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T0826

ID: 1403201243 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 544 (536)
Sequences: 1892 (1591.5)
Seq/Len: 3.530
Nf(neff/√len): 68.7

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: 3.530).

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
259_L431_D3.3501.00
271_P506_E3.3471.00
517_T537_L3.0801.00
520_G535_D2.8771.00
248_G257_T2.6831.00
237_V430_I2.3051.00
307_L518_V2.2651.00
330_V334_V2.2611.00
431_D435_R2.2511.00
237_V449_Y2.2151.00
250_N269_N2.2091.00
433_V447_V2.2071.00
284_L289_S2.1281.00
335_P338_D2.0731.00
285_P288_F2.0621.00
331_C335_P2.0551.00
397_K424_L2.0421.00
509_Y536_I1.9261.00
280_T283_S1.9161.00
311_V522_M1.9071.00
176_D179_S1.8981.00
276_C280_T1.8841.00
435_R438_E1.8831.00
280_T284_L1.8791.00
331_C334_V1.8440.99
363_D436_K1.8350.99
284_L290_T1.8310.99
273_V509_Y1.8270.99
382_S422_T1.8160.99
327_C331_C1.8110.99
367_N440_R1.7970.99
284_L288_F1.7850.99
438_E442_D1.7640.99
277_G280_T1.7580.99
286_C291_F1.7510.99
190_L193_P1.7430.99
285_P289_S1.7390.99
331_C336_N1.7390.99
115_S118_L1.7320.99
450_V511_H1.7230.99
110_T114_E1.7050.99
263_R431_D1.7020.99
171_M174_Y1.6800.99
173_Q177_Y1.6790.99
259_L262_A1.6760.99
182_R185_K1.6730.99
168_G172_L1.6540.99
338_D342_L1.6390.98
235_V447_V1.6390.98
242_T423_V1.6280.98
392_T425_Y1.6110.98
124_V128_V1.5950.98
281_A284_L1.5900.98
279_S282_H1.5710.98
286_C289_S1.5660.98
285_P291_F1.5630.98
242_T246_N1.5590.98
455_E459_E1.5570.98
383_H452_D1.5540.98
174_Y178_A1.5530.98
165_C168_G1.5410.97
292_D297_D1.5330.97
172_L176_D1.5280.97
330_V335_P1.5210.97
474_S477_T1.5160.97
287_M297_D1.5100.97
284_L292_D1.5000.97
338_D344_L1.4990.97
234_V522_M1.4900.97
232_R444_E1.4840.97
285_P290_T1.4830.97
171_M175_Q1.4780.96
126_W129_C1.4670.96
64_V68_I1.4650.96
286_C290_T1.4610.96
287_M291_F1.4600.96
242_T426_V1.4510.96
26_V37_E1.4460.96
454_G457_L1.4430.96
217_L220_A1.4410.96
189_H193_P1.4350.96
289_S292_D1.4350.96
356_N425_Y1.4300.96
126_W132_V1.4280.95
285_P293_R1.4280.95
334_V338_D1.4280.95
255_Q424_L1.4260.95
187_V190_L1.4250.95
332_G335_P1.4250.95
462_M465_H1.4240.95
216_Q219_M1.4230.95
317_E371_K1.4220.95
393_E396_R1.4040.95
213_P217_L1.4000.95
259_L428_Q1.3880.94
191_I198_G1.3880.94
276_C286_C1.3720.94
289_S294_T1.3710.94
131_G135_A1.3700.94
396_R401_T1.3630.94
267_I482_V1.3590.94
246_N423_V1.3580.94
398_F421_N1.3520.93
334_V337_T1.3520.93
382_S423_V1.3510.93
255_Q261_A1.3510.93
463_Y466_A1.3500.93
294_T297_D1.3460.93
174_Y179_S1.3400.93
435_R439_N1.3370.93
293_R296_Y1.3350.93
208_K211_N1.3320.93
170_A174_Y1.3320.93
456_S460_N1.3310.93
191_I195_N1.3280.93
337_T340_T1.3220.92
172_L177_Y1.3190.92
20_S28_N1.3190.92
339_V342_L1.3140.92
169_I173_Q1.3110.92
333_K336_N1.3100.92
275_S280_T1.3090.92
392_T395_E1.3090.92
258_P427_D1.3080.92
242_T247_W1.2950.91
25_L28_N1.2880.91
114_E118_L1.2860.91
25_L29_Y1.2860.91
27_L32_F1.2840.91
29_Y36_V1.2830.91
195_N198_G1.2760.91
257_T261_A1.2730.90
276_C279_S1.2710.90
233_F443_L1.2640.90
214_Y217_L1.2630.90
181_F185_K1.2630.90
244_A478_H1.2620.90
280_T286_C1.2500.89
330_V336_N1.2500.89
363_D440_R1.2490.89
26_V29_Y1.2480.89
244_A269_N1.2480.89
114_E117_R1.2420.89
469_Y472_A1.2360.89
395_E428_Q1.2310.88
462_M467_A1.2290.88
236_L374_V1.2270.88
268_V537_L1.2220.88
434_I447_V1.2210.88
474_S478_H1.2180.88
287_M290_T1.2170.88
126_W130_L1.2150.87
