GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
hknoali

ID: 1500207465 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 371 (344)
Sequences: 680 (467.6)
Seq/Len: 1.977
Nf(neff/√len): 25.2

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: 1.977).

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
202_S223_V3.3721.00
191_L234_V2.5321.00
292_V304_C2.4201.00
203_D228_R2.2341.00
192_G234_V2.1741.00
288_L317_I2.1200.99
345_L364_M2.1010.99
303_T322_D2.0950.99
286_M289_K1.9780.99
314_E365_A1.9730.99
284_L317_I1.9610.99
291_A362_L1.9590.99
302_K322_D1.9360.99
238_V335_G1.9280.99
295_V304_C1.9190.98
179_E182_R1.8440.98
179_E344_R1.7460.97
293_T297_K1.7310.97
263_I301_A1.6250.95
194_K230_S1.5880.94
292_V306_V1.5490.93
187_L203_D1.5470.93
301_A322_D1.5180.92
263_I299_S1.5180.92
318_T361_K1.5160.91
290_E293_T1.5160.91
292_V296_V1.5130.91
291_A341_M1.5000.91
202_S220_L1.4930.91
220_L223_V1.4920.91
320_S361_K1.4840.90
199_G224_Q1.4730.90
76_T113_I1.4550.89
287_C341_M1.4430.89
49_F53_Y1.4320.88
354_I360_T1.4220.88
323_G359_G1.4210.88
326_K360_T1.4170.87
290_E340_G1.4100.87
290_E297_K1.4070.87
276_I315_V1.4070.87
185_R235_R1.4020.87
172_A176_K1.3740.85
321_D359_G1.3720.85
206_R223_V1.3540.84
193_Q326_K1.3460.83
321_D360_T1.3360.83
186_D191_L1.3280.82
266_I305_R1.3250.82
167_A171_I1.3230.82
241_M292_V1.3200.82
192_G293_T1.3170.82
341_M352_L1.3130.81
291_A319_V1.3130.81
343_E347_F1.3090.81
342_R346_E1.3080.81
287_C364_M1.3050.81
301_A323_G1.3050.81
98_I205_A1.2980.80
194_K234_V1.2950.80
273_P310_Q1.2950.80
179_E185_R1.2930.80
31_W34_S1.2890.80
235_R344_R1.2800.79
321_D325_F1.2680.78
22_F26_P1.2510.77
199_G340_G1.2420.76
355_D358_N1.2410.76
92_A192_G1.2340.75
287_C291_A1.2260.75
287_C345_L1.2180.74
115_A303_T1.2180.74
29_F35_S1.2130.74
202_S224_Q1.2130.74
192_G335_G1.2070.73
87_F91_I1.2050.73
277_S280_N1.2010.73
351_S365_A1.1990.72
258_L292_V1.1990.72
204_L250_E1.1970.72
193_Q293_T1.1920.72
31_W35_S1.1840.71
269_E274_E1.1810.71
200_L237_I1.1760.70
185_R340_G1.1730.70
235_R323_G1.1560.68
268_E305_R1.1550.68
192_G336_H1.1530.68
290_E294_N1.1450.67
224_Q238_V1.1380.67
299_S304_C1.1320.66
206_R224_Q1.1280.66
250_E289_K1.1240.65
192_G203_D1.1180.65
193_Q231_L1.1150.64
274_E308_I1.1090.64
201_K223_V1.1080.64
158_E335_G1.1080.64
190_T231_L1.1060.63
231_L235_R1.1060.63
180_R235_R1.1030.63
199_G202_S1.1030.63
159_R366_I1.0980.63
271_K310_Q1.0970.62
203_D323_G1.0890.62
289_K335_G1.0840.61
27_F31_W1.0780.60
317_I346_E1.0760.60
191_L216_A1.0730.60
186_D237_I1.0710.60
155_K191_L1.0630.59
25_L29_F1.0620.59
267_Y305_R1.0620.59
343_E366_I1.0610.59
302_K365_A1.0600.59
76_T353_H1.0590.58
112_L116_A1.0580.58
186_D242_K1.0580.58
75_S116_A1.0560.58
315_V368_N1.0550.58
293_T360_T1.0550.58
248_K312_W1.0540.58
102_V141_L1.0530.58
179_E235_R1.0520.58
316_V365_A1.0500.57
338_L341_M1.0470.57
205_A219_E1.0460.57
232_N299_S1.0460.57
184_A291_A1.0450.57
207_K231_L1.0440.57
241_M304_C1.0430.57
340_G343_E1.0420.57
117_V205_A1.0420.57
325_F360_T1.0400.56
303_T349_N1.0350.56
316_V362_L1.0340.56
313_K353_H1.0330.56
196_S204_L1.0320.55
268_E307_D1.0320.55
118_A367_P1.0300.55
301_A321_D1.0300.55
164_L171_I1.0280.55
124_V319_V1.0250.55
192_G289_K1.0240.55
219_E223_V1.0240.55
21_I28_Y1.0230.54
154_R313_K1.0230.54
203_D234_V1.0220.54
51_S55_F1.0210.54
190_T193_Q1.0210.54
345_L350_G1.0190.54
201_K219_E1.0140.54
24_I30_I1.0110.53
115_A291_A1.0100.53
191_L230_S1.0060.53
51_S54_R1.0050.53
189_D235_R1.0030.52
279_L347_F1.0010.52
205_A251_L1.0010.52
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  
3ehhA20.52831000.6Contact Map
4r39A40.50499.90.751Contact Map
4bixA20.549999.80.767Contact Map
2c2aA10.560699.80.772Contact Map
4i5sA20.695499.80.774Contact Map
4q20A20.544599.80.776Contact Map
3ehgA10.336999.80.782Contact Map
3zxqA20.328899.80.783Contact Map
3d36A20.525699.70.785Contact Map
3a0rA10.811399.70.787Contact 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 0.0442 seconds.