May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org

hGR Question Mark Shorter

ID: 1478553509 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 63 (54)
Sequences: 65 (49.1)
Seq/Len: 1.204
Nf(neff/√len): 6.7

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: 1.204).

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_T14_Q1.8430.94
4_Y25_P1.7370.92
5_D32_E1.7080.91
2_Y28_P1.6390.88
6_M20_I1.6090.87
38_Q53_F1.4850.80
30_G43_D1.4740.80
1_M9_A1.3960.74
39_G54_P1.3090.67
8_T46_T1.2310.60
31_S48_L1.2260.60
14_Q38_Q1.2050.58
33_N37_C1.2020.58
13_Q33_N1.1950.57
21_F25_P1.1940.57
24_I31_S1.1330.51
1_M46_T1.1240.50
35_N38_Q1.1120.49
6_M12_S1.0980.48
5_D17_Q1.0900.47
35_N54_P1.0900.47
1_M26_P1.0650.44
22_N44_N1.0650.44
7_N42_D1.0420.42
48_L51_L1.0410.42
9_A39_G1.0300.41
8_T13_Q1.0160.40
14_Q18_K1.0150.40
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  
1qtqA10.412713.50.894Contact Map
5bnzA2010.90.898Contact Map
4h3sA10.44444.50.915Contact Map
4r3zC10.39684.20.916Contact Map
4p2bA10.33333.20.921Contact Map
3abhA20.04762.40.926Contact Map
4m70E40.52381.90.93Contact Map
3on9A20.33331.80.931Contact Map
3gnpA10.17461.60.933Contact Map
1h1nA20.39681.40.935Contact 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 1.4041 seconds.