OPENSEQ.org
CcmD-01

ID: 1517604753 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 69 (63)
Sequences: 724 (510.9)
Seq/Len: 11.492
Nf(neff/√len): 64.4

Jackhmmer Results: (2016_04)
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: 11.492).

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
8_W12_F4.4101.00
19_F23_L2.9801.00
35_L39_S2.0831.00
5_F35_L2.0201.00
14_M22_W1.7021.00
43_H47_L1.6461.00
4_A53_Q1.6411.00
3_P6_A1.5851.00
30_I34_V1.5801.00
26_V30_I1.4551.00
6_A10_E1.4481.00
17_Y23_L1.3040.99
5_F39_S1.2660.99
60_L63_A1.2630.99
5_F56_R1.2600.99
17_Y24_A1.2540.99
14_M21_V1.2420.98
37_V58_A1.2100.98
27_M64_Q1.1660.97
23_L35_L1.1580.97
61_R64_Q1.1500.97
52_Q61_R1.1270.97
10_E13_A1.1090.96
31_P39_S1.0450.94
14_M20_F1.0380.94
40_V62_A1.0210.93
46_I50_V1.0110.93
10_E42_Q1.0040.93
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  
4tllA20.014522.80.878Contact Map
4aw6A40.97117.60.884Contact Map
2kncB10.840611.90.893Contact Map
4i5sA20.478310.20.896Contact Map
5amrA1090.898Contact Map
4tphA20.66676.60.905Contact Map
4p6vB10.62326.60.905Contact Map
4tllB20.04356.50.905Contact Map
3sksA10.75365.70.907Contact Map
4u2pA40.55075.70.907Contact 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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