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T0826

ID: 1403200141 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 544 (535)
Sequences: 3639 (3200.1)
Seq/Len: 6.802
Nf(neff/√len): 138.4

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: 6.802).

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_D4.4601.00
271_P506_E3.9051.00
520_G535_D3.3761.00
237_V449_Y3.0021.00
367_N440_R2.8801.00
43_G47_D2.8331.00
259_L262_A2.6931.00
517_T537_L2.6471.00
363_D436_K2.4551.00
335_P338_D2.4501.00
431_D435_R2.3211.00
234_V522_M2.2861.00
248_G257_T2.2831.00
330_V334_V2.2481.00
235_V447_V2.2011.00
317_E371_K2.1841.00
255_Q261_A2.1571.00
435_R438_E2.1321.00
237_V430_I2.1061.00
338_D344_L2.0691.00
509_Y536_I2.0511.00
280_T284_L2.0261.00
438_E442_D2.0031.00
273_V509_Y1.9901.00
311_V522_M1.9901.00
232_R444_E1.9521.00
331_C335_P1.9071.00
437_L447_V1.9041.00
266_E438_E1.9041.00
239_G242_T1.8871.00
190_L193_P1.8671.00
138_Y142_K1.8601.00
234_V311_V1.8421.00
236_L374_V1.8391.00
284_L289_S1.8001.00
88_V98_Y1.7781.00
397_K424_L1.7311.00
233_F445_S1.7251.00
233_F373_A1.7241.00
392_T425_Y1.7171.00
250_N269_N1.7081.00
337_T340_T1.7001.00
257_T261_A1.6751.00
338_D342_L1.6711.00
331_C336_N1.6511.00
356_N425_Y1.6351.00
176_D179_S1.6251.00
339_V342_L1.6011.00
277_G280_T1.6011.00
446_V483_M1.5851.00
276_C280_T1.5741.00
442_D484_W1.5691.00
235_V445_S1.5560.99
331_C334_V1.5460.99
434_I447_V1.5360.99
280_T283_S1.5350.99
187_V190_L1.5230.99
435_R439_N1.5210.99
25_L28_N1.5170.99
139_I143_V1.5160.99
188_T191_I1.5100.99
450_V511_H1.5080.99
382_S423_V1.4980.99
432_K435_R1.4850.99
382_S422_T1.4740.99
330_V335_P1.4720.99
115_S118_L1.4680.99
312_Q340_T1.4670.99
114_E118_L1.4650.99
338_D343_N1.4600.99
307_L518_V1.4400.99
248_G261_A1.4390.99
189_H193_P1.4370.99
361_K364_E1.4350.99
285_P289_S1.4320.99
428_Q432_K1.4060.99
188_T193_P1.4050.99
433_V447_V1.4040.99
230_L444_E1.4040.99
242_T423_V1.3980.99
363_D367_N1.3900.99
239_G426_V1.3880.99
114_E117_R1.3770.98
284_L290_T1.3770.98
43_G46_A1.3700.98
319_T375_L1.3550.98
280_T378_H1.3500.98
334_V337_T1.3500.98
383_H452_D1.3490.98
442_D447_V1.3480.98
285_P288_F1.3470.98
238_V284_L1.3440.98
172_L176_D1.3440.98
110_T114_E1.3390.98
338_D341_S1.3370.98
126_W132_V1.3360.98
485_F488_A1.3340.98
393_E396_R1.3340.98
260_L430_I1.3320.98
236_L448_H1.3310.98
284_L288_F1.3300.98
339_V343_N1.3300.98
262_A431_D1.3260.98
258_P427_D1.3230.98
163_F166_A1.3210.98
239_G449_Y1.3210.98
359_L363_D1.3190.98
382_S426_V1.3190.98
171_M174_Y1.3090.98
320_W378_H1.3080.98
173_Q177_Y1.3020.98
259_L434_I1.3020.98
287_M450_V1.2980.98
286_C291_F1.2820.97
285_P291_F1.2780.97
246_N420_D1.2780.97
333_K336_N1.2750.97
263_R431_D1.2750.97
292_D297_D1.2750.97
285_P290_T1.2730.97
395_E428_Q1.2690.97
182_R185_K1.2680.97
191_I195_N1.2680.97
25_L29_Y1.2670.97
242_T426_V1.2630.97
21_L28_N1.2520.97
174_Y179_S1.2460.97
268_V537_L1.2420.97
244_A478_H1.2390.96
66_H69_A1.2390.96
28_N31_F1.2370.96
330_V338_D1.2320.96
356_N432_K1.2310.96
339_V344_L1.2230.96
273_V481_M1.2200.96
28_N32_F1.2180.96
193_P196_F1.2170.96
213_P217_L1.2150.96
24_S28_N1.2140.96
28_N33_A1.2110.96
275_S280_T1.2080.96
276_C286_C1.2080.96
