OPENSEQ.org
knl1

ID: 1517068441 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 451 (408)
Sequences: 1065 (924.2)
Seq/Len: 2.610
Nf(neff/√len): 45.8

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: 2.610).

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
255_S270_L1.9920.99
192_T195_A1.9010.99
208_E212_N1.7990.99
257_D265_Y1.7820.98
193_R196_E1.7600.98
206_E210_Q1.7510.98
253_E257_D1.7420.98
192_T199_L1.6900.98
192_T219_Q1.6860.98
126_T129_G1.6640.97
259_A275_G1.6290.97
256_D260_V1.6230.97
212_N219_Q1.6110.97
192_T196_E1.5510.96
275_G291_K1.5510.96
238_E242_D1.5460.95
259_A263_F1.5440.95
250_D264_V1.5420.95
261_F274_F1.5200.95
202_L230_M1.5150.95
79_S82_D1.4800.94
62_Q66_A1.4700.94
195_A199_L1.4640.93
205_E215_E1.4590.93
266_D296_N1.4330.92
185_V189_D1.4300.92
192_T205_E1.4210.92
261_F269_E1.4180.92
234_T238_E1.4120.92
246_V272_I1.4110.92
263_F270_L1.4010.91
255_S261_F1.3940.91
279_V289_I1.3780.90
249_W275_G1.3590.90
259_A266_D1.3540.89
212_N215_E1.3460.89
270_L277_S1.3420.89
206_E209_F1.3400.89
188_W191_E1.3350.88
219_Q231_Q1.3300.88
260_V270_L1.3260.88
196_E212_N1.3210.88
258_Q263_F1.3200.88
249_W277_S1.3180.88
249_W260_V1.3150.87
192_T227_I1.3150.87
107_F110_Y1.3120.87
249_W257_D1.3110.87
249_W261_F1.3080.87
89_N203_K1.3070.87
66_A69_Q1.2910.86
130_K133_L1.2900.86
63_D66_A1.2700.85
196_E237_T1.2690.85
71_I74_L1.2670.85
203_K207_E1.2610.84
215_E241_L1.2550.84
107_F111_L1.2540.84
95_K170_E1.2540.84
259_A270_L1.2500.83
26_P29_S1.2500.83
266_D275_G1.2490.83
253_E259_A1.2490.83
253_E263_F1.2420.83
207_E211_R1.2390.83
108_G112_N1.2360.83
220_K230_M1.2360.83
220_K249_W1.2340.82
251_V257_D1.2260.82
236_R241_L1.2260.82
258_Q276_E1.2200.81
74_L77_S1.2190.81
104_L110_Y1.2170.81
233_Q236_R1.2140.81
263_F277_S1.2140.81
103_E107_F1.2140.81
260_V274_F1.2130.81
291_K297_F1.2100.81
249_W270_L1.2080.81
140_S144_E1.2020.80
159_L162_I1.2000.80
196_E199_L1.2000.80
257_D277_S1.1980.80
270_L275_G1.1960.80
215_E219_Q1.1960.80
266_D298_Q1.1950.80
111_L115_K1.1890.79
82_D115_K1.1880.79
136_K151_K1.1870.79
208_E226_Q1.1830.79
200_E204_T1.1820.78
256_D278_V1.1800.78
65_E68_R1.1770.78
124_V128_Q1.1750.78
227_I232_K1.1740.78
183_N187_E1.1740.78
289_I294_D1.1700.78
192_T241_L1.1680.77
159_L170_E1.1680.77
238_E241_L1.1680.77
174_K178_D1.1660.77
72_E80_N1.1640.77
220_K224_L1.1630.77
210_Q214_L1.1620.77
179_E182_D1.1610.77
227_I230_M1.1610.77
202_L206_E1.1600.77
99_C110_Y1.1580.76
111_L114_I1.1550.76
151_K154_E1.1540.76
199_L203_K1.1530.76
115_K126_T1.1530.76
337_V340_I1.1480.76
245_S249_W1.1480.76
266_D277_S1.1470.76
266_D291_K1.1430.75
