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Prasanth Kumar

ID: 1499887159 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 364 (300)
Sequences: 4289 (2784)
Seq/Len: 14.297
Nf(neff/√len): 160.7

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: 14.297).

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
67_S103_T5.5761.00
94_N177_W3.9621.00
237_L241_Q3.5481.00
152_W157_K3.1611.00
94_N143_S3.0891.00
146_I176_S2.9691.00
84_L89_N2.8661.00
119_F122_G2.3701.00
126_C203_C2.3351.00
240_L244_L2.1461.00
236_M240_L2.0631.00
68_V100_L2.0381.00
281_W311_A2.0351.00
232_L278_C2.0271.00
99_D140_G1.9801.00
152_W156_C1.9141.00
96_A99_D1.9041.00
171_V175_F1.9021.00
75_L100_L1.8921.00
99_D318_N1.8781.00
276_A321_I1.8721.00
124_P128_L1.8701.00
146_I172_G1.8491.00
150_E154_V1.7971.00
131_Y135_L1.7901.00
70_T316_I1.7831.00
244_L248_A1.7601.00
234_I238_C1.7381.00
90_W173_I1.7321.00
75_L93_V1.7111.00
313_S317_Y1.6841.00
98_A139_T1.6431.00
101_A136_C1.6101.00
123_H127_V1.6091.00
269_M325_M1.6091.00
165_D168_L1.5511.00
157_K160_G1.5251.00
72_G100_L1.5131.00
68_V103_T1.5041.00
152_W241_Q1.5021.00
131_Y188_I1.4811.00
94_N173_I1.4701.00
86_H89_N1.4661.00
74_V319_P1.4641.00
185_A189_F1.4551.00
145_A238_C1.4291.00
98_A177_W1.4241.00
142_W179_W1.3970.99
172_G176_S1.3930.99
91_I147_I1.3900.99
177_W319_P1.3900.99
167_K171_V1.3790.99
244_L247_R1.3690.99
143_S177_W1.3570.99
126_C319_P1.3540.99
241_Q244_L1.3500.99
70_T318_N1.3450.99
143_S173_I1.3430.99
263_E267_T1.3400.99
144_L235_I1.3290.99
149_W238_C1.3180.99
98_A140_G1.3010.99
75_L97_V1.2990.99
85_R89_N1.2960.99
51_W55_L1.2900.99
72_G76_A1.2840.99
148_S238_C1.2700.99
91_I169_A1.2670.99
232_L236_M1.2650.99
78_T93_V1.2640.99
154_V158_P1.2570.99
74_V96_A1.2480.99
303_M307_P1.2340.98
91_I150_E1.2320.98
243_W247_R1.2230.98
286_F290_F1.2200.98
155_V159_F1.2150.98
152_W238_C1.2150.98
272_V325_M1.2140.98
108_T111_I1.2080.98
122_G125_M1.2010.98
329_F333_I1.1990.98
222_V226_T1.1970.98
103_T326_N1.1890.98
167_K170_I1.1730.98
95_L322_Y1.1670.97
239_Y319_P1.1650.97
100_L103_T1.1630.97
183_W222_V1.1610.97
228_C277_Y1.1610.97
145_A234_I1.1580.97
221_I225_V1.1480.97
70_T96_A1.1450.97
96_A322_Y1.1370.97
99_D314_A1.1370.97
155_V158_P1.1360.97
112_V121_L1.1330.97
74_V322_Y1.1300.97
91_I143_S1.1250.97
74_V323_V1.1220.97
148_S235_I1.1200.96
170_I174_A1.1190.96
174_A178_I1.1090.96
135_L181_A1.1020.96
284_Y311_A1.1010.96
67_S316_I1.1000.96
243_W246_I1.0950.96
46_H49_P1.0880.96
186_P219_Y1.0820.96
81_F332_C1.0820.96
185_A188_I1.0750.95
228_C282_G1.0750.95
306_L310_F1.0710.95
103_T147_I1.0660.95
139_T143_S1.0620.95
237_L240_L1.0600.95
139_T180_S1.0540.95
74_V281_W1.0530.95
119_F126_C1.0460.94
51_W54_H1.0450.94
321_I325_M1.0390.94
241_Q245_A1.0350.94
149_W153_L1.0340.94
142_W180_S1.0330.94
77_A329_F1.0330.94
171_V174_A1.0320.94
49_P52_V1.0310.94
249_V253_Q1.0270.94
235_I238_C1.0270.94
140_G318_N1.0230.93
173_I180_S1.0170.93
138_I223_L1.0170.93
145_A235_I1.0170.93
271_V275_F1.0150.93
191_W246_I1.0130.93
239_Y274_I1.0070.93
74_V329_F1.0040.93
46_H50_R1.0040.93
242_V270_V1.0020.92
74_V78_T1.0020.92
151_R314_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: (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  
1u19A20.94781000.335Contact Map
4pxzA10.76371000.349Contact Map
4iarA10.7721000.351Contact Map
4zwjA401000.355Contact Map
2rh1A10.78851000.362Contact Map
3uonA10.77471000.364Contact Map
3pblA20.74731000.365Contact Map
4s0vA10.77751000.375Contact Map
3vw7A10.77751000.375Contact Map
3oduA20.82691000.376Contact 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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