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T0826

ID: 1403215952 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 544 (533)
Sequences: 737 (528.8)
Seq/Len: 1.383
Nf(neff/√len): 22.9

HHblits Results: (2013_03)
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: 1.383).

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
237_V430_I4.2791.00
517_T537_L4.0471.00
382_S422_T3.8801.00
250_N269_N3.7381.00
248_G257_T3.6711.00
307_L518_V3.3691.00
327_C331_C3.1681.00
433_V447_V2.7431.00
397_K424_L2.6351.00
392_T425_Y2.6041.00
520_G535_D2.5581.00
363_D436_K2.5331.00
450_V511_H2.4851.00
516_S534_M2.3911.00
242_T423_V2.3220.99
435_R438_E2.2820.99
530_Y535_D2.1150.99
242_T426_V2.1000.98
103_M106_N2.0790.98
311_V522_M2.0620.98
273_V509_Y2.0380.98
396_R401_T2.0160.98
259_L428_Q1.9910.98
276_C286_C1.9000.96
242_T382_S1.8510.96
499_C540_C1.8140.95
234_V374_V1.7890.95
131_G135_A1.7570.94
489_F517_T1.7360.93
429_F433_V1.7220.93
245_A475_G1.6890.92
263_R431_D1.6840.92
356_N425_Y1.6730.92
242_T247_W1.6520.91
20_S27_L1.6480.91
22_Y27_L1.6280.90
234_V446_V1.6250.90
287_M450_V1.6160.90
248_G255_Q1.6060.89
395_E428_Q1.5960.89
242_T451_S1.5880.89
236_L374_V1.5860.89
259_L431_D1.5790.88
450_V514_Y1.5480.87
230_L444_E1.5420.87
318_V334_V1.5370.86
520_G530_Y1.5270.86
218_D221_V1.5210.86
252_Y420_D1.5100.85
31_F35_V1.5080.85
247_W379_T1.5070.85
283_S464_L1.4890.84
348_C353_C1.4830.84
446_V489_F1.4770.83
246_N420_D1.4760.83
402_C410_C1.4410.81
317_E371_K1.4260.80
59_F165_C1.4050.79
401_T418_T1.3980.78
173_Q177_Y1.3890.78
455_E476_Q1.3850.77
233_F443_L1.3810.77
62_N162_S1.3780.77
216_Q219_M1.3720.76
256_T420_D1.3660.76
255_Q424_L1.3560.75
244_A478_H1.3500.75
519_L527_S1.3490.75
52_T177_Y1.3450.74
509_Y536_I1.3450.74
236_L450_V1.3440.74
48_I51_Y1.3440.74
382_S423_V1.3360.74
87_A127_I1.3300.73
243_R464_L1.3290.73
462_M467_A1.3250.73
79_P139_I1.3240.73
296_Y423_V1.3240.73
359_L363_D1.3140.72
429_F536_I1.3110.72
278_T320_W1.3100.72
483_M537_L1.3020.71
243_R283_S1.3010.71
274_R477_T1.2930.70
254_R420_D1.2890.70
246_N416_V1.2890.70
129_C136_L1.2790.69
254_R417_N1.2760.69
287_M514_Y1.2750.69
110_T114_E1.2710.68
311_V320_W1.2680.68
403_D418_T1.2680.68
396_R399_T1.2620.68
246_N475_G1.2570.67
55_V168_G1.2550.67
255_Q261_A1.2520.67
79_P135_A1.2420.66
118_L379_T1.2390.65
117_R386_T1.2360.65
483_M517_T1.2360.65
79_P138_Y1.2290.65
234_V518_V1.2260.64
252_Y256_T1.2240.64
420_D484_W1.2200.64
214_Y305_D1.2140.63
117_R380_I1.2080.63
395_E425_Y1.2040.62
248_G261_A1.2010.62
309_D512_D1.2010.62
387_Y455_E1.1980.62
381_G449_Y1.1980.62
497_F501_K1.1980.62
233_F366_L1.1940.61
474_S477_T1.1910.61
244_A269_N1.1910.61
