GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0819

ID: 1402705425 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 373 (360)
Sequences: 5539 (4224.1)
Seq/Len: 15.386
Nf(neff/√len): 222.6

Jackhmmer Results: (2014_04_16)
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: 15.386).

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
235_I265_A3.8281.00
288_R357_D3.8191.00
330_H365_E3.6641.00
76_A270_A3.4301.00
292_I360_A3.1211.00
348_I359_L2.8281.00
179_V214_D2.6711.00
110_A158_P2.4801.00
285_S288_R2.4191.00
179_V183_Q2.3981.00
240_S245_A2.3801.00
174_P177_R2.3461.00
285_S353_D2.3201.00
292_I295_D2.2171.00
182_A218_V2.1411.00
53_L57_Q2.1411.00
289_I350_T2.1411.00
101_I219_I2.1181.00
83_T239_L2.1091.00
219_I240_S2.0731.00
285_S356_M2.0691.00
91_G97_L2.0601.00
101_I192_V2.0521.00
296_S364_P2.0421.00
70_N262_V1.9541.00
352_P355_E1.9471.00
118_G163_A1.9441.00
48_A271_D1.9021.00
111_P153_G1.8911.00
126_V131_G1.8771.00
290_G308_V1.8761.00
123_N135_T1.8561.00
145_L181_F1.8321.00
330_H362_A1.7911.00
182_A191_L1.7841.00
289_I356_M1.7811.00
111_P132_R1.7801.00
77_L88_I1.7571.00
86_A242_P1.7491.00
17_S20_F1.7491.00
288_R292_I1.7401.00
80_H272_Q1.7361.00
114_T133_L1.7351.00
64_K355_E1.7281.00
45_F281_K1.7201.00
89_A245_A1.7131.00
323_V326_L1.6841.00
76_A266_I1.6771.00
299_A311_D1.6721.00
75_Q85_P1.6641.00
146_E180_A1.6461.00
144_D147_G1.6441.00
292_I364_P1.6421.00
310_V348_I1.6391.00
80_H228_Y1.6251.00
111_P134_V1.6151.00
84_S87_N1.6111.00
55_I260_I1.6101.00
152_V157_A1.6021.00
175_A179_V1.5891.00
161_Y192_V1.5871.00
112_V126_V1.5801.00
77_L237_Y1.5681.00
89_A238_T1.5621.00
52_L56_R1.5361.00
190_L244_T1.5341.00
219_I238_T1.5301.00
101_I159_L1.5211.00
67_D71_H1.5211.00
123_N127_A1.5161.00
197_Y225_S1.5151.00
106_V131_G1.5091.00
272_Q276_K1.5071.00
111_P157_A1.5061.00
183_Q215_K1.5041.00
99_G103_R1.5011.00
98_L221_A1.5001.00
186_P189_T1.5001.00
287_Q291_R1.4961.00
288_R353_D1.4711.00
81_L237_Y1.4661.00
102_V161_Y1.4631.00
92_E258_S1.4611.00
74_K249_D1.4561.00
72_D266_I1.4501.00
78_A84_S1.4491.00
294_A302_P1.4451.00
246_Q250_K1.4241.00
325_R329_D1.4171.00
139_A144_D1.4151.00
353_D357_D1.4091.00
111_P156_N1.4030.99
196_A223_T1.3820.99
247_A250_K1.3740.99
358_L362_A1.3720.99
280_L284_N1.3720.99
200_T282_I1.3660.99
36_A332_I1.3660.99
98_L125_H1.3620.99
96_G256_G1.3600.99
311_D344_R1.3590.99
113_V160_V1.3590.99
55_I264_A1.3540.99
310_V359_L1.3430.99
47_P274_Y1.3420.99
290_G300_P1.3410.99
77_L269_L1.3350.99
139_A142_R1.3350.99
87_N242_P1.3210.99
54_A267_A1.3190.99
294_A300_P1.3040.99
73_L77_L1.3000.99
238_T248_F1.2850.99
202_P283_A1.2840.99
235_I261_G1.2830.99
79_R270_A1.2770.99
276_K280_L1.2750.99
152_V185_L1.2690.99
292_I296_S1.2560.99
134_V153_G1.2520.99
288_R360_A1.2500.99
324_D329_D1.2380.98
142_R177_R1.2350.98
351_A355_E1.2300.98
75_Q79_R1.2280.98
322_I326_L1.2270.98
153_G157_A1.2180.98
162_L173_W1.2160.98
249_D252_R1.2120.98
81_L239_L1.2080.98
88_I239_L1.2070.98
50_S271_D1.2040.98
97_L238_T1.2040.98
94_I221_A1.2010.98
136_V151_A1.1970.98
70_N90_I1.1840.98
258_S261_G1.1830.98
309_A342_L1.1820.98
34_I358_L1.1810.98
166_D169_M1.1800.98
20_F23_P1.1750.98
106_V112_V1.1740.98
295_D364_P1.1720.98
172_W304_A1.1620.97
36_A355_E1.1610.97
149_L184_A1.1590.97
271_D274_Y1.1540.97
180_A184_A1.1530.97
100_Q252_R1.1490.97
356_M360_A1.1480.97
43_S278_V1.1460.97
143_E148_L1.1410.97
262_V266_I1.1320.97
357_D361_A1.1310.97
40_A255_F1.1280.97
53_L56_R1.1270.97
216_P243_G1.1230.97
284_N353_D1.1220.97
289_I308_V1.1220.97
73_L265_A1.1120.96
277_E281_K1.1100.96
325_R366_V1.1070.96
115_S143_E1.1060.96
185_L191_L1.1050.96
104_L251_I1.1010.96
222_R237_Y1.0990.96
358_L361_A1.0960.96
332_I358_L1.0920.96
228_Y272_Q1.0890.96
290_G294_A1.0880.96
208_P211_S1.0860.96
47_P52_L1.0860.96
77_L90_I1.0840.96
159_L192_V1.0840.96
147_G150_A1.0790.95
252_R256_G1.0770.95
175_A210_E1.0660.95
179_V215_K1.0560.95
77_L81_L1.0500.94
145_L149_L1.0480.94
212_L239_L1.0450.94
176_E179_V1.0440.94
51_V267_A1.0350.94
147_G151_A1.0290.94
177_R180_A1.0270.94
49_P53_L1.0210.93
50_S53_L1.0130.93
334_I346_I1.0120.93
227_A279_T1.0090.93
285_S357_D1.0050.93
98_L161_Y1.0040.93
179_V211_S1.0000.92
332_I362_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: (07Jun14)
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  
1fg7A10.92231000.446Contact Map
3getA20.96251000.451Contact Map
3ffhA20.94641000.452Contact Map
3hdoA20.92491000.476Contact Map
3ly1A40.93831000.485Contact Map
3eucA20.9331000.49Contact Map
3cq5A30.93571000.491Contact Map
1lc5A10.92761000.5Contact Map
3ftbA40.87671000.501Contact Map
3p1tA40.86331000.504Contact 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 0.0356 seconds.