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T0826

ID: 1403223478 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 544 (537)
Sequences: 967 (750.6)
Seq/Len: 1.801
Nf(neff/√len): 32.4

Jackhmmer Results: (2014_04_16)
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: 1.801).

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_I4.6001.00
517_T537_L4.4661.00
382_S422_T4.4541.00
248_G257_T4.1331.00
307_L518_V4.0191.00
250_N269_N3.9561.00
397_K424_L3.3551.00
327_C331_C3.1661.00
433_V447_V3.0801.00
435_R438_E2.9521.00
363_D436_K2.9351.00
450_V511_H2.8661.00
520_G535_D2.7131.00
259_L431_D2.5351.00
248_G255_Q2.3901.00
259_L428_Q2.3891.00
392_T425_Y2.2961.00
273_V509_Y2.2871.00
396_R401_T2.2801.00
242_T423_V2.2741.00
263_R431_D2.2531.00
530_Y535_D2.2180.99
363_D440_R2.1310.99
242_T426_V2.1130.99
245_A475_G2.0750.99
356_N425_Y2.0700.99
429_F433_V2.0130.99
131_G135_A2.0070.99
311_V522_M1.9920.99
290_T304_Q1.9890.99
242_T247_W1.9680.98
430_I447_V1.9590.98
395_E428_Q1.9160.98
462_M467_A1.9100.98
252_Y420_D1.8870.98
520_G530_Y1.8870.98
236_L514_Y1.8830.98
59_F165_C1.8490.97
242_T382_S1.8310.97
255_Q424_L1.8140.97
234_V374_V1.8140.97
499_C540_C1.8120.97
255_Q261_A1.7830.97
396_R399_T1.7650.96
233_F443_L1.7630.96
82_L138_Y1.7570.96
62_N162_S1.7430.96
103_M106_N1.7260.96
246_N416_V1.7130.96
276_C286_C1.7110.96
248_G261_A1.7070.95
465_H468_P1.7020.95
474_S477_T1.6940.95
79_P139_I1.6940.95
244_A269_N1.6850.95
52_T177_Y1.6810.95
516_S534_M1.6810.95
236_L374_V1.6660.95
247_W379_T1.6370.94
249_L257_T1.6320.94
254_R420_D1.6100.93
22_Y27_L1.5780.92
234_V446_V1.5770.92
358_L429_F1.5690.92
97_I467_A1.5630.92
401_T418_T1.5540.91
216_Q219_M1.5430.91
79_P135_A1.5280.91
49_F177_Y1.5220.90
395_E425_Y1.5180.90
519_L526_N1.5180.90
117_R380_I1.4990.89
393_E396_R1.4980.89
292_D534_M1.4960.89
15_L138_Y1.4960.89
348_C353_C1.4870.89
257_T261_A1.4750.88
317_E371_K1.4700.88
273_V481_M1.4680.88
214_Y305_D1.4640.88
274_R477_T1.4620.88
151_E155_R1.4540.87
256_T420_D1.4530.87
246_N420_D1.4400.87
244_A478_H1.4330.86
110_T114_E1.4280.86
263_R435_R1.4250.86
246_N475_G1.4040.85
287_M450_V1.4040.85
318_V334_V1.3920.84
287_M514_Y1.3890.84
474_S478_H1.3830.84
203_K257_T1.3800.83
354_L392_T1.3660.83
117_R386_T1.3650.83
306_N332_G1.3640.82
254_R417_N1.3590.82
241_T451_S1.3570.82
532_K538_A1.3570.82
10_L14_A1.3560.82
23_S65_F1.3550.82
230_L444_E1.3460.81
173_Q177_Y1.3450.81
311_V374_V1.3400.81
403_D418_T1.3390.81
489_F517_T1.3390.81
271_P505_A1.3330.80
79_P138_Y1.3280.80
509_Y536_I1.3250.80
249_L260_L1.3160.79
195_N327_C1.3130.79
263_R438_E1.3090.79
362_F433_V1.3060.79
