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glubp

ID: 1501768596 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 226 (223)
Sequences: 24260 (16534.1)
Seq/Len: 108.789
Nf(neff/√len): 1107.2

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: 108.789).

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
113_A151_A4.2241.00
8_A62_V3.6551.00
4_K44_E3.0691.00
38_E206_T2.7261.00
71_I76_K2.4921.00
136_F145_E2.4791.00
34_A212_T2.3341.00
6_V44_E2.2311.00
142_A154_V2.2191.00
58_Q78_A2.2051.00
56_A62_V2.1611.00
36_A43_Y2.1531.00
83_D205_K2.1431.00
56_A61_N2.1141.00
79_I188_A2.0951.00
38_E203_A2.0011.00
34_A37_K1.9911.00
156_H161_I1.9801.00
30_D219_K1.9741.00
197_R201_N1.9681.00
80_D197_R1.9571.00
121_V135_Q1.9521.00
6_V46_K1.9021.00
121_V125_K1.8781.00
145_E150_R1.8751.00
138_N141_N1.8661.00
212_T215_E1.8541.00
20_Q25_V1.8261.00
189_F197_R1.8151.00
82_S201_N1.8131.00
83_D201_N1.8011.00
71_I186_G1.7821.00
189_F200_V1.7781.00
214_N218_K1.7501.00
4_K42_D1.7281.00
73_D76_K1.6871.00
34_A207_L1.6701.00
103_S106_D1.6611.00
7_V32_W1.6361.00
95_K149_N1.6191.00
30_D220_W1.6121.00
87_K184_Q1.5931.00
93_M161_I1.5891.00
34_A38_E1.5881.00
205_K209_E1.5601.00
190_P193_S1.5541.00
35_I203_A1.5541.00
203_A207_L1.5511.00
91_L158_T1.5391.00
29_V33_A1.5331.00
203_A206_T1.5241.00
7_V64_L1.5221.00
112_V153_A1.5211.00
111_V134_R1.5201.00
136_F142_A1.5201.00
55_P59_T1.5111.00
39_L203_A1.5011.00
111_V152_D1.4911.00
18_F25_V1.4891.00
48_M56_A1.4771.00
53_I65_A1.4691.00
102_K106_D1.4681.00
94_V153_A1.4641.00
110_K152_D1.4291.00
123_Y127_N1.4201.00
145_E151_A1.4081.00
38_E210_N1.4081.00
28_D85_Y1.4060.99
113_A142_A1.3890.99
144_M148_T1.3820.99
116_S137_P1.3690.99
92_V153_A1.3430.99
69_I188_A1.3360.99
198_D202_G1.3160.99
144_M147_G1.3130.99
89_G158_T1.3120.99
199_K202_G1.3050.99
66_L187_I1.3020.99
212_T216_I1.2970.99
158_T162_L1.2930.99
64_L189_F1.2840.99
95_K98_N1.2700.99
94_V176_V1.2680.99
96_A174_K1.2640.99
146_L154_V1.2610.99
199_K203_A1.2500.99
146_L173_F1.2380.98
33_A45_L1.2320.98
19_K47_P1.2280.98
208_R213_Y1.2230.98
55_P58_Q1.2120.98
111_V132_D1.2100.98
194_D198_D1.2010.98
49_D52_G1.1860.98
81_F188_A1.1850.98
147_G172_Q1.1840.98
113_A136_F1.1760.98
80_D192_G1.1720.98
202_G206_T1.1590.97
38_E212_T1.1580.97
116_S135_Q1.1400.97
54_I79_I1.1360.97
206_T210_N1.1170.96
134_R145_E1.1140.96
72_T75_R1.1080.96
32_W66_L1.0950.96
142_A145_E1.0940.96
8_A53_I1.0920.96
80_D191_K1.0910.96
114_V121_V1.0800.95
20_Q23_L1.0770.95
31_L213_Y1.0690.95
80_D194_D1.0610.95
137_P141_N1.0580.95
90_L120_S1.0480.94
94_V174_K1.0480.94
27_F217_Y1.0440.94
201_N205_K1.0410.94
52_G56_A1.0350.94
25_V30_D1.0290.94
207_L212_T1.0160.93
41_L199_K1.0030.93
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  
1wdnA10.98671000.004Contact Map
4powA20.99121000.008Contact Map
3k4uA611000.023Contact Map
3kzgA40.9691000.026Contact Map
4ohnA10.99561000.027Contact Map
3h7mA10.99561000.029Contact Map
3hv1A20.99561000.032Contact Map
3kbrA10.96021000.036Contact Map
4c0rA20.99561000.037Contact Map
3i6vA10.94691000.042Contact 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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