3734

ID: 1517742139 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 117 (108)
Sequences: 1127 (790.6)
Seq/Len: 10.435
Nf(neff/√len): 76.1

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: 10.435).

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
32_C90_V2.4361.00
58_L101_R2.3811.00
95_D98_A2.3201.00
2_I32_C2.2701.00
90_V94_V2.1441.00
5_V43_V1.9351.00
7_P10_E1.7241.00
3_Y35_D1.7091.00
8_L12_N1.6921.00
1_M61_E1.6841.00
60_D100_Q1.6711.00
13_A16_G1.6651.00
59_L99_V1.6421.00
60_D63_R1.6331.00
8_L104_E1.6191.00
34_P70_W1.5641.00
55_V104_E1.4431.00
58_L103_L1.4381.00
38_T85_T1.4181.00
14_G96_R1.3990.99
4_H19_Y1.3980.99
92_G98_A1.3930.99
107_W113_A1.3680.99
34_P38_T1.3580.99
55_V102_V1.3270.99
6_V10_E1.3190.99
96_R99_V1.2970.99
5_V54_L1.2730.99
59_L98_A1.2730.99
8_L53_P1.2670.99
5_V47_Y1.2630.99
11_W99_V1.2400.98
72_A86_L1.2400.98
44_N113_A1.2360.98
64_L68_C1.2330.98
59_L64_L1.2320.98
71_E87_F1.2280.98
40_L44_N1.2180.98
32_C59_L1.2180.98
6_V55_V1.2060.98
43_V105_V1.2040.98
12_N15_R1.1920.98
15_R102_V1.1670.97
71_E88_P1.1540.97
15_R96_R1.1420.97
4_H23_S1.1140.96
7_P50_A1.1070.96
22_D26_R1.0940.96
2_I61_E1.0880.96
5_V39_T1.0550.95
11_W43_V1.0440.94
33_S42_V1.0400.94
20_A93_P1.0390.94
1_M100_Q1.0220.93
56_A105_V1.0210.93
42_V47_Y1.0160.93
46_F73_A1.0060.93
34_P37_E1.0040.93
1_M58_L1.0000.92
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  
2o0qA10.91451000.098Contact Map
1wfxA10.760739.10.899Contact Map
1gff210.8974110.922Contact Map
1xqiA30.46157.80.928Contact Map
4aneA60.41887.70.928Contact Map
3js9A30.53857.60.928Contact Map
2bpa210.88897.30.928Contact Map
1wkjA20.44446.90.929Contact Map
4dz6A60.56416.70.93Contact Map
1h05A10.3596.60.93Contact 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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