311_V316_V1.3040.78
218_D221_V1.2990.78
233_F366_L1.2880.77
503_K507_N1.2850.77
526_N529_T1.2810.77
468_P476_Q1.2770.76
316_V522_M1.2760.76
195_N331_C1.2750.76
11_G14_A1.2690.76
431_D435_R1.2600.75
391_Y401_T1.2490.74
359_L436_K1.2450.74
450_V514_Y1.2420.73
111_T325_S1.2400.73
359_L363_D1.2330.73
214_Y333_K1.2320.73
242_T451_S1.2280.72
387_Y455_E1.2260.72
87_A127_I1.2230.72
117_R389_E1.2190.71
379_T429_F1.2170.71
290_T515_F1.2170.71
411_T414_T1.2150.71
276_C472_A1.2140.71
446_V489_F1.2110.71
272_Q508_E1.2100.71
280_T383_H1.1930.69
420_D484_W1.1860.68
321_L361_K1.1830.68
309_D334_V1.1830.68
311_V518_V1.1820.68
267_I482_V1.1800.68
312_Q335_P1.1680.67
402_C410_C1.1660.67
165_C168_G1.1660.67
319_T373_A1.1630.66
391_Y396_R1.1630.66
455_E476_Q1.1590.66
358_L377_L1.1540.65
274_R474_S1.1510.65
374_V518_V1.1500.65
136_L140_A1.1490.65
392_T429_F1.1470.65
214_Y217_L1.1420.64
234_V518_V1.1420.64
268_V505_A1.1390.64
219_M313_R1.1380.64
456_S476_Q1.1310.63
258_P427_D1.1300.63
319_T335_P1.1230.62
361_K364_E1.1200.62
383_H452_D1.1180.62
519_L524_I1.1140.61
362_F366_L1.1110.61
391_Y422_T1.1110.61
235_V433_V1.1090.61
314_A522_M1.1090.61
483_M537_L1.1060.61
237_V447_V1.1030.60
363_D367_N1.0940.59
284_L478_H1.0890.59
266_E501_K1.0870.59
309_D333_K1.0870.59
118_L379_T1.0730.57
366_L445_S1.0700.57
129_C136_L1.0600.56
11_G84_I1.0590.56
305_D313_R1.0570.55
273_V480_P1.0540.55
485_F497_F1.0520.55
327_C336_N1.0500.55
356_N432_K1.0490.55
130_L430_I1.0480.54
280_T452_D1.0440.54
140_A144_K1.0420.54
301_A304_Q1.0420.54
243_R468_P1.0410.54
485_F489_F1.0410.54
63_F163_F1.0400.54
309_D512_D1.0380.53
231_R521_L1.0350.53
76_V79_P1.0340.53
390_R449_Y1.0320.53
92_E99_F1.0290.52
392_T395_E1.0260.52
10_L18_F1.0240.52
269_N482_V1.0240.52
402_C456_S1.0240.52
234_V522_M1.0210.51
468_P473_P1.0210.51
179_S183_N1.0200.51
306_N309_D1.0170.51
220_A526_N1.0170.51
381_G390_R1.0150.51
91_Q305_D1.0140.51
497_F501_K1.0140.51
414_T418_T1.0130.51
392_T428_Q1.0110.50
249_L269_N1.0100.50
256_T260_L1.0100.50
415_L418_T1.0100.50
247_W333_K1.0090.50
278_T320_W1.0070.50
106_N468_P1.0040.50
383_H453_H1.0040.50
437_L447_V1.0020.49
218_D529_T1.0000.49
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  
4kavA10.61031000.664Contact Map
2vqrA10.54411000.764Contact Map
3b5qA20.54411000.769Contact Map
2w5qA10.5791000.772Contact Map
2w8dA20.58091000.773Contact Map
2qzuA10.56251000.773Contact Map
4mhxA20.52761000.779Contact Map
3lxqA20.57351000.78Contact Map
1aukA10.51841000.781Contact Map
1fsuA10.52941000.781Contact 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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