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NikRcovariance

ID: 1500905713 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 133 (133)
Sequences: 755 (519.9)
Seq/Len: 5.677
Nf(neff/√len): 45.1

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: 5.677).

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
91_N94_D2.9601.00
87_H95_C2.8861.00
56_L101_L2.8051.00
30_E33_R2.2941.00
62_H76_H2.2661.00
76_H95_C2.1841.00
8_L36_L2.1291.00
116_I124_G2.1271.00
89_H95_C2.1051.00
94_D122_R2.0941.00
30_E37_R1.9651.00
25_Y34_D1.9391.00
76_H89_H1.8551.00
77_H114_D1.8401.00
62_H89_H1.7911.00
104_D107_D1.7901.00
49_G106_G1.7821.00
52_G108_V1.7291.00
16_L31_A1.6961.00
110_H114_D1.6180.99
35_I39_A1.6110.99
54_A101_L1.5670.99
15_T44_A1.5590.99
57_S127_Q1.5550.99
13_L17_D1.5320.99
76_H87_H1.4690.99
1_M5_T1.4440.98
62_H95_C1.4270.98
16_L36_L1.4090.98
77_H107_D1.4030.98
17_D28_R1.3140.97
77_H92_H1.3110.97
30_E34_D1.2780.96
78_H110_H1.2630.96
72_V76_H1.2590.96
80_D107_D1.2390.95
62_H87_H1.2370.95
34_D121_V1.2320.95
18_S47_Q1.2070.94
4_V7_T1.2060.94
83_V102_K1.1980.94
25_Y30_E1.1860.93
58_Y99_A1.1500.92
71_I115_V1.1480.92
50_T104_D1.1280.91
63_E92_H1.1280.91
44_A132_E1.1260.91
2_Q5_T1.1100.90
1_M10_D1.1000.89
18_S22_R1.0930.89
58_Y115_V1.0870.89
87_H97_E1.0700.87
15_T24_G1.0560.87
107_D110_H1.0530.86
32_I98_I1.0520.86
112_A124_G1.0370.85
53_F90_I1.0340.85
60_Y97_E1.0260.84
20_S25_Y1.0200.84
79_H90_I1.0120.83
16_L20_S1.0110.83
86_L98_I1.0040.83
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  
2wvfA211000.075Contact Map
2hzaA20.9851000.096Contact Map
2bj7A211000.133Contact Map
1q5yA40.631699.90.464Contact Map
2nzcA40.616599.80.53Contact Map
3kxeC20.541498.80.722Contact Map
2k5jA20.541498.70.727Contact Map
4me7E20.59498.70.732Contact Map
2cpgA30.330898.40.756Contact Map
2k9iA20.3534980.777Contact 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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