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T0843

ID: 1404412385 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 369 (351)
Sequences: 32380 (21779.6)
Seq/Len: 92.251
Nf(neff/√len): 1162.5

HHblits Results: (2013_03)
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: 92.251).

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
266_F359_E4.6331.00
270_E362_V4.0361.00
310_A367_S3.9911.00
114_E149_E3.8601.00
19_A23_A3.2971.00
266_F355_E3.2781.00
135_D138_R3.2321.00
140_A148_R3.0501.00
39_A251_E2.8691.00
354_T357_D2.7021.00
16_D20_E2.6091.00
74_E121_T2.5271.00
306_K309_A2.4861.00
112_D116_K2.4791.00
140_A156_V2.4741.00
74_E118_S2.4581.00
262_E355_E2.4371.00
360_H364_T2.3991.00
259_L263_N2.3441.00
110_L142_I2.3201.00
112_D115_R2.3141.00
74_E97_T2.3001.00
110_L138_R2.2971.00
266_F270_E2.2831.00
270_E359_E2.2731.00
138_R141_G2.2621.00
265_A269_K2.2081.00
270_E273_G2.1991.00
12_P16_D2.1771.00
124_I147_E2.1291.00
73_D122_R2.0891.00
38_S42_A2.0861.00
141_G149_E2.0831.00
74_E95_R2.0771.00
114_E150_H2.0561.00
100_D112_D2.0491.00
15_L19_A2.0341.00
347_L361_V2.0131.00
39_A247_L2.0111.00
306_K310_A2.0041.00
74_E120_A1.9751.00
152_F155_A1.9301.00
52_V58_G1.9151.00
310_A364_T1.9061.00
312_I364_T1.8441.00
48_R202_D1.8391.00
307_M314_A1.8011.00
79_P100_D1.7971.00
147_E156_V1.7541.00
255_E258_R1.7461.00
305_R309_A1.7431.00
259_L262_E1.7351.00
123_A157_I1.7271.00
147_E152_F1.7081.00
62_A179_M1.7071.00
160_C180_C1.7061.00
102_D105_T1.7031.00
118_S121_T1.7011.00
258_R262_E1.7001.00
114_E142_I1.6941.00
199_L205_H1.6841.00
355_E359_E1.6821.00
109_D112_D1.6711.00
99_V116_K1.6601.00
137_D141_G1.6471.00
126_V139_L1.6431.00
299_D302_A1.6411.00
124_I152_F1.6231.00
76_L121_T1.6121.00
13_T248_A1.6111.00
148_R178_N1.6071.00
114_E118_S1.6051.00
15_L23_A1.5931.00
53_H57_S1.5881.00
270_E363_A1.5781.00
142_I150_H1.5701.00
270_E366_R1.5661.00
111_D114_E1.5641.00
125_I157_I1.5621.00
268_D293_Y1.5561.00
360_H363_A1.5441.00
59_L84_A1.5291.00
306_K368_G1.5171.00
202_D206_E1.5071.00
68_A94_R1.4891.00
248_A251_E1.4891.00
113_L139_L1.4861.00
47_P202_D1.4721.00
114_E138_R1.4531.00
274_V366_R1.4521.00
16_D19_A1.4371.00
18_V22_F1.4331.00
266_F358_R1.4311.00
58_G181_V1.4171.00
261_R265_A1.4050.99
102_D109_D1.3760.99
302_A306_K1.3620.99
263_N358_R1.3570.99
111_D115_R1.3490.99
268_D272_T1.3480.99
59_L181_V1.3470.99
73_D120_A1.3460.99
303_F365_I1.3340.99
359_E363_A1.3330.99
312_I361_V1.3300.99
13_T252_T1.3220.99
20_E24_S1.3110.99
97_T116_K1.3020.99
296_K343_R1.2930.99
273_G366_R1.2820.99
263_N355_E1.2720.99
117_I142_I1.2600.99
157_I181_V1.2540.99
363_A367_S1.2520.99
278_E296_K1.2420.98
39_A42_A1.2380.98
267_Y349_V1.2330.98
269_K273_G1.2330.98
59_L157_I1.2320.98
76_L116_K1.2140.98
40_L196_L1.2120.98
357_D360_H1.2040.98
66_L155_A1.1930.98
362_V366_R1.1910.98
307_M364_T1.1900.98
15_L22_F1.1850.98
182_F196_L1.1830.98
117_I121_T1.1800.98
267_Y270_E1.1740.98
305_R308_E1.1730.98
111_D138_R1.1660.97
35_E39_A1.1630.97
31_P35_E1.1500.97
266_F362_V1.1460.97
118_S150_H1.1330.97
259_L355_E1.1320.97
69_P73_D1.1250.97
269_K272_T1.1200.96
55_G181_V1.1200.96
262_E266_F1.1160.96
361_V365_I1.1150.96
117_I152_F1.1140.96
263_N266_F1.1090.96
34_A38_S1.0970.96
60_C64_R1.0770.95
62_A157_I1.0770.95
137_D172_P1.0750.95
99_V112_D1.0750.95
356_Q359_E1.0690.95
20_E32_R1.0640.95
36_F246_G1.0550.95
79_P98_W1.0530.95
179_M199_L1.0520.95
35_E247_L1.0450.94
20_E23_A1.0440.94
12_P23_A1.0330.94
304_H314_A1.0290.94
274_V362_V1.0230.93
303_F345_V1.0190.93
75_V89_I1.0170.93
248_A252_T1.0160.93
303_F368_G1.0140.93
169_R172_P1.0100.93
307_M312_I1.0090.93
239_T242_N1.0050.93
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: (28Jun14)
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  
3dr4A40.96481000.267Contact Map
3frkA20.95661000.268Contact Map
4lc3A20.97021000.273Contact Map
3b8xA20.96481000.277Contact Map
2fnuA20.97021000.283Contact Map
1mdoA10.96211000.285Contact Map
2c81A10.96481000.286Contact Map
4qgrA20.95661000.292Contact Map
1b9hA10.96211000.294Contact Map
3bb8A20.97561000.294Contact 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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