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scpA

ID: 1499502092 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 274 (242)
Sequences: 2780 (1755.9)
Seq/Len: 11.488
Nf(neff/√len): 112.9

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: 11.488).

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
200_R249_V4.3861.00
245_V252_A3.3081.00
209_W264_R3.2721.00
27_D32_E2.9621.00
256_E259_Q2.9171.00
213_T260_D2.7391.00
195_A198_R2.4991.00
195_A233_Y2.4661.00
113_A117_F2.4601.00
254_Q261_I2.3801.00
191_P194_D2.3741.00
31_Y40_A2.3261.00
56_R59_E2.2571.00
211_V260_D2.2511.00
195_A237_T2.1571.00
251_E264_R2.0671.00
47_V53_S2.0351.00
121_K124_V2.0151.00
43_R123_D1.9521.00
196_R244_L1.9191.00
127_K130_E1.9091.00
254_Q258_F1.8931.00
241_S250_L1.8751.00
40_A44_S1.7721.00
68_A75_L1.7451.00
200_R244_L1.7161.00
48_D51_Q1.6921.00
59_E63_A1.6781.00
163_L167_M1.6641.00
209_W262_Y1.6271.00
241_S263_L1.5991.00
63_A67_Q1.5741.00
112_A116_A1.5511.00
131_A135_R1.5371.00
254_Q259_Q1.4231.00
81_V85_W1.4151.00
162_D165_G1.4151.00
114_Q118_R1.4111.00
211_V214_S1.4081.00
145_R148_P1.4060.99
45_Q56_R1.3730.99
34_P37_V1.3650.99
49_L89_L1.3630.99
31_Y37_V1.3590.99
203_L250_L1.3510.99
51_Q54_I1.3510.99
25_V32_E1.3360.99
190_Y195_A1.3330.99
123_D127_K1.3300.99
54_I57_L1.3190.99
53_S116_A1.3160.99
50_L120_A1.2960.99
35_L39_L1.2730.99
69_R75_L1.2690.99
53_S56_R1.2530.99
253_R264_R1.2490.99
212_L216_A1.2280.98
250_L263_L1.2230.98
88_Y92_R1.2170.98
254_Q263_L1.2130.98
204_P265_T1.2100.98
251_E266_R1.2100.98
199_L241_S1.2090.98
207_E214_S1.2000.98
42_A48_D1.1980.98
127_K131_A1.1950.98
66_Q69_R1.1950.98
243_E246_K1.1930.98
241_S252_A1.1810.98
83_A235_A1.1800.98
132_L135_R1.1760.98
199_L237_T1.1740.98
212_L261_I1.1730.98
50_L93_L1.1720.98
88_Y91_S1.1690.97
65_V75_L1.1670.97
52_L93_L1.1580.97
67_Q70_R1.1520.97
43_R76_A1.1510.97
170_Y174_R1.1450.97
46_K65_V1.1400.97
116_A120_A1.1360.97
52_L112_A1.1260.97
93_L112_A1.1250.97
30_G47_V1.1250.97
28_I31_Y1.1230.97
94_L215_V1.1210.97
77_A87_A1.1200.96
45_Q60_Q1.1150.96
188_T236_S1.1110.96
64_F68_A1.1080.96
123_D244_L1.1080.96
36_H39_L1.1060.96
202_L215_V1.1050.96
112_A120_A1.0920.96
73_F76_A1.0620.95
136_P140_R1.0600.95
133_K137_I1.0510.94
124_V248_G1.0500.94
72_R75_L1.0470.94
190_Y233_Y1.0450.94
71_V87_A1.0380.94
235_A239_S1.0350.94
133_K136_P1.0330.94
230_P233_Y1.0310.94
211_V262_Y1.0280.94
199_L248_G1.0230.93
23_A26_I1.0220.93
203_L265_T1.0210.93
36_H126_R1.0200.93
168_S172_T1.0120.93
72_R79_Y1.0030.93
115_L118_R1.0030.93
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  
4i98A10.53651000.44Contact Map
3w6jA20.55471000.442Contact Map
3zgxC20.24451000.609Contact Map
4i99C20.240999.30.8Contact Map
1w1wE40.255595.80.906Contact Map
2l02A20.270162.50.942Contact Map
2l01A20.2774260.954Contact Map
2w2uA20.26286.30.965Contact Map
4a5xA20.266460.966Contact Map
4y66A30.27015.70.966Contact 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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