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Mas

ID: 1499850496 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 325 (271)
Sequences: 14396 (7841)
Seq/Len: 53.122
Nf(neff/√len): 476.3

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: 53.122).

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
46_G81_L5.4201.00
72_H157_W4.1431.00
205_V209_I3.4691.00
147_Y151_L2.7001.00
72_H122_L2.6531.00
131_C136_Y2.5561.00
125_A156_L2.5141.00
208_T212_V2.3631.00
125_A152_V2.1551.00
103_Y106_V2.1541.00
202_L206_S2.1541.00
131_C135_L2.1091.00
104_T107_T2.0861.00
54_L71_T2.0671.00
79_S115_G2.0521.00
110_V114_F2.0391.00
114_F161_C2.0301.00
229_V283_V2.0291.00
76_A118_T1.9931.00
151_L155_L1.9291.00
131_C209_I1.9231.00
68_V153_C1.9201.00
118_T160_S1.9071.00
136_Y139_W1.8771.00
124_T206_S1.8511.00
145_P148_Q1.8191.00
77_D119_G1.8181.00
51_G55_W1.7971.00
246_L250_L1.7891.00
150_A154_A1.7821.00
165_T169_V1.7741.00
236_I279_I1.7621.00
77_D276_N1.7561.00
133_S137_P1.7441.00
47_F78_I1.7161.00
122_L153_C1.7081.00
72_H153_C1.6631.00
57_L71_T1.6591.00
62_R67_T1.6551.00
33_P37_W1.6471.00
209_I212_V1.6331.00
46_G274_S1.6291.00
241_A269_S1.6181.00
135_L213_K1.5961.00
209_I213_K1.5941.00
204_L208_T1.5181.00
69_Y149_S1.4991.00
211_V215_R1.4541.00
271_I275_A1.4511.00
49_E274_S1.4471.00
276_N280_Y1.4421.00
146_K150_A1.4331.00
131_C206_S1.4291.00
68_V150_A1.4231.00
212_V216_K1.4231.00
236_I275_A1.4151.00
123_L203_M1.4131.00
132_L143_H1.4060.99
200_T238_L1.4000.99
76_A119_G1.3820.99
110_V168_Y1.3500.99
71_T75_I1.3480.99
147_Y150_A1.3370.99
48_V51_G1.3300.99
207_S210_L1.3280.99
51_G78_I1.3060.99
129_E144_R1.2950.99
114_F164_T1.2950.99
122_L157_W1.2880.99
65_P149_S1.2840.99
213_K216_K1.2790.99
47_F81_L1.2770.99
127_S207_S1.2730.99
76_A157_W1.2690.99
58_C71_T1.2650.99
124_T202_L1.2570.99
54_L78_I1.2510.99
139_W142_C1.2400.98
223_S227_Y1.2330.98
152_V156_L1.2210.98
133_S140_Y1.2130.98
118_T122_L1.2040.98
120_L124_T1.2030.98
261_L265_S1.2010.98
52_I56_F1.1950.98
121_Y159_L1.1920.98
113_L164_T1.1880.98
254_Y257_T1.1840.98
80_L273_S1.1810.98
68_V146_K1.1760.98
134_V137_P1.1670.97
53_L74_S1.1660.97
242_M246_L1.1640.97
74_S77_D1.1630.97
121_Y156_L1.1600.97
129_E133_S1.1580.97
76_A115_G1.1530.97
156_L160_S1.1490.97
69_Y126_I1.1470.97
118_T157_W1.1440.97
117_N195_S1.1220.97
83_C86_I1.1180.96
133_S138_I1.1140.96
54_L75_I1.1140.96
214_I224_S1.1120.96
192_A197_L1.1040.96
53_L277_P1.1040.96
160_S164_T1.0990.96
167_E170_M1.0920.96
211_V227_Y1.0790.95
43_S81_L1.0730.95
139_W143_H1.0720.95
193_I199_F1.0630.95
226_L229_V1.0560.95
289_K292_K1.0560.95
54_L74_S1.0550.95
155_L159_L1.0500.94
73_L122_L1.0430.94
294_S298_V1.0430.94
56_F287_K1.0420.94
244_M265_S1.0410.94
64_N67_T1.0390.94
290_R293_E1.0380.94
120_L237_F1.0350.94
135_L209_I1.0320.94
162_L166_M1.0300.94
55_W59_F1.0240.93
128_V206_S1.0220.93
122_L156_L1.0160.93
69_Y122_L1.0140.93
69_Y125_A1.0030.93
151_L154_A1.0010.92
72_H76_A1.0000.92
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  
4pxzA10.78771000.334Contact Map
2rh1A10.80921000.343Contact Map
3uonA10.81231000.35Contact Map
3oduA20.86151000.352Contact Map
3emlA10.82151000.352Contact Map
3vw7A10.79381000.352Contact Map
4grvA10.82461000.353Contact Map
2z73A20.95081000.353Contact Map
3pblA20.78771000.354Contact Map
4eiyA10.83691000.355Contact 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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