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DegP

ID: 1513765045 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 474 (432)
Sequences: 2836 (1780.8)
Seq/Len: 6.565
Nf(neff/√len): 85.7

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: 6.565).

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
242_N246_E6.3011.00
46_E185_R6.0891.00
367_L376_V4.8971.00
338_S366_G4.3181.00
184_L248_I4.0881.00
139_I153_M3.9251.00
149_F167_I3.7571.00
180_D183_A3.4231.00
177_K246_E3.2801.00
208_V225_I3.2521.00
164_L281_V3.2271.00
322_N326_A3.2171.00
130_N156_K3.1731.00
182_D271_N3.1401.00
51_S175_A3.0801.00
231_I265_G2.8971.00
120_D123_K2.8911.00
443_N446_E2.8441.00
152_K168_Q2.8151.00
436_A447_L2.7831.00
180_D271_N2.7731.00
118_I143_L2.7691.00
404_N444_I2.7381.00
340_N357_M2.7261.00
316_V336_I2.6811.00
413_V427_L2.6681.00
364_T375_N2.5651.00
339_L354_V2.5321.00
337_T368_L2.5211.00
40_S188_D2.4521.00
42_A185_R2.4501.00
151_A165_I2.3921.00
362_K377_N2.3761.00
330_I365_L2.3411.00
127_V277_T2.3231.00
58_E138_V2.3101.00
42_A188_D2.3031.00
431_D464_R2.2721.00
176_I241_V2.2531.00
362_K379_E2.2271.00
239_A247_L2.2231.00
127_V273_V2.2121.00
184_L208_V2.1641.00
117_V247_L2.1481.00
316_V330_I2.1441.00
125_Y154_V2.1191.00
330_I367_L2.1131.00
442_K446_E2.1111.00
138_V150_D2.1051.00
339_L357_M2.0881.00
125_Y164_L2.0871.00
291_L378_L2.0271.00
119_I277_T2.0151.00
125_Y281_V1.9921.00
48_V176_I1.9871.00
404_N411_V1.9631.00
41_L189_Y1.9401.00
43_P185_R1.8941.00
117_V239_A1.8921.00
152_K166_Q1.8311.00
402_M447_L1.8191.00
364_T377_N1.8131.00
126_V167_I1.8081.00
366_G375_N1.8021.00
189_Y205_S1.7801.00
297_E347_F1.7631.00
285_Q382_Q1.7451.00
278_S282_E1.7401.00
338_S341_G1.7331.00
208_V248_I1.7201.00
367_L374_V1.7141.00
140_K148_K1.6941.00
463_Q466_D1.6911.00
51_S176_I1.6661.00
321_P326_A1.6541.00
312_R343_P1.6351.00
338_S343_P1.6121.00
427_L462_I1.6081.00
250_I273_V1.5961.00
118_I173_L1.5931.00
289_G380_L1.5881.00
298_L308_V1.5881.00
302_L306_M1.5690.99
125_Y166_Q1.5650.99
181_S271_N1.5540.99
441_V450_V1.5400.99
162_I250_I1.5340.99
178_M274_K1.5120.99
45_L203_V1.5120.99
48_V241_V1.5110.99
287_K382_Q1.5010.99
134_D158_P1.4990.99
233_R257_P1.4850.99
446_E449_K1.4790.99
337_T366_G1.4700.99
439_Q450_V1.4650.99
176_I247_L1.4600.99
126_V165_I1.4520.99
296_T302_L1.4390.99
403_S414_N1.4320.99
330_I376_V1.4310.99
312_R345_S1.4210.99
130_N134_D1.4090.99
446_E450_V1.4060.99
145_D149_F1.4040.99
401_E415_N1.4040.99
444_I448_R1.4030.99
184_L225_I1.3940.98
342_K353_Q1.3890.98
117_V176_I1.3880.98
164_L277_T1.3830.98
291_L323_S1.3830.98
178_M270_S1.3800.98
203_V207_I1.3560.98
357_M380_L1.3500.98
340_N363_L1.3500.98
340_N361_S1.3400.98
117_V241_V1.3340.98
162_I270_S1.3320.98
294_M318_Q1.3240.98
411_V444_I1.3170.98
118_I167_I1.3100.98
55_I141_V1.2990.97
160_S276_L1.2950.97
57_V113_L1.2920.97
441_V446_E1.2840.97
327_K381_Q1.2790.97
143_L149_F1.2710.97
44_M241_V1.2680.97
48_V193_I1.2640.97
283_Y287_K1.2590.97
302_L305_A1.2580.97
363_L380_L1.2560.97
357_M361_S1.2470.96
56_N112_A1.2450.96
274_K278_S1.2400.96
358_P361_S1.2340.96
59_G110_F1.2340.96
123_K166_Q1.2250.96
50_P174_T1.2200.96
298_L311_Q1.2180.96
178_M273_V1.2170.96
293_I314_A1.2080.95
299_N302_L1.2060.95
328_A378_L1.2060.95
90_Q94_F1.1930.95
190_T248_I1.1840.95
41_L205_S1.1820.95
229_A265_G1.1810.95
296_T317_S1.1800.95
44_M191_V1.1640.94
419_G423_A1.1640.94
127_V270_S1.1610.94
345_S349_A1.1550.94
295_G350_L1.1350.93
339_L365_L1.1330.93
195_N253_A1.1240.93
191_V243_L1.1210.92
290_E320_L1.1200.92
411_V441_V1.1070.92
227_T240_L1.1050.92
72_F75_F1.1030.92
169_N173_L1.0890.91
45_L191_V1.0830.91
331_K370_D1.0830.91
278_S281_V1.0810.91
273_V277_T1.0770.90
435_G461_N1.0750.90
318_Q332_A1.0690.90
49_M201_E1.0670.90
136_A139_I1.0660.90
291_L380_L1.0640.90
140_K150_D1.0620.89
159_R383_S1.0570.89
413_V431_D1.0560.89
130_N158_P1.0460.89
306_M335_V1.0440.88
117_V250_I1.0410.88
40_S43_P1.0390.88
143_L147_R1.0380.88
409_Q442_K1.0380.88
445_A449_K1.0260.87
344_I353_Q1.0220.87
155_G280_M1.0220.87
334_D369_R1.0190.87
211_L225_I1.0180.87
90_Q93_P1.0170.87
257_P262_I1.0110.86
324_S381_Q1.0080.86
54_S112_A1.0080.86
183_A244_N1.0050.86
57_V112_A1.0010.85
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  
1ky9A20.84181000.401Contact Map
3pv2A40.79961000.431Contact Map
4a8cA120.82491000.455Contact Map
3stjA120.63081000.545Contact Map
4flnA30.80591000.546Contact Map
4ic6A30.66671000.598Contact Map
1lcyA10.61181000.598Contact Map
3qo6A30.66461000.601Contact Map
4ri0A30.64351000.613Contact Map
1te0A20.66461000.622Contact 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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