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PKC C1A

ID: 1501861118 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 100 (88)
Sequences: 181 (102.8)
Seq/Len: 2.057
Nf(neff/√len): 11.0

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: 2.057).

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
74_V79_H2.7711.00
82_V87_P1.7330.97
29_K84_F1.6550.96
29_K35_K1.6330.95
90_D96_D1.6310.95
43_F49_F1.5580.93
57_I61_G1.5370.93
32_H41_A1.5340.93
13_S16_V1.4230.88
47_P56_F1.4140.88
48_T56_F1.3360.84
49_F56_F1.3340.84
90_D94_D1.3040.82
73_V79_H1.2950.81
26_L30_N1.2890.81
33_E38_K1.2870.80
42_R72_F1.2600.79
52_H81_F1.2540.78
76_K79_H1.2300.76
57_I77_R1.2250.76
26_L99_R1.2180.75
27_R33_E1.2090.74
74_V77_R1.1720.71
38_K68_Q1.1710.71
31_V34_V1.1530.69
31_V49_F1.1460.69
52_H77_R1.1290.67
97_D100_S1.1180.66
82_V86_C1.1160.66
22_R58_W1.1110.65
30_N65_F1.1090.65
46_Q62_K1.1070.65
90_D95_T1.1020.64
28_Q41_A1.1020.64
70_C78_C1.0980.64
24_G88_G1.0910.63
43_F48_T1.0910.63
29_K83_T1.0820.62
26_L35_K1.0810.62
30_N41_A1.0730.61
63_Q76_K1.0710.61
43_F47_P1.0670.61
30_N51_S1.0390.57
28_Q33_E1.0390.57
43_F46_Q1.0250.56
81_F92_G1.0110.54
75_H86_C1.0090.54
47_P58_W1.0070.54
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  
3pfqA101000.313Contact Map
2ennA10.7799.90.443Contact Map
4l9mA10.8899.90.456Contact Map
2yuuA10.8199.80.48Contact Map
2rowA10.7999.80.535Contact Map
3uejA20.6599.70.563Contact Map
2db6A10.7399.70.568Contact Map
1y8fA10.5199.70.574Contact Map
2enzA10.6599.60.58Contact Map
2fnfX10.5899.60.585Contact 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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