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Run for P6 and P7

ID: 1504735914 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 655 (602)
Sequences: 9520 (8103.5)
Seq/Len: 15.814
Nf(neff/√len): 330.3

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: 15.814).

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
473_R504_A4.0151.00
268_V279_L3.2891.00
163_S166_K3.2311.00
511_A519_N2.8511.00
417_Q615_P2.8461.00
121_I150_L2.7261.00
616_E620_S2.6861.00
124_Q153_L2.6661.00
108_A134_T2.5621.00
446_A456_I2.5501.00
136_N171_P2.5351.00
134_T174_A2.5341.00
464_T629_L2.5221.00
114_L181_Q2.4991.00
513_L633_L2.4111.00
172_T175_E2.4031.00
468_W625_A2.3991.00
258_L362_L2.3631.00
403_R523_Q2.3621.00
485_P489_Q2.3521.00
256_Q260_D2.3391.00
118_M154_V2.3361.00
137_Y142_G2.3281.00
355_L494_V2.3241.00
607_W619_L2.3231.00
113_P116_T2.3031.00
342_F347_F2.2571.00
607_W623_F2.2511.00
396_D530_H2.2491.00
136_N139_E2.2361.00
133_M173_I2.2321.00
111_Q133_M2.2111.00
255_W326_V2.2021.00
596_V605_L2.1991.00
132_G135_D2.1981.00
122_W173_I2.1951.00
459_T516_R2.1871.00
462_A505_V2.1511.00
258_L359_W2.1401.00
251_I359_W2.1381.00
76_L79_L2.1301.00
442_L453_P2.1141.00
268_V321_W2.1121.00
166_K179_H2.1121.00
357_S492_A2.0951.00
475_T502_L2.0521.00
261_H358_E2.0341.00
522_Q526_R2.0051.00
461_Y556_V1.9941.00
428_E611_E1.9881.00
473_R506_E1.9781.00
257_R260_D1.9771.00
449_F514_L1.9771.00
252_N256_Q1.9671.00
115_E133_M1.9571.00
432_A605_L1.9541.00
428_E616_E1.9491.00
112_T133_M1.9471.00
262_H358_E1.9131.00
117_E120_A1.8831.00
121_I154_V1.8831.00
317_A320_V1.8771.00
620_S624_A1.8441.00
416_A618_M1.8331.00
117_E157_R1.8221.00
107_F130_R1.8191.00
397_L541_E1.8171.00
247_D250_R1.8081.00
276_Q279_L1.8061.00
627_C631_H1.7921.00
398_D402_A1.7881.00
396_D532_L1.7821.00
138_F168_F1.7741.00
514_L638_A1.7651.00
170_K179_H1.7611.00
461_Y594_H1.7541.00
112_T181_Q1.7481.00
636_E639_A1.7481.00
466_G507_L1.7461.00
430_L620_S1.7331.00
438_K631_H1.7321.00
455_G521_Q1.7291.00
119_A173_I1.7241.00
443_K598_E1.7231.00
57_A73_F1.7081.00
397_L533_V1.6991.00
407_L475_T1.6981.00
263_E376_S1.6921.00
594_H607_W1.6821.00
399_Y403_R1.6731.00
512_T515_E1.6691.00
155_R161_E1.6551.00
108_A133_M1.6551.00
118_M177_A1.6501.00
112_T116_T1.6431.00
461_Y558_F1.6391.00
323_L346_I1.6381.00
477_N554_M1.6301.00
264_M267_A1.6181.00
394_Q398_D1.6131.00
59_F63_K1.6101.00
116_T120_A1.5991.00
625_A651_P1.5981.00
537_T540_R1.5831.00
247_D363_Y1.5751.00
276_Q280_P1.5661.00
114_L117_E1.5621.00
248_L328_A1.5581.00
535_G539_Q1.5571.00
120_A157_R1.5441.00
125_L150_L1.5431.00
621_D625_A1.5431.00
615_P618_M1.5361.00
609_A619_L1.5301.00
502_L538_V1.5191.00
303_E306_A1.5161.00
269_V346_I1.5091.00
459_T520_L1.5041.00
463_E629_L1.5011.00
250_R363_Y1.5011.00
401_T541_E1.4751.00
251_I338_L1.4711.00
403_R526_R1.4681.00
291_D330_R1.4661.00
444_E448_E1.4641.00
397_L401_T1.4631.00
257_R362_L1.4631.00
538_V542_L1.4581.00
435_D438_K1.4471.00
119_A133_M1.4431.00
143_D146_L1.4431.00
424_S612_G1.4411.00
225_S271_P1.4381.00
118_M173_I1.4381.00
150_L167_I1.4371.00
57_A61_K1.4261.00
453_P603_L1.4181.00
460_A630_L1.4161.00
468_W622_M1.4151.00
441_K631_H1.4141.00
326_V338_L1.4131.00
214_T217_Q1.4101.00
326_V340_I1.4060.99
640_W643_T1.4050.99
505_V520_L1.3970.99
170_K175_E1.3930.99
112_T115_E1.3930.99
462_A476_I1.3920.99
410_A550_Q1.3880.99
399_Y527_D1.3850.99
111_Q115_E1.3850.99
463_E516_R1.3840.99
458_L476_I1.3820.99
167_I176_L1.3790.99
426_R612_G1.3770.99
277_Q280_P1.3740.99
122_W142_G1.3710.99
614_F619_L1.3570.99
115_E177_A1.3560.99
166_K169_D1.3500.99