363_D367_N1.1880.61
392_T429_F1.1860.60
82_L138_Y1.1820.60
241_T464_L1.1800.60
236_L376_I1.1800.60
18_F500_L1.1770.60
234_V316_V1.1760.60
306_N331_C1.1750.59
456_S476_Q1.1720.59
386_T418_T1.1720.59
311_V518_V1.1700.59
24_S57_L1.1690.59
23_S65_F1.1650.58
243_R476_Q1.1630.58
239_G378_H1.1590.58
411_T414_T1.1590.58
195_N327_C1.1560.58
132_V164_L1.1560.58
32_F35_V1.1530.57
239_G449_Y1.1510.57
362_F377_L1.1500.57
356_N392_T1.1490.57
238_V284_L1.1450.56
31_F53_M1.1420.56
104_L203_K1.1360.56
91_Q118_L1.1350.55
309_D333_K1.1350.55
21_L58_F1.1300.55
16_I38_L1.1290.55
236_L514_Y1.1280.55
45_G48_I1.1270.55
290_T304_Q1.1200.54
392_T395_E1.1160.54
354_L392_T1.1120.53
390_R449_Y1.1100.53
19_L22_Y1.1060.53
214_Y333_K1.1060.53
393_E396_R1.1020.52
456_S473_P1.0960.52
243_R437_L1.0940.51
274_R474_S1.0920.51
43_G46_A1.0920.51
92_E99_F1.0920.51
321_L358_L1.0910.51
58_F460_N1.0910.51
218_D527_S1.0890.51
277_G285_P1.0890.51
29_Y35_V1.0850.50
249_L260_L1.0850.50
391_Y395_E1.0840.50
468_P476_Q1.0790.50
420_D455_E1.0790.50
11_G14_A1.0790.50
50_L60_L1.0790.50
20_S24_S1.0770.50
243_R400_P1.0720.49
195_N331_C1.0710.49
306_N330_V1.0710.49
290_T515_F1.0700.49
281_A301_A1.0700.49
96_N510_S1.0690.49
256_T260_L1.0680.49
423_V426_V1.0670.49
331_C336_N1.0630.48
68_I77_L1.0620.48
76_V79_P1.0590.48
238_V288_F1.0570.48
321_L337_T1.0540.47
249_L267_I1.0530.47
465_H476_Q1.0520.47
26_V147_V1.0520.47
235_V433_V1.0490.47
258_P427_D1.0480.47
242_T257_T1.0470.47
137_A262_A1.0430.46
314_A522_M1.0410.46
36_V40_P1.0400.46
374_V518_V1.0400.46
483_M518_V1.0390.46
49_F177_Y1.0370.46
164_L171_M1.0360.45
249_L257_T1.0360.45
277_G288_F1.0350.45
242_T422_T1.0340.45
437_L447_V1.0320.45
283_S511_H1.0310.45
465_H519_L1.0270.45
362_F366_L1.0260.44
75_K79_P1.0230.44
323_N378_H1.0220.44
181_F281_A1.0220.44
254_R484_W1.0210.44
391_Y422_T1.0210.44
44_T48_I1.0180.44
63_F163_F1.0180.44
359_L436_K1.0170.44
239_G381_G1.0110.43
45_G59_F1.0080.43
243_R266_E1.0070.43
91_Q123_Y1.0050.42
62_N158_L1.0040.42
247_W260_L1.0040.42
239_G455_E1.0030.42
332_G489_F1.0030.42
241_T283_S1.0020.42
293_R329_G1.0020.42
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: (14Jun14)
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  
4kavA10.61031000.67Contact Map
2vqrA10.54411000.789Contact Map
3b5qA20.54231000.79Contact Map
3lxqA20.57171000.791Contact Map
2w5qA10.57351000.793Contact Map
2qzuA10.56071000.793Contact Map
2w8dA20.57721000.794Contact Map
4mhxA20.53491000.8Contact Map
1fsuA10.52391000.802Contact Map
1aukA10.51471000.802Contact 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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