GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0808 100-200 -force run

ID: 1404888676 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 101 (99)
Sequences: 80 (69.2)
Seq/Len: 0.808
Nf(neff/√len): 7.0

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: 0.808).

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
87_E90_H2.3260.98
48_V56_G2.2970.98
66_Y78_N2.0700.95
64_L95_A1.6050.78
47_Y89_M1.6040.78
55_W69_P1.5140.72
22_G30_F1.4820.69
50_D53_D1.4510.67
90_H93_Y1.4130.64
8_I36_L1.4060.64
7_S38_A1.3910.62
10_I13_A1.3470.59
85_E93_Y1.3390.58
8_I53_D1.3160.56
16_V36_L1.3030.55
33_I80_I1.2750.52
41_V80_I1.2710.52
23_V89_M1.2530.50
56_G60_P1.2500.50
20_L31_G1.2460.50
55_W96_A1.2420.49
44_K80_I1.2340.49
21_Q81_T1.2270.48
85_E96_A1.2220.48
27_G32_E1.2210.48
56_G59_G1.1990.46
48_V82_V1.1890.45
47_Y99_G1.1830.44
60_P90_H1.1770.44
18_I53_D1.1750.44
57_R95_A1.1550.42
5_V91_S1.1490.41
26_S31_G1.1210.39
59_G90_H1.1060.38
64_L72_D1.1000.37
78_N98_F1.0800.36
18_I30_F1.0790.36
3_V33_I1.0710.35
62_V76_F1.0700.35
8_I91_S1.0660.35
77_Y93_Y1.0640.34
5_V19_D1.0600.34
66_Y94_M1.0540.34
91_S99_G1.0360.32
19_D80_I1.0210.31
6_G93_Y1.0210.31
66_Y81_T1.0190.31
62_V94_M1.0180.31
70_E84_K1.0140.31
36_L68_L1.0130.31
32_E40_N1.0050.30
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  
4fchA20.861480.945Contact Map
3ghmA10.7037.90.945Contact Map
2xomA10.38617.20.946Contact Map
2vzsA206.80.947Contact Map
4kmqA10.36636.50.947Contact Map
1x9pA10.9016.20.948Contact Map
3mtxA20.40594.10.952Contact Map
3hnmA40.455440.952Contact Map
4c91A20.53473.70.953Contact Map
4ar2A10.95053.70.953Contact 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 0.0121 seconds.