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T0854

ID: 1405362914 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 212 (201)
Sequences: 13054 (10284)
Seq/Len: 64.945
Nf(neff/√len): 725.4

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: 64.945).

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
172_G177_D5.0571.00
11_K167_E4.1711.00
156_K160_H2.8641.00
127_R132_D2.7321.00
104_D134_Y2.5431.00
146_N150_H2.5121.00
158_L168_A2.4731.00
182_E198_A2.4201.00
12_A163_I2.4031.00
156_K159_E2.3581.00
111_G136_S2.2441.00
100_R104_D2.1771.00
116_T122_M2.1671.00
10_I187_P2.1411.00
15_Y112_L2.1161.00
115_C153_P2.0761.00
202_E206_E2.0581.00
179_L183_A2.0151.00
181_A188_F2.0081.00
107_K136_S1.9951.00
45_S48_N1.9701.00
113_G137_I1.9361.00
158_L186_V1.9271.00
178_R188_F1.8161.00
146_N152_E1.8071.00
164_G167_E1.7821.00
112_L135_F1.7451.00
14_I115_C1.7311.00
170_F181_A1.6751.00
99_F204_H1.6701.00
158_L165_P1.6641.00
13_V171_V1.6601.00
20_V171_V1.6501.00
187_P198_A1.6091.00
137_I160_H1.5921.00
107_K134_Y1.5751.00
13_V106_L1.5601.00
163_I168_A1.5571.00
203_H206_E1.4921.00
154_L172_G1.4801.00
13_V110_V1.4781.00
14_I157_V1.4601.00
12_A161_F1.4401.00
105_T109_R1.4161.00
17_C22_F1.4020.99
21_M99_F1.3980.99
14_I170_F1.3780.99
98_G101_E1.3670.99
62_E65_A1.3670.99
18_D24_S1.3430.99
105_T208_I1.3360.99
113_G161_F1.3330.99
34_R85_D1.3290.99
17_C122_M1.3260.99
95_M131_L1.2910.99
168_A186_V1.2770.99
139_M160_H1.2610.99
102_A208_I1.2450.98
123_D132_D1.2370.98
170_F177_D1.2220.98
34_R38_M1.2220.98
14_I168_A1.2180.98
154_L170_F1.1870.98
169_L189_V1.1840.98
139_M157_V1.1770.98
115_C157_V1.1730.98
178_R197_A1.1720.98
154_L177_D1.1620.97
122_M140_T1.1540.97
10_I169_L1.1480.97
116_T140_T1.1420.97
175_E179_L1.1410.97
199_Y210_L1.1400.97
189_V201_M1.1380.97
105_T108_G1.1380.97
78_V82_G1.1350.97
114_V135_F1.1280.97
12_A168_A1.1190.96
104_D108_G1.1170.96
12_A111_G1.0990.96
18_D118_R1.0970.96
101_E205_R1.0940.96
145_T152_E1.0920.96
106_L110_V1.0910.96
123_D127_R1.0910.96
20_V177_D1.0810.95
38_M85_D1.0770.95
154_L186_V1.0760.95
201_M207_I1.0750.95
17_C114_V1.0730.95
35_I39_M1.0720.95
152_E156_K1.0530.95
107_K112_L1.0500.94
38_M79_R1.0460.94
151_P155_L1.0460.94
17_C118_R1.0410.94
170_F186_V1.0350.94
14_I186_V1.0330.94
101_E104_D1.0300.94
76_E79_R1.0300.94
154_L180_S1.0220.93
102_A204_H1.0200.93
137_I161_F1.0100.93
34_R37_E1.0040.93
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: (12Jul14)
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  
2om6A20.96231000.258Contact Map
2nyvA10.94341000.29Contact Map
3ed5A10.94341000.311Contact Map
4eekA10.94341000.312Contact Map
2hszA20.96231000.316Contact Map
3l5kA10.96231000.32Contact Map
4g9bA10.94811000.322Contact Map
3qxgA20.93871000.323Contact Map
3smvA10.94341000.324Contact Map
2zg6A20.86791000.327Contact 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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