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4F35

ID: 1507574531 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 449 (435)
Sequences: 8340 (4771.4)
Seq/Len: 19.172
Nf(neff/√len): 228.8

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: 19.172).

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
71_E74_A4.0051.00
117_K120_V3.7021.00
99_H300_E3.5381.00
330_V334_N3.4241.00
258_T286_A3.1671.00
421_K424_E2.8781.00
129_T145_M2.8751.00
423_S427_R2.8051.00
184_L194_A2.6641.00
74_A325_Q2.6571.00
88_L310_L2.6391.00
169_L414_V2.5731.00
96_A290_L2.5121.00
344_G347_V2.4601.00
109_K113_M2.4531.00
424_E427_R2.3691.00
297_H300_E2.3251.00
109_K112_A2.2921.00
42_I60_V2.2881.00
331_F335_A2.1701.00
64_A322_V2.1211.00
254_I286_A2.0711.00
357_V433_N2.0651.00
246_K250_V2.0601.00
200_S203_D2.0581.00
205_M209_L1.9921.00
434_I438_G1.9851.00
38_M63_M1.9741.00
149_V172_V1.9681.00
321_N325_Q1.9661.00
170_L174_Y1.9601.00
131_L135_W1.9371.00
249_V253_G1.9301.00
18_L44_V1.9091.00
105_V109_K1.9081.00
166_V424_E1.8961.00
206_K210_P1.8951.00
92_A287_I1.8731.00
356_V372_L1.8521.00
202_T206_K1.8461.00
353_A397_A1.8341.00
130_A212_A1.8061.00
41_F45_L1.7951.00
264_F268_I1.7891.00
178_I215_M1.7841.00
36_I328_T1.7821.00
299_K303_K1.7781.00
89_G283_A1.7771.00
123_F220_I1.7651.00
61_P76_L1.7301.00
28_F32_V1.7281.00
126_F175_S1.7231.00
218_M439_L1.7191.00
182_A212_A1.7111.00
129_T176_A1.6991.00
335_A338_D1.6971.00
218_M435_A1.6891.00
119_S224_Y1.6651.00
89_G287_I1.6341.00
215_M436_C1.6301.00
30_H34_L1.6251.00
185_V201_F1.6171.00
213_M217_P1.6121.00
95_A98_H1.6021.00
264_F267_P1.5781.00
358_F362_F1.5731.00
426_M430_L1.5621.00
133_S179_G1.5611.00
361_E433_N1.5501.00
203_D206_K1.5471.00
16_V41_F1.5461.00
405_P415_F1.5461.00
350_L441_T1.5451.00
323_L328_T1.5391.00
95_A304_T1.5281.00
346_F445_M1.5171.00
354_T437_I1.5051.00
299_K302_Q1.4731.00
38_M60_V1.4611.00
443_I447_F1.4581.00
105_V248_K1.4561.00
125_L149_V1.4561.00
369_A398_A1.4461.00
130_A216_L1.4271.00
353_A393_L1.4221.00
84_I310_L1.4151.00
45_L48_T1.4151.00
209_L213_M1.4141.00
442_A446_L1.3930.99
324_K330_V1.3920.99
88_L92_A1.3860.99
334_N337_S1.3850.99
15_D45_L1.3850.99
260_F264_F1.3790.99
321_N324_K1.3760.99
170_L428_V1.3610.99
38_M64_A1.3610.99
237_L240_A1.3590.99
256_G260_F1.3550.99
403_M433_N1.3530.99
354_T441_T1.3460.99
437_I441_T1.3460.99
430_L434_I1.3380.99
173_A414_V1.3340.99
335_A339_M1.3340.99
343_M347_V1.3320.99
51_L55_V1.3310.99
323_L329_S1.3290.99
126_F219_A1.3260.99
96_A251_T1.3210.99
182_A209_L1.3190.99
440_L444_A1.3160.99
29_E32_V1.3110.99
389_L393_L1.3100.99
393_L444_A1.3070.99
203_D388_V1.2960.99
93_L258_T1.2850.99
134_M182_A1.2830.99
44_V48_T1.2820.99
380_A390_L1.2620.99
222_I435_A1.2620.99
354_T358_F1.2530.99
104_K108_D1.2500.99
137_S140_A1.2480.99
221_A225_F1.2480.99
385_M390_L1.2450.98
442_A445_M1.2430.98
82_S280_T1.2400.98
254_I289_M1.2390.98
146_L413_I1.2350.98
126_F171_G1.2310.98
244_W248_K1.2290.98
13_L17_A1.2260.98
126_F216_L1.2250.98
257_L261_L1.2220.98
365_N401_A1.2180.98
245_D248_K1.2180.98
423_S426_M1.2150.98
214_M439_L1.2040.98
178_I219_A1.2020.98
360_T365_N1.2010.98
48_T51_L1.1940.98
211_T439_L1.1890.98
125_L152_V1.1870.98
52_H56_T1.1860.98
75_A318_C1.1840.98
65_V75_A1.1830.98
169_L420_I1.1790.98
192_I373_I1.1780.98
62_V288_L1.1780.98
222_I226_L1.1720.98
78_N318_C1.1710.98
403_M426_M1.1670.97
188_P366_T1.1670.97
252_L256_G1.1520.97
376_F394_I1.1470.97
236_E240_A1.1440.97
9_S13_L1.1310.97
98_H304_T1.1280.97
18_L40_A1.1200.96
114_A124_M1.1170.96
175_S179_G1.1160.96
123_F127_G1.1140.96
225_F228_K1.1130.96
334_N338_D1.1130.96
227_L428_V1.1110.96
54_T308_G1.1090.96
23_Y34_L1.1050.96
171_G223_L1.1020.96
105_V108_D1.0980.96
373_I391_S1.0960.96
361_E403_M1.0960.96
93_L286_A1.0960.96
20_L23_Y1.0910.96
74_A77_N1.0900.96
357_V437_I1.0870.96
210_P443_I1.0860.96
37_S40_A1.0830.96
51_L56_T1.0830.96
250_V295_V1.0720.95
57_A315_G1.0690.95
129_T172_V1.0670.95
142_A176_A1.0670.95
95_A99_H1.0670.95
31_N34_L1.0620.95
119_S220_I1.0590.95
173_A411_N1.0580.95
193_A391_S1.0570.95
35_G322_V1.0550.95
166_V170_L1.0490.94
45_L56_T1.0460.94
22_L40_A1.0450.94
244_W249_V1.0440.94
65_V281_L1.0420.94
78_N321_N1.0320.94
358_F433_N1.0300.94
71_E75_A1.0290.94
359_L368_S1.0260.94
132_L141_T1.0210.93
32_V331_F1.0200.93
61_P315_G1.0190.93
146_L417_S1.0190.93
147_P151_G1.0170.93
139_T364_S1.0140.93
38_M42_I1.0090.93
180_G187_S1.0050.93
100_Q251_T1.0040.93
438_G442_A1.0040.93
59_L63_M1.0040.93
403_M430_L1.0000.92
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  
4f35D40.9711000.303Contact Map
4r1iA20.94881000.661Contact Map
4r0cA4099.90.706Contact Map
2kncA10.115812.10.967Contact Map
4pd6A10.777311.80.967Contact Map
2m20A20.1189.50.968Contact Map
3tdsE50.49673.50.974Contact Map
2rddB10.08243.20.975Contact Map
2ksfA10.23613.10.975Contact Map
2a65A10.50112.60.976Contact 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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