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MRED_ECOLI

ID: 1423731022 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 162 (157)
Sequences: 735 (521)
Seq/Len: 4.682
Nf(neff/√len): 41.6

Jackhmmer Results: (2015_01_07)
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: 4.682).

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
47_I85_A3.5781.00
111_S141_N3.5051.00
108_M142_G3.4911.00
19_A42_I2.4851.00
56_V82_S2.2001.00
43_L54_V2.0711.00
44_L107_V1.8471.00
49_A153_R1.7891.00
11_V155_V1.7010.99
94_L98_L1.6640.99
22_L38_W1.6390.99
60_F82_S1.6360.99
96_R156_R1.6260.99
149_F156_R1.5980.99
49_A156_R1.5890.99
20_L39_V1.5500.99
43_L85_A1.5470.99
24_I72_S1.5330.99
115_D138_S1.4820.98
45_Y153_R1.4800.98
34_F136_W1.4760.98
40_L111_S1.4380.98
40_L84_I1.3820.97
55_N85_A1.3670.96
66_L81_M1.3660.96
137_S140_V1.3570.96
13_W62_M1.3330.96
16_F62_M1.3170.95
87_L113_V1.3140.95
45_Y156_R1.3110.95
153_R156_R1.2880.95
48_L88_V1.2770.94
58_T62_M1.2750.94
24_I69_I1.2660.94
15_S19_A1.2610.94
23_Q66_L1.2430.93
27_W34_F1.2250.92
13_W58_T1.2160.92
44_L88_V1.2150.92
25_M30_N1.2110.92
77_R131_R1.2100.92
68_L73_T1.2050.92
38_W102_Q1.2020.91
37_N81_M1.2000.91
15_S46_W1.1970.91
99_A102_Q1.1940.91
72_S79_L1.1910.91
47_I111_S1.1820.90
76_V119_F1.1580.89
112_L141_N1.1390.88
37_N98_L1.1380.88
80_A118_V1.1320.88
51_P55_N1.1320.88
37_N141_N1.1270.87
45_Y96_R1.1030.86
15_S152_M1.0980.86
122_E126_I1.0910.85
29_D105_L1.0860.85
10_W101_W1.0840.85
137_S141_N1.0830.85
25_M34_F1.0610.83
17_L155_V1.0530.82
11_V161_V1.0510.82
79_L143_V1.0450.82
77_R129_S1.0430.81
49_A149_F1.0350.81
90_L135_F1.0290.80
84_I161_V1.0230.80
47_I90_L1.0230.80
96_R153_R1.0220.79
86_Y121_A1.0150.79
50_L153_R1.0060.78
83_I117_I1.0040.78
110_L118_V1.0030.78
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: (31Jan15)
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  
4hzuS10.9568720.911Contact Map
4rfsS10.932147.60.923Contact Map
3p5nA20.907432.70.93Contact Map
3rlbA20.950618.40.938Contact Map
4tkrA20.944414.90.94Contact Map
4huqS10.913610.90.944Contact Map
4brcA20.34572.80.958Contact Map
4dveA30.9632.70.958Contact Map
3tx3A20.33332.60.958Contact Map
3f7cA10.38892.10.96Contact 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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