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4nn2

ID: 1500381588 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 124 (123)
Sequences: 1759 (1103.1)
Seq/Len: 14.301
Nf(neff/√len): 99.5

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: 14.301).

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
94_Y117_L2.9161.00
71_M84_G2.7511.00
68_G82_T2.7091.00
71_M93_T2.5871.00
5_C8_C2.5721.00
32_H35_C2.4911.00
119_C122_H2.4811.00
7_F31_A2.0591.00
95_H98_C2.0081.00
90_C95_H1.9771.00
33_Y44_Q1.9631.00
90_C98_C1.9331.00
41_G68_G1.9071.00
73_C76_C1.8051.00
84_G93_T1.7511.00
75_L104_A1.7511.00
67_R84_G1.6261.00
19_G22_H1.5331.00
39_S68_G1.5091.00
85_C90_C1.4641.00
92_K121_N1.4261.00
64_E69_K1.4241.00
76_C80_G1.4070.99
64_E67_R1.4010.99
76_C95_H1.3770.99
84_G91_V1.3510.99
25_N28_K1.3430.99
85_C95_H1.3310.99
64_E68_G1.2980.99
39_S82_T1.2520.99
65_I68_G1.2450.98
110_M116_K1.2250.98
30_A33_Y1.2020.98
40_S84_G1.1960.98
17_A20_K1.1880.98
68_G71_M1.1850.98
5_C35_C1.1800.98
34_K97_H1.1760.98
6_G29_A1.1650.97
85_C98_C1.1540.97
76_C85_C1.1500.97
5_C32_H1.1460.97
39_S96_Y1.1230.97
76_C90_C1.1100.96
96_Y99_G1.1040.96
31_A58_I1.0940.96
18_R21_L1.0870.96
34_K96_Y1.0810.95
111_S114_I1.0580.95
3_P21_L1.0560.95
46_T49_S1.0250.93
12_E94_Y1.0140.93
32_H36_M1.0020.92
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  
4nn2A211000.041Contact Map
2lq6A10.508199.20.53Contact Map
4gneA10.717794.80.788Contact Map
4lk9A10.822693.60.799Contact Map
3v43A10.822689.20.821Contact Map
2kwjA10.814588.40.824Contact Map
2ysmA10.766185.90.83Contact Map
2g6qA10.395283.50.836Contact Map
1wewA10.548482.60.837Contact Map
4cosA10.403282.50.838Contact 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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