GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
KNL1_vertebrates -force run

ID: 1517037681 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 451 (318)
Sequences: 13121 (11921.2)
Seq/Len: 41.261
Nf(neff/√len): 668.5

Jackhmmer Results: (2016_04)
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: 41.261).

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 > 50% 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
71_I74_L2.1371.00
199_L202_L1.9251.00
192_T195_A1.9001.00
247_S250_D1.8611.00
234_T238_E1.8311.00
152_I156_D1.7931.00
138_V142_Q1.7821.00
145_R148_L1.7601.00
152_I155_M1.7361.00
159_L162_I1.7331.00
206_E209_F1.7241.00
215_E219_Q1.7231.00
166_L169_V1.7091.00
138_V141_A1.7081.00
173_T177_E1.6851.00
254_W257_D1.6651.00
145_R149_Q1.6561.00
227_I230_M1.6421.00
78_A81_Q1.6271.00
227_I231_Q1.6021.00
66_A70_K1.5971.00
234_T237_T1.5901.00
199_L203_K1.5641.00
229_F233_Q1.5381.00
159_L163_D1.5331.00
236_R240_L1.5251.00
64_C67_R1.5201.00
213_L216_L1.5191.00
247_S251_V1.5101.00
220_K224_L1.4941.00
226_Q229_F1.4921.00
207_E211_R1.4901.00
194_T198_E1.4811.00
108_G112_N1.4701.00
80_N84_L1.4651.00
351_C354_L1.4431.00
187_E191_E1.4401.00
57_I60_Y1.4371.00
167_I170_E1.4361.00
131_V134_Y1.4311.00
225_A229_F1.4281.00
73_E77_S1.4171.00
104_L108_G1.4070.99
124_V128_Q1.4040.99
192_T196_E1.3980.99
63_D68_R1.3890.99
70_K75_K1.3840.99
112_N116_S1.3820.99
172_E177_E1.3740.99
64_C68_R1.3700.99
257_D260_V1.3680.99
233_Q238_E1.3650.99
134_Y138_V1.3610.99
185_V188_W1.3570.99
158_I161_K1.3540.99
172_E175_N1.3490.99
222_Q226_Q1.3480.99
214_L218_V1.3450.99
147_K151_K1.3430.99
79_S82_D1.3360.99
235_N239_E1.3350.99
347_V351_C1.3320.99
166_L170_E1.3160.99
173_T176_L1.3150.99
163_D167_I1.3150.99
76_L80_N1.3140.99
175_N179_E1.3140.99
161_K165_C1.3080.99
220_K223_T1.3040.99
201_Q205_E1.3030.99
183_N187_E1.3020.99
185_V189_D1.3000.99
68_R72_E1.3000.99
221_E225_A1.2970.99
200_E203_K1.2960.99
193_R196_E1.2920.99
58_Q62_Q1.2920.99
260_V265_Y1.2910.99
223_T227_I1.2850.99
209_F213_L1.2800.99
213_L217_E1.2790.99
74_L78_A1.2710.99
207_E210_Q1.2520.99
127_H131_V1.2500.99
228_D232_K1.2390.98
143_N147_K1.2360.98
94_E98_H1.2340.98
204_T208_E1.2300.98
259_A263_F1.2290.98
253_E256_D1.2280.98
239_E243_Q1.2260.98
136_K140_S1.2220.98
212_N217_E1.2220.98
132_A136_K1.2170.98
169_V173_T1.2170.98
63_D66_A1.2090.98
226_Q231_Q1.2080.98
78_A82_D1.2070.98
132_A135_G1.2040.98
79_S83_K1.2040.98
186_E189_D1.2010.98
56_K60_Y1.2000.98
124_V127_H1.1990.98
193_R197_K1.1940.98
154_E158_I1.1900.98
206_E210_Q1.1860.98
151_K154_E1.1860.98
109_I113_K1.1830.98
59_I63_D1.1750.98
241_L244_L1.1740.98
72_E75_K1.1700.97
111_L115_K1.1680.97
231_Q235_N1.1680.97
141_A145_R1.1680.97
197_K201_Q1.1620.97
235_N238_E1.1560.97
144_E149_Q1.1560.97
350_H353_L1.1540.97
77_S80_N1.1490.97
70_K73_E1.1460.97
261_F264_V1.1410.97
174_K177_E1.1400.97
363_T366_P1.1350.97
128_Q132_A1.1330.97
168_E172_E1.1320.97
139_Q143_N1.1290.97
156_D160_K1.1290.97
60_Y64_C1.1260.97
134_Y137_L1.1260.97
221_E224_L1.1250.97
70_K74_L1.1250.97
195_A199_L1.1210.97
189_D193_R1.1210.97
240_L245_S1.1190.96
357_E360_Y1.1180.96
106_A110_Y1.1170.96
350_H355_G1.1150.96
139_Q142_Q1.1150.96
344_F347_V1.1120.96
146_E149_Q1.1120.96
162_I166_L1.1090.96
208_E212_N1.1090.96
155_M159_L1.1090.96
249_W253_E1.1090.96
148_L152_I1.1080.96
345_S349_N1.1030.96
56_K59_I1.1030.96
165_C168_E1.1020.96
184_L187_E1.1020.96
174_K178_D1.1010.96
358_I361_L1.0990.96
167_I171_I1.0980.96
198_E203_K1.0960.96
72_E76_L1.0900.96
224_L228_D1.0900.96
44_E48_L1.0880.96
126_T130_K1.0880.96
203_K207_E1.0880.96
186_E190_S1.0880.96
182_D186_E1.0850.96
246_V250_D1.0820.96
69_Q73_E1.0780.95
58_Q61_R1.0710.95
125_F128_Q1.0690.95
352_R356_E1.0680.95
171_I175_N1.0640.95
140_S144_E1.0640.95
144_E147_K1.0640.95
202_L205_E1.0620.95
219_Q222_Q1.0580.95
184_L189_D1.0540.95
347_V350_H1.0530.95
214_L217_E1.0530.95
238_E242_D1.0520.95
256_D260_V1.0510.94
61_R65_E1.0510.94
135_G139_Q1.0510.94
230_M234_T1.0510.94
342_Q346_L1.0510.94
157_K160_K1.0510.94
130_K133_L1.0500.94
252_V256_D1.0500.94
209_F212_N1.0480.94
149_Q153_D1.0450.94
74_L77_S1.0410.94
334_Q338_P1.0350.94
205_E210_Q1.0320.94
212_N215_E1.0310.94
260_V263_F1.0310.94
55_P58_Q1.0300.94
223_T226_Q1.0290.94
205_E208_E1.0270.94
81_Q84_L1.0260.94
78_A85_L1.0240.93
360_Y364_W1.0180.93
262_T266_D1.0150.93
125_F129_G1.0140.93
198_E201_Q1.0120.93
111_L114_I1.0030.93
83_K87_D1.0030.93
77_S82_D1.0020.92
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  
4nfaA10.450199.60.666Contact Map
1i84S20.261698.90.77Contact Map
3vkgA20.951298.40.809Contact Map
1c1gA40.629798.20.817Contact Map
2dfsA20.390297.10.854Contact Map
4uxvA10.8115970.856Contact Map
2v71A20.354896.60.864Contact Map
4linA120.609896.40.867Contact Map
3tnuB10.210696.20.87Contact Map
3tnuA10.199696.10.87Contact 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.

Page generated in 0.0293 seconds.