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D395G VCP

ID: 1502228033 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 806 (749)
Sequences: 1246 (763.4)
Seq/Len: 1.664
Nf(neff/√len): 27.9

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: 1.664).

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
701_E735_H7.6761.00
657_L687_L7.0991.00
654_V673_E4.2511.00
425_K451_D3.9881.00
650_E677_K3.3701.00
378_L397_E3.0471.00
381_L411_L2.9671.00
654_V672_L2.9321.00
39_V84_M2.9171.00
657_L675_L2.6861.00
657_L690_I2.6751.00
701_E734_D2.5901.00
374_A401_N2.4091.00
661_L672_L2.2951.00
641_Q693_R2.2530.99
475_T533_N2.2500.99
686_D746_S2.2230.99
213_L254_I2.2030.99
664_S731_I2.1340.99
494_Q498_E2.1050.99
575_F622_A2.0210.99
28_V170_P1.9690.98
388_M415_C1.9670.98
58_L103_Q1.9530.98
491_E700_R1.9410.98
51_L71_V1.9260.98
654_V658_K1.9190.98
601_I633_I1.9110.98
647_L747_V1.8990.98
655_A658_K1.8680.97
479_I573_V1.8680.97
206_I253_L1.8470.97
732_R735_H1.8300.97
579_L621_G1.8180.97
474_V533_N1.8170.97
690_I740_M1.8100.97
531_I573_V1.8010.96
333_D362_R1.7960.96
302_F346_A1.7920.96
146_I176_V1.7830.96
738_E741_R1.7730.96
559_V600_V1.7660.96
671_D674_F1.7620.96
168_T174_C1.7330.95
661_L666_V1.7330.95
39_V57_V1.7070.95
674_F733_R1.7050.95
657_L672_L1.6950.94
547_L559_V1.6830.94
547_L576_F1.6800.94
522_C601_I1.6760.94
547_L562_I1.6620.94
286_L331_L1.6480.93
678_M740_M1.6350.93
674_F677_K1.6240.93
546_E560_R1.6220.93
561_E564_D1.5990.92
479_I526_L1.5960.92
542_I562_I1.5960.92
28_V35_D1.5940.92
269_I303_I1.5820.91
413_A416_S1.5800.91
585_A631_P1.5790.91
522_C683_S1.5780.91
249_T522_C1.5650.91
682_F743_A1.5620.91
482_L523_G1.5610.91
378_L382_Q1.5540.90
748_S751_D1.5480.90
284_S288_K1.5360.90
464_L572_C1.5310.89
545_P603_Q1.5270.89
305_E348_N1.5170.89
667_A670_V1.5140.89
554_E557_A1.5090.89
753_R757_M1.5080.88
511_S535_C1.5010.88
406_H456_L1.5000.88
403_T411_L1.4980.88
544_G555_S1.4930.88
644_Y647_L1.4910.88
604_I633_I1.4900.88
664_S691_C1.4840.87
380_I408_G1.4690.87
657_L691_C1.4600.86
650_E676_A1.4540.86
596_A599_R1.4530.86
57_V84_M1.4360.85
325_V356_A1.4280.85
334_G356_A1.4230.84
747_V751_D1.4040.83
543_K612_S1.4020.83
545_P560_R1.4010.83
528_A545_P1.4000.83
683_S747_V1.3940.83
752_I755_Y1.3720.81
733_R737_E1.3710.81
559_V582_I1.3690.81
626_P644_Y1.3670.81
531_I620_I1.3650.81
67_A71_V1.3620.80
378_L396_L1.3600.80
749_D753_R1.3590.80
668_K730_E1.3580.80
391_A394_V1.3540.80
67_A70_I1.3540.80
553_G556_E1.3510.80
507_G664_S1.3460.79
270_N602_N1.3360.79
664_S695_C1.3350.79
517_Y626_P1.3300.78
472_P528_A1.3290.78
275_M320_V1.3270.78
674_F678_M1.3260.78
579_L629_I1.3130.77
544_G560_R1.3070.77
608_M639_L1.3060.76
698_A735_H1.3060.76
24_N28_V1.3040.76
751_D754_K1.2960.76
678_M737_E1.2950.76
