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scEMC2

ID: 1504851007 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 292 (276)
Sequences: 1370 (929.4)
Seq/Len: 4.964
Nf(neff/√len): 55.9

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: 4.964).

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
101_N104_G4.5251.00
178_Q181_K4.3711.00
66_Q69_D3.1681.00
144_S147_S3.0081.00
247_V251_S2.9441.00
149_L169_A2.3551.00
227_L250_I2.2601.00
173_Y181_K1.9861.00
166_W185_C1.9831.00
256_R265_L1.9321.00
212_L215_K1.9181.00
282_K286_E1.9061.00
183_C203_L1.8831.00
75_N92_K1.8431.00
203_L207_L1.8041.00
169_A173_Y1.7811.00
222_L225_K1.7681.00
169_A185_C1.7681.00
155_L165_L1.6960.99
231_L251_S1.6920.99
57_L61_L1.6200.99
93_A109_L1.6010.99
106_I110_E1.5950.99
234_V244_W1.5630.99
71_Q99_N1.5070.99
153_V169_A1.5010.98
58_F74_Y1.4940.98
152_V169_A1.4760.98
89_V108_Y1.4450.98
170_S186_L1.4420.98
234_V243_G1.4320.98
145_Q172_I1.4030.97
287_L290_N1.3750.97
231_L247_V1.3630.97
74_Y91_M1.3580.97
183_C206_T1.3520.97
146_E176_M1.3240.96
224_E254_L1.3190.96
156_T166_W1.3010.95
218_T223_L1.2950.95
167_W202_R1.2790.95
173_Y178_Q1.2670.94
183_C187_E1.2660.94
58_F88_M1.2640.94
227_L247_V1.2590.94
189_V199_C1.2570.94
149_L176_M1.2530.94
201_G205_E1.2470.94
15_N18_A1.2330.93
267_A289_L1.2330.93
274_S282_K1.2200.93
30_L34_M1.2190.93
20_T29_Q1.2170.93
107_E111_N1.2120.93
26_Q33_E1.2060.92
137_K147_S1.2040.92
170_S185_C1.2030.92
233_S236_L1.2030.92
149_L173_Y1.1950.92
280_K283_I1.1950.92
28_L35_K1.1950.92
14_M18_A1.1940.92
268_S272_E1.1890.92
250_I254_L1.1860.92
26_Q29_Q1.1850.91
149_L172_I1.1820.91
230_A246_L1.1720.91
286_E290_N1.1560.90
29_Q36_I1.1560.90
22_F33_E1.1540.90
285_A289_L1.1440.89
85_S88_M1.1400.89
230_A247_V1.1400.89
71_Q92_K1.1390.89
233_S243_G1.1320.89
60_V64_R1.1300.89
31_E35_K1.1230.88
18_A34_M1.1220.88
22_F34_M1.1200.88
26_Q34_M1.1160.88
248_N281_D1.1110.88
25_E28_L1.1070.87
284_T287_L1.1060.87
131_K152_V1.1060.87
25_E29_Q1.1010.87
232_R235_E1.0990.87
38_M42_D1.0960.87
281_D285_A1.0940.86
100_G177_G1.0900.86
162_D165_L1.0810.86
27_L30_L1.0780.85
26_Q32_N1.0780.85
32_N36_I1.0750.85
15_N19_Y1.0710.85
155_L170_S1.0710.85
63_Y93_A1.0680.85
24_P28_L1.0670.85
22_F25_E1.0650.84
271_K275_A1.0650.84
138_T172_I1.0620.84
103_K107_E1.0530.84
65_N177_G1.0520.83
32_N39_K1.0450.83
27_L31_E1.0410.83
13_I23_N1.0330.82
137_K144_S1.0300.82
75_N79_D1.0240.81
31_E34_M1.0140.80
89_V112_L1.0120.80
25_E34_M1.0120.80
25_E30_L1.0100.80
24_P36_I1.0080.80
88_M226_A1.0080.80
160_P194_P1.0080.80
283_I287_L1.0070.80
25_E32_N1.0010.79
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  
3dssA10.8871000.406Contact Map
3q7aA10.8871000.411Contact Map
4l9pA10.88361000.413Contact Map
4ui9C201000.42Contact Map
1w3bA20.90411000.423Contact Map
2h6fA10.88361000.434Contact Map
4ui9J101000.437Contact Map
4eqfA10.83561000.44Contact Map
3draA10.87671000.444Contact Map
2xpiA20.90411000.449Contact 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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