175_Q178_A1.2110.87
173_Q176_D1.2090.87
188_T191_I1.2070.87
172_L175_Q1.1980.86
29_Y33_A1.1960.86
163_F166_A1.1940.86
28_N33_A1.1870.86
424_L428_Q1.1850.86
236_L514_Y1.1830.86
180_F185_K1.1820.85
288_F292_D1.1800.85
179_S183_N1.1770.85
28_N32_F1.1760.85
280_T383_H1.1760.85
27_L30_A1.1760.85
276_C283_S1.1760.85
330_V333_K1.1740.85
170_A179_S1.1740.85
233_F445_S1.1740.85
284_L291_F1.1740.85
463_Y467_A1.1730.85
168_G176_D1.1710.85
248_G255_Q1.1660.84
171_M178_A1.1660.84
29_Y37_E1.1630.84
262_A431_D1.1620.84
290_T304_Q1.1580.84
166_A169_I1.1570.84
63_F66_H1.1560.84
174_Y177_Y1.1510.83
289_S296_Y1.1490.83
284_L293_R1.1460.83
28_N37_E1.1450.83
233_F373_A1.1420.83
277_G282_H1.1380.82
187_V191_I1.1340.82
288_F294_T1.1330.82
383_H453_H1.1320.82
202_S206_D1.1300.82
282_H286_C1.1290.82
335_P340_T1.1290.82
222_V225_R1.1260.81
481_M514_Y1.1250.81
235_V445_S1.1220.81
277_G281_A1.1220.81
171_M176_D1.1220.81
213_P216_Q1.1210.81
301_A304_Q1.1200.81
289_S293_R1.1190.81
263_R434_I1.1190.81
446_V483_M1.1160.81
456_S459_E1.1160.81
275_S279_S1.1160.81
286_C292_D1.1140.80
168_G171_M1.1130.80
404_T417_N1.1130.80
65_F68_I1.1120.80
230_L444_E1.1090.80
132_V135_A1.1080.80
276_C281_A1.1080.80
33_A36_V1.1070.80
191_I199_A1.1050.80
232_R446_V1.1040.80
281_A288_F1.1030.80
171_M177_Y1.1030.80
289_S297_D1.1020.79
128_V132_V1.1020.79
32_F37_E1.0990.79
138_Y142_K1.0990.79
169_I172_L1.0970.79
285_P297_D1.0940.79
283_S286_C1.0930.79
213_P218_D1.0900.78
22_Y27_L1.0860.78
248_G261_A1.0860.78
272_Q508_E1.0850.78
437_L447_V1.0840.78
442_D447_V1.0830.78
234_V446_V1.0830.78
287_M294_T1.0830.78
356_N432_K1.0820.78
530_Y535_D1.0820.78
358_L429_F1.0790.77
300_K304_Q1.0780.77
276_C282_H1.0780.77
59_F165_C1.0770.77
338_D341_S1.0770.77
11_G14_A1.0760.77
25_L32_F1.0760.77
168_G173_Q1.0760.77
193_P199_A1.0720.77
284_L287_M1.0660.76
287_M293_R1.0620.76
465_H468_P1.0580.76
32_F36_V1.0570.75
398_F401_T1.0570.75
264_G267_I1.0570.75
464_L467_A1.0560.75
246_N420_D1.0550.75
118_L123_Y1.0530.75
316_V372_D1.0520.75
113_A118_L1.0480.75
252_Y420_D1.0480.75
234_V448_H1.0470.74
92_E99_F1.0460.74
27_L36_V1.0460.74
338_D343_N1.0450.74
271_P505_A1.0430.74
334_V343_N1.0420.74
337_T342_L1.0400.74
330_V338_D1.0380.74
414_T418_T1.0370.73
292_D296_Y1.0360.73
335_P342_L1.0350.73
396_R399_T1.0330.73
395_E425_Y1.0290.73
26_V30_A1.0240.72
170_A173_Q1.0240.72
499_C540_C1.0230.72
40_P45_G1.0220.72
240_E452_D1.0210.72
47_D50_L1.0200.72
287_M450_V1.0190.72
240_E383_H1.0170.71
234_V374_V1.0160.71
331_C338_D1.0160.71
363_D367_N1.0150.71
137_A141_V1.0150.71
103_M106_N1.0130.71
175_Q179_S1.0130.71
188_T198_G1.0100.71
136_L140_A1.0100.71
246_N256_T1.0100.71
324_D378_H1.0060.70
280_T452_D1.0040.70
287_M292_D1.0040.70
188_T199_A1.0030.70
33_A37_E1.0020.70
245_A475_G1.0010.70
275_S282_H1.0010.70
358_L377_L1.0010.70
29_Y32_F1.0010.70
140_A144_K1.0000.70
135_A138_Y1.0000.70
238_V284_L1.0000.70
479_I509_Y1.0000.70
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  
4kavA10.60851000.521Contact Map
2w8dA20.57721000.553Contact Map
2w5qA10.5791000.554Contact Map
3lxqA20.58461000.56Contact Map
3b5qA20.53681000.593Contact Map
2vqrA10.54411000.599Contact Map
2qzuA10.56071000.601Contact Map
1fsuA10.53121000.607Contact Map
1aukA10.51651000.61Contact Map
3ed4A40.56071000.61Contact 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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