264_G267_I1.2040.96
118_L122_G1.2040.96
392_T395_E1.2040.96
424_L428_Q1.2020.96
321_L365_V1.2010.96
359_L433_V1.1980.95
363_D440_R1.1970.95
187_V191_I1.1940.95
398_F402_C1.1910.95
173_Q179_S1.1860.95
187_V193_P1.1830.95
330_V333_K1.1830.95
242_T246_N1.1830.95
451_S479_I1.1790.95
124_V128_V1.1790.95
174_Y177_Y1.1770.95
171_M175_Q1.1760.95
140_A144_K1.1740.95
345_P348_C1.1730.95
29_Y33_A1.1720.95
172_L175_Q1.1720.95
280_T285_P1.1710.95
331_C338_D1.1680.95
272_Q508_E1.1670.95
112_A118_L1.1660.95
481_M514_Y1.1650.94
301_A304_Q1.1640.94
377_L433_V1.1530.94
168_G172_L1.1500.94
172_L177_Y1.1480.94
263_R430_I1.1430.94
234_V446_V1.1400.94
455_E459_E1.1340.93
286_C289_S1.1330.93
396_R401_T1.1310.93
279_S282_H1.1260.93
181_F185_K1.1240.93
474_S477_T1.1230.93
252_Y420_D1.1230.93
281_A284_L1.1200.93
188_T198_G1.1190.93
236_L376_I1.1100.92
429_F433_V1.1100.92
174_Y178_A1.1100.92
293_R296_Y1.1080.92
267_I484_W1.1050.92
32_F37_E1.1040.92
337_T342_L1.1040.92
462_M465_H1.1010.92
398_F421_N1.1000.92
362_F366_L1.1000.92
337_T341_S1.0990.92
358_L377_L1.0990.92
214_Y217_L1.0970.92
254_R420_D1.0970.92
362_F377_L1.0960.92
173_Q176_D1.0940.92
170_A174_Y1.0940.92
248_G255_Q1.0940.92
364_E368_K1.0910.92
327_C331_C1.0880.91
277_G282_H1.0880.91
448_H483_M1.0850.91
310_I519_L1.0850.91
257_T260_L1.0840.91
151_E154_T1.0840.91
234_V316_V1.0840.91
159_A163_F1.0830.91
428_Q431_D1.0810.91
238_V376_I1.0810.91
137_A141_V1.0810.91
282_H286_C1.0780.91
179_S185_K1.0780.91
239_G430_I1.0780.91
171_M177_Y1.0770.91
334_V338_D1.0750.91
175_Q178_A1.0740.91
335_P340_T1.0730.91
136_L140_A1.0670.90
216_Q219_M1.0670.90
75_K78_I1.0630.90
232_R446_V1.0620.90
280_T383_H1.0590.90
56_V63_F1.0560.90
311_V519_L1.0560.90
282_H285_P1.0550.90
47_D50_L1.0540.90
111_T114_E1.0540.90
300_K304_Q1.0520.89
284_L292_D1.0520.89
164_L168_G1.0510.89
233_F443_L1.0500.89
189_H192_V1.0500.89
208_K211_N1.0500.89
30_A33_A1.0490.89
26_V29_Y1.0470.89
238_V450_V1.0440.89
275_S282_H1.0430.89
217_L220_A1.0420.89
129_C132_V1.0400.89
332_G335_P1.0390.89
91_Q95_F1.0390.89
64_V68_I1.0380.89
118_L123_Y1.0370.89
188_T199_A1.0370.89
333_K338_D1.0370.89
321_L375_L1.0370.89
28_N37_E1.0350.88
27_L32_F1.0350.88
287_M291_F1.0350.88
474_S478_H1.0340.88
27_L30_A1.0310.88
190_L194_S1.0310.88
21_L27_L1.0310.88
32_F36_V1.0300.88
294_T297_D1.0290.88
189_H195_N1.0280.88
40_P45_G1.0260.88
519_L524_I1.0240.88
195_N199_A1.0230.88
289_S306_N1.0230.88
43_G48_I1.0230.88
26_V37_E1.0140.87
319_T373_A1.0140.87
200_G204_Y1.0120.87
242_T260_L1.0100.87
192_V195_N1.0090.87
454_G457_L1.0070.87
276_C279_S1.0070.87
191_I194_S1.0070.87
330_V336_N1.0050.86
209_R213_P1.0020.86
155_R159_A1.0010.86
57_L67_V1.0010.86
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  
4kavA10.60851000.478Contact Map
2w8dA20.5791000.526Contact Map
2w5qA10.5791000.526Contact Map
3lxqA20.5791000.534Contact Map
3b5qA20.53681000.552Contact Map
2vqrA10.54411000.557Contact Map
2qzuA10.56251000.563Contact Map
1fsuA10.52761000.568Contact Map
1aukA10.51651000.57Contact Map
3ed4A40.55881000.571Contact 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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