119_A131_V1.3490.99
402_A405_D1.3480.99
458_L524_L1.3440.99
216_I219_A1.3410.99
290_T327_R1.3370.99
424_S610_V1.3330.99
329_S339_H1.3320.99
441_K635_E1.3260.99
107_F132_G1.3240.99
59_F62_H1.3160.99
398_D401_T1.3140.99
133_M174_A1.3110.99
464_T626_Y1.3080.99
460_A633_L1.3020.99
433_K604_L1.2970.99
231_G335_R1.2950.99
377_F380_Y1.2890.99
251_I363_Y1.2880.99
52_N55_R1.2800.99
88_D91_A1.2780.99
632_R645_P1.2740.99
117_E158_I1.2730.99
246_L251_I1.2720.99
558_F596_V1.2710.99
160_V180_V1.2640.99
114_L180_V1.2610.99
108_A174_A1.2610.99
165_G169_D1.2590.99
537_T541_E1.2520.99
311_M327_R1.2500.99
347_F494_V1.2500.99
547_G550_Q1.2480.99
629_L644_A1.2440.98
293_R333_D1.2410.98
107_F110_P1.2410.98
433_K602_E1.2390.98
110_P133_M1.2340.98
506_E511_A1.2300.98
438_K441_K1.2270.98
318_P345_L1.2230.98
53_P73_F1.2180.98
357_S361_R1.2170.98
524_L528_L1.2080.98
510_G642_E1.2030.98
55_R59_F1.1990.98
65_P68_M1.1980.98
330_R336_V1.1980.98
79_L87_V1.1960.98
154_V180_V1.1890.98
365_E368_A1.1850.98
246_L336_V1.1820.98
618_M621_D1.1820.98
442_L456_I1.1800.98
507_L511_A1.1750.98
214_T377_F1.1750.98
466_G469_S1.1740.98
215_D384_L1.1730.98
218_Q385_E1.1730.98
111_Q174_A1.1710.98
328_A338_L1.1660.97
449_F518_R1.1640.97
315_V325_D1.1620.97
508_S511_A1.1610.97
454_S478_L1.1550.97
457_L560_S1.1530.97
526_R529_D1.1490.97
458_L558_F1.1480.97
533_V541_E1.1480.97
245_N334_G1.1470.97
270_L277_Q1.1410.97
122_W176_L1.1410.97
220_Y496_D1.1330.97
460_A626_Y1.1330.97
439_W443_K1.1290.97
441_K634_T1.1280.97
451_L517_G1.1260.97
267_A278_I1.1230.97
248_L252_N1.1220.97
457_L558_F1.1200.96
311_M314_Q1.1190.96
307_I329_S1.1160.96
445_R449_F1.1160.96
430_L616_E1.1150.96
439_W453_P1.1150.96
150_L176_L1.1130.96
406_D504_A1.1120.96
58_D62_H1.1100.96
362_L370_L1.1090.96
430_L623_F1.1080.96
119_A123_C1.1080.96
162_L176_L1.1080.96
147_A164_L1.1060.96
479_T559_T1.1000.96
515_E518_R1.0980.96
147_A167_I1.0980.96
373_L493_L1.0980.96
151_A167_I1.0970.96
639_A643_T1.0950.96
559_T562_L1.0940.96
380_Y383_A1.0900.96
432_A623_F1.0890.96
263_E266_R1.0880.96
324_F340_I1.0880.96
465_L556_V1.0860.96
435_D631_H1.0850.96
347_F352_M1.0840.96
350_W481_F1.0830.96
351_S494_V1.0820.96
533_V538_V1.0810.95
252_N286_Q1.0800.95
306_A310_E1.0780.95
264_M494_V1.0750.95
173_I176_L1.0740.95
467_A625_A1.0710.95
260_D281_Q1.0690.95
222_L226_G1.0650.95
149_R153_L1.0600.95
259_I324_F1.0600.95
451_L456_I1.0580.95
480_Q501_T1.0550.95
439_W603_L1.0550.95
151_A155_R1.0520.95
213_L217_Q1.0520.95
279_L282_V1.0500.94
342_F346_I1.0500.94
472_S506_E1.0490.94
128_V131_V1.0450.94
519_N523_Q1.0450.94
272_N275_Q1.0440.94
254_A359_W1.0440.94
118_M180_V1.0390.94
457_L603_L1.0380.94
594_H605_L1.0370.94
394_Q397_L1.0350.94
445_R634_T1.0350.94
308_R339_H1.0350.94
511_A515_E1.0350.94
217_Q220_Y1.0290.94
360_T364_H1.0290.94
645_P652_R1.0270.94
556_V559_T1.0240.93
261_H362_L1.0240.93
207_R263_E1.0210.93
110_P119_A1.0180.93
207_R211_F1.0170.93
624_A627_C1.0150.93
633_L644_A1.0120.93
254_A362_L1.0110.93
428_E609_A1.0100.93
311_M341_S1.0080.93
328_A336_V1.0080.93
154_V160_V1.0050.93
528_L531_P1.0050.93
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  
2jgpA10.78781000.298Contact Map
4tx3B10.67181000.473Contact Map
2vsqA10.67331000.478Contact Map
1l5aA30.64271000.483Contact Map
4znmA201000.497Contact Map
4jn3A20.64891000.497Contact Map
4hvmA40.58631000.509Contact Map
2xhgA10.6581000.523Contact Map
1q9jA20.56491000.603Contact Map
3fotA10.66871000.634Contact 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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