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3zja

ID: 1500381994 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 114 (113)
Sequences: 1937 (1503.1)
Seq/Len: 17.142
Nf(neff/√len): 141.4

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: 17.142).

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
34_E100_A2.4321.00
8_A109_L2.2571.00
32_A62_E2.2461.00
43_G82_K2.1941.00
39_T98_H2.1881.00
64_P67_G2.0501.00
92_S108_K1.9871.00
37_S98_H1.8961.00
38_V45_V1.8861.00
88_K91_Q1.8731.00
34_E60_R1.8601.00
55_M79_M1.8411.00
26_T68_Q1.8301.00
32_A65_A1.8201.00
46_T57_E1.8191.00
4_S26_T1.8191.00
35_L99_F1.8091.00
21_G109_L1.7871.00
41_E94_A1.7731.00
61_I71_F1.7481.00
98_H104_P1.6961.00
95_V109_L1.6731.00
47_V61_I1.6621.00
5_V23_L1.6381.00
43_G84_K1.6311.00
69_L76_N1.5811.00
46_T81_E1.5801.00
6_D26_T1.5441.00
61_I69_L1.5161.00
94_A108_K1.5151.00
4_S28_E1.4951.00
23_L71_F1.4631.00
21_G95_V1.4551.00
49_E56_K1.4481.00
50_T53_G1.4201.00
33_D102_S1.4060.99
10_I19_A1.4020.99
87_P111_V1.3620.99
23_L78_L1.3610.99
33_D101_H1.3570.99
94_A106_A1.3570.99
21_G80_F1.3350.99
24_T70_V1.3030.99
44_E81_E1.2950.99
10_I21_G1.2360.98
33_D103_D1.2270.98
9_Y73_S1.2220.98
85_Q91_Q1.2180.98
35_L97_L1.2050.98
40_S45_V1.1850.98
93_V109_L1.1780.98
10_I93_V1.1530.97
7_A24_T1.1410.97
24_T68_Q1.1310.97
51_I56_K1.1170.96
89_Q113_A1.1070.96
58_V76_N1.1070.96
13_P16_D1.0990.96
33_D100_A1.0820.96
21_G78_L1.0660.95
39_T104_P1.0650.95
44_E82_K1.0630.95
72_K75_G1.0550.95
34_E62_E1.0510.94
6_D24_T1.0350.94
40_S80_F1.0300.94
5_V8_A1.0300.94
61_I76_N1.0140.93
92_S110_P1.0080.93
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  
3zjaA111000.06Contact Map
1x9lA111000.105Contact Map
2k6wA10.97371000.119Contact Map
1ufgA10.894771.10.876Contact Map
3umnA30.88665.30.881Contact Map
1ifrA10.868463.30.882Contact Map
2lllA10.8947600.885Contact Map
2x3cA10.9035590.886Contact Map
3isyA10.877246.50.894Contact Map
3jt0A20.8684340.902Contact 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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