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ID: 1501096432 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 264 (199)
Sequences: 54751 (39843.8)
Seq/Len: 275.131
Nf(neff/√len): 2824.5

Jackhmmer Results: (2016_04)
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: 275.131).

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 > 50% 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
106_F122_A4.3321.00
182_V234_C3.9521.00
115_V157_T3.7621.00
109_L238_V3.5171.00
123_S154_T2.8401.00
213_T218_M2.7071.00
112_H115_V2.6521.00
121_H228_C2.6351.00
234_C237_K2.6091.00
115_V155_I2.4521.00
223_T242_H2.2041.00
96_I185_V2.0921.00
177_E180_D2.0531.00
108_M116_A2.0351.00
114_N157_T1.9051.00
234_C239_I1.8991.00
97_V108_M1.8821.00
120_T145_D1.8781.00
93_K185_V1.8391.00
185_V233_T1.7831.00
184_I223_T1.7531.00
90_A177_E1.7101.00
182_V232_I1.7021.00
121_H152_E1.6811.00
97_V116_A1.6741.00
131_D134_E1.6641.00
109_L241_M1.6561.00
100_T131_D1.6281.00
109_L117_V1.5651.00
109_L231_I1.5301.00
117_V238_V1.5071.00
114_N161_S1.5041.00
136_E157_T1.4781.00
188_S227_Q1.4271.00
96_I107_T1.4040.99
82_G85_F1.3940.99
164_F170_H1.3820.99
170_H173_T1.3810.99
141_K159_K1.3640.99
158_L162_E1.3540.99
119_P122_A1.3430.99
181_G197_V1.3380.99
213_T216_T1.3240.99
169_P237_K1.3210.99
41_G44_G1.2740.99
95_N233_T1.2640.99
205_Y208_L1.2600.99
214_A218_M1.2550.99
213_T217_L1.2520.99
118_L123_S1.2520.99
111_V117_V1.2430.98
113_D161_S1.2410.98
192_N195_V1.2400.98
153_I241_M1.2220.98
110_G164_F1.2200.98
182_V199_A1.2180.98
242_H245_G1.2150.98
123_S140_A1.2080.98
173_T176_T1.2080.98
143_L151_L1.2020.98
42_T45_C1.1950.98
140_A143_L1.1910.98
116_A158_L1.1900.98
219_Y242_H1.1660.97
96_I231_I1.1660.97
110_G162_E1.1630.97
189_K225_A1.1620.97
248_S251_F1.1550.97
182_V239_I1.1520.97
132_G162_E1.1490.97
231_I238_V1.1430.97
44_G47_G1.1350.97
186_N227_Q1.1220.97
184_I242_H1.1150.96
181_G198_G1.0840.96
97_V132_G1.0840.96
140_A156_V1.0830.96
230_G242_H1.0820.96
172_P237_K1.0740.95
119_P241_M1.0660.95
172_P175_I1.0590.95
181_G235_T1.0580.95
201_T204_G1.0560.95
135_V141_K1.0540.95
107_T230_G1.0520.95
202_E206_L1.0510.94
89_V92_A1.0510.94
119_P243_V1.0490.94
123_S156_V1.0450.94
128_I131_D1.0430.94
118_L154_T1.0420.94
180_D234_C1.0340.94
137_V157_T1.0260.94
110_G116_A1.0230.93
216_T219_Y1.0180.93
204_G207_N1.0170.93
93_K194_Y1.0130.93
140_A144_E1.0060.93
98_T105_E1.0030.93
139_D157_T1.0010.92
141_K157_T1.0010.92
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  
3stiA30.67051000.464Contact Map
1ky9A20.66671000.467Contact Map
3stjA120.68561000.47Contact Map
1lcyA10.68941000.475Contact Map
1l1jA20.69321000.482Contact Map
4ri0A30.68941000.483Contact Map
3tjoA30.6781000.485Contact Map
4ic6A30.72731000.485Contact Map
3numA10.65151000.485Contact Map
3lgiA30.73861000.485Contact 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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