OPENSEQ.org
rhodo monomer

ID: 1517760685 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 153 (144)
Sequences: 1852 (1210.6)
Seq/Len: 12.861
Nf(neff/√len): 100.9

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: 12.861).

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
70_W105_S3.5751.00
58_L112_A2.7281.00
34_E127_G2.6781.00
12_I149_T2.5391.00
146_L150_T2.4691.00
68_L72_F2.3571.00
51_R121_G2.3461.00
21_G62_L2.3001.00
32_D54_Q2.2041.00
96_A147_S2.1811.00
113_A117_K2.1021.00
15_V69_A2.0821.00
140_L144_M2.0321.00
105_S109_G2.0241.00
46_M49_L2.0211.00
10_L72_F2.0111.00
100_G147_S1.9261.00
95_V99_A1.9221.00
118_I123_S1.8921.00
14_A68_L1.8481.00
100_G143_V1.8101.00
117_K122_T1.7631.00
17_A65_A1.7471.00
41_P46_M1.7211.00
128_K132_M1.7141.00
16_I141_A1.6461.00
14_A72_F1.5811.00
74_L78_H1.5591.00
13_L142_I1.5521.00
110_F114_Q1.5201.00
94_M98_L1.5051.00
5_D8_R1.4821.00
47_Q121_G1.4681.00
52_L56_R1.3830.99
7_A75_W1.3540.99
47_Q51_R1.3540.99
13_L145_V1.3130.99
100_G144_M1.3010.99
111_L133_T1.2940.99
31_Y52_L1.2890.99
24_F53_W1.2700.99
115_R119_A1.2280.98
106_G109_G1.2220.98
114_Q129_F1.2170.98
93_W148_V1.2170.98
55_T60_I1.2100.98
9_G150_T1.1970.98
92_P95_V1.1770.98
123_S130_W1.1640.97
9_G146_L1.1620.97
30_A33_A1.1390.97
81_V86_A1.1200.96
109_G112_A1.1150.96
78_H81_V1.0940.96
98_L102_F1.0840.96
23_L107_W1.0800.95
81_V85_G1.0710.95
107_W111_L1.0580.95
6_L146_L1.0570.95
117_K124_K1.0560.95
34_E56_R1.0490.94
114_Q130_W1.0390.94
92_P96_A1.0380.94
3_T7_A1.0370.94
80_D85_G1.0330.94
56_R60_I1.0330.94
27_R134_N1.0320.94
63_T108_H1.0200.93
7_A150_T1.0160.93
80_D86_A1.0110.93
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  
2wdqC30.75162.80.95Contact Map
2kncB10.22881.30.959Contact Map
2wdqD30.66671.20.959Contact Map
2lp1A10.25491.20.96Contact Map
2llmA10.27451.20.96Contact Map
3zuxA10.588210.962Contact Map
3s8fA10.72550.90.962Contact Map
2lzrA10.13730.90.963Contact Map
3w9iA60.24840.90.963Contact Map
3x29A20.47060.90.963Contact 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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