253_E266_D1.1360.75
315_K319_Q1.1350.74
71_I127_H1.1340.74
206_E219_Q1.1330.74
63_D130_K1.1310.74
73_E77_S1.1300.74
254_W296_N1.1270.74
55_P58_Q1.1230.73
274_F278_V1.1220.73
185_V191_E1.1220.73
127_H170_E1.1220.73
187_E191_E1.1190.73
197_K200_E1.1180.73
116_S127_H1.1170.73
217_E221_E1.1150.73
203_K220_K1.1150.73
356_E359_E1.1120.72
200_E220_K1.1060.72
229_F233_Q1.1060.72
221_E225_A1.1050.72
107_F114_I1.1040.72
276_E289_I1.1040.72
258_Q293_I1.1000.71
148_L154_E1.0990.71
273_T276_E1.0930.70
82_D90_K1.0920.70
257_D275_G1.0900.70
253_E297_F1.0900.70
246_V277_S1.0890.70
173_T177_E1.0880.70
333_T337_V1.0870.70
55_P59_I1.0860.70
277_S300_L1.0860.70
205_E219_Q1.0860.70
408_L411_T1.0850.70
107_F113_K1.0850.70
237_T241_L1.0820.69
103_E106_A1.0820.69
212_N226_Q1.0790.69
109_I113_K1.0760.69
215_E226_Q1.0750.69
129_G133_L1.0700.68
10_I13_F1.0690.68
118_F137_L1.0680.68
276_E295_V1.0680.68
192_T215_E1.0660.68
263_F266_D1.0660.68
56_K121_M1.0650.68
90_K93_W1.0640.67
92_L96_M1.0600.67
59_I63_D1.0600.67
57_I60_Y1.0600.67
208_E215_E1.0590.67
199_L202_L1.0590.67
266_D292_I1.0570.67
258_Q270_L1.0570.67
258_Q277_S1.0530.66
256_D274_F1.0530.66
244_L250_D1.0510.66
278_V293_I1.0500.66
193_R233_Q1.0490.66
270_L296_N1.0470.66
157_K186_E1.0450.65
93_W115_K1.0450.65
67_R71_I1.0450.65
266_D269_E1.0450.65
196_E203_K1.0430.65
256_D261_F1.0360.64
90_K102_E1.0350.64
81_Q84_L1.0330.64
375_V378_I1.0330.64
252_V257_D1.0330.64
384_F393_F1.0320.64
93_W96_M1.0310.64
244_L263_F1.0300.64
199_L206_E1.0280.64
249_W253_E1.0250.63
344_F355_G1.0200.63
205_E231_Q1.0200.63
348_V351_C1.0200.63
53_Y61_R1.0200.63
156_D160_K1.0200.63
253_E277_S1.0190.63
189_D192_T1.0190.63
205_E212_N1.0180.62
220_K227_I1.0180.62
84_L109_I1.0170.62
63_D69_Q1.0170.62
205_E226_Q1.0170.62
271_T278_V1.0150.62
213_L219_Q1.0150.62
34_N38_N1.0150.62
259_A277_S1.0140.62
327_W333_T1.0140.62
245_S277_S1.0140.62
270_L294_D1.0110.62
192_T220_K1.0090.61
209_F241_L1.0090.61
371_M379_E1.0090.61
274_F289_I1.0080.61
133_L137_L1.0080.61
277_S294_D1.0070.61
8_I16_L1.0070.61
373_I376_N1.0040.61
90_K96_M1.0040.61
119_T129_G1.0030.61
214_L217_E1.0020.61
199_L208_E1.0020.61
116_S159_L1.0010.60
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  
4nfaA10.45011000.62Contact Map
1i84S20.155298.40.866Contact Map
1c1gA40.616497.70.888Contact Map
4linA120.61297.20.899Contact Map
2dfsA20.350397.10.899Contact Map
3na7A10.523396.50.907Contact Map
4iloA20.467896.40.908Contact Map
3ojaB10.403596.40.909Contact Map
3vkgA20.636496.10.911Contact Map
2v71A20.3415960.911Contact 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 0.0193 seconds.