GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Geovibrio sp L21-Ace-BES -force run

ID: 1513960019 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 147 (126)
Sequences: 204 (181.3)
Seq/Len: 1.619
Nf(neff/√len): 16.2

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: 1.619).

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
40_N87_V2.0600.99
121_K125_P2.0230.98
59_G87_V1.8940.97
42_T46_D1.6840.94
13_L21_G1.6800.94
26_V117_I1.6390.93
40_N116_Y1.6220.92
31_Y47_L1.5500.90
7_G10_L1.5220.89
94_I105_C1.5050.88
60_E118_F1.4830.87
20_I83_S1.4740.86
55_E64_Y1.4530.85
59_G111_S1.4320.84
40_N111_S1.3970.82
20_I61_H1.3790.81
14_L17_V1.3580.80
19_I112_M1.3470.79
87_V111_S1.3320.78
20_I117_I1.3090.76
11_I24_A1.3000.75
43_A120_Y1.2970.75
16_V92_T1.2920.75
51_R111_S1.2760.73
9_T28_I1.2750.73
42_T62_D1.2530.71
40_N56_S1.2500.71
94_I104_S1.2360.70
102_N107_V1.2340.70
25_A29_P1.2210.69
15_V24_A1.2170.68
14_L19_I1.2160.68
42_T85_E1.2000.67
54_V87_V1.2000.67
9_T14_L1.1790.65
35_R106_G1.1690.64
54_V58_F1.1630.63
98_T102_N1.1620.63
24_A108_G1.1560.62
27_A34_F1.1540.62
47_L120_Y1.1530.62
97_K105_C1.1450.61
41_T44_K1.1350.60
8_F12_E1.1270.59
47_L109_V1.1250.59
5_S26_V1.1240.59
90_S119_T1.1200.59
7_G29_P1.1150.58
51_R105_C1.1130.58
31_Y35_R1.1090.58
97_K102_N1.1040.57
15_V26_V1.1010.57
106_G119_T1.0960.56
21_G98_T1.0910.56
32_A125_P1.0770.54
56_S118_F1.0690.53
64_Y87_V1.0680.53
90_S108_G1.0580.52
56_S124_S1.0520.52
87_V109_V1.0320.50
20_I34_F1.0280.49
44_K81_V1.0230.49
42_T80_G1.0220.48
20_I79_D1.0060.47
47_L55_E1.0060.47
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  
3sokA20.850399.60.652Contact Map
2hi2A10.891299.60.652Contact Map
1oqwA20.891299.60.668Contact Map
2m7gA10.41599.50.673Contact Map
2m3kA10.714399.40.701Contact Map
4noaA10.639599.30.717Contact Map
4d40A20990.747Contact Map
3g20A20.755198.80.764Contact Map
1x6zA10.721195.40.87Contact Map
3gn9A30.700790.70.891Contact 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 0.034 seconds.