51_L102_I1.2900.75
502_K506_F1.2900.75
289_A301_I1.2840.75
210_R379_E1.2770.74
693_R696_K1.2770.74
512_K640_D1.2720.74
403_T456_L1.2710.74
329_L334_G1.2700.74
502_K505_K1.2670.73
646_P649_D1.2670.73
688_T692_Q1.2660.73
149_G670_V1.2650.73
667_A730_E1.2560.72
305_E313_R1.2550.72
701_E732_R1.2540.72
469_V533_N1.2520.72
313_R356_A1.2510.72
342_I376_G1.2480.72
493_V497_V1.2470.72
675_L691_C1.2310.70
42_S79_D1.2280.70
371_I569_A1.2280.70
546_E606_T1.2260.70
523_G686_D1.2240.70
223_P230_F1.2220.69
26_L170_P1.2210.69
543_K550_M1.2130.69
520_P575_F1.2110.68
541_S572_C1.2100.68
495_Y511_S1.2050.68
493_V535_C1.2020.68
475_T479_I1.2000.67
576_F691_C1.1980.67
592_D595_G1.1980.67
325_V329_L1.1960.67
753_R756_E1.1930.67
459_S569_A1.1910.67
402_E456_L1.1910.67
587_G598_D1.1890.66
557_A658_K1.1860.66
254_I459_S1.1860.66
454_W457_S1.1840.66
649_D652_S1.1830.66
450_D643_I1.1830.66
471_V533_N1.1820.66
531_I537_A1.1810.66
413_A422_A1.1810.66
543_K555_S1.1790.65
235_V423_I1.1780.65
603_Q608_M1.1730.65
476_W533_N1.1660.64
247_P334_G1.1640.64
329_L348_N1.1640.64
750_N753_R1.1620.64
68_V71_V1.1610.64
560_R606_T1.1600.64
402_E453_R1.1590.63
351_N378_L1.1550.63
662_R741_R1.1550.63
450_D454_W1.1530.63
751_D758_F1.1500.63
543_K614_K1.1490.63
325_V334_G1.1460.62
398_Q449_M1.1400.62
102_I587_G1.1370.61
583_A629_I1.1360.61
348_N356_A1.1350.61
492_L511_S1.1340.61
176_V180_T1.1300.61
574_L670_V1.1290.60
581_S686_D1.1260.60
60_K103_Q1.1260.60
277_K603_Q1.1260.60
320_V324_I1.1240.60
450_D453_R1.1220.60
203_Y221_E1.1210.60
348_N359_R1.1200.60
227_P230_F1.1190.59
208_G456_L1.1130.59
636_P685_A1.1110.59
207_G408_G1.1100.59
538_N554_E1.1100.59
245_G248_G1.1090.58
372_P380_I1.1090.58
482_L686_D1.1090.58
617_V647_L1.1080.58
756_E760_Q1.1080.58
111_G174_C1.1050.58
629_I704_E1.1050.58
111_G114_I1.1030.58
575_F609_D1.1030.58
283_E361_G1.1030.58
274_I286_L1.1020.58
28_V34_E1.0990.57
280_G283_E1.0980.57
24_N27_I1.0970.57
528_A573_V1.0960.57
547_L558_N1.0940.57
422_A451_D1.0930.57
485_V643_I1.0920.57
315_K570_A1.0920.57
259_A300_I1.0910.57
359_R362_R1.0910.57
570_A645_I1.0900.56
493_V631_P1.0880.56
329_L356_A1.0840.56
650_E654_V1.0830.56
59_L92_L1.0830.56
82_I102_I1.0810.56
583_A604_I1.0810.56
493_V561_E1.0780.55
488_E742_F1.0780.55
507_G731_I1.0770.55
254_I460_N1.0770.55
610_G632_A1.0750.55
39_V82_I1.0750.55
691_C736_F1.0720.55
255_A344_M1.0700.54
689_E693_R1.0690.54
209_C212_Q1.0680.54
304_D307_D1.0670.54
114_I176_V1.0670.54
608_M611_M1.0660.54
545_P552_F1.0650.54
536_Q541_S1.0630.54
520_P622_A1.0620.54
495_Y499_H1.0610.53
165_V168_T1.0600.53
51_L57_V1.0590.53
325_V332_M1.0590.53
98_D102_I1.0580.53
647_L683_S1.0570.53
549_T557_A1.0570.53
431_D437_I1.0570.53
45_K48_E1.0560.53
661_L736_F1.0520.52
406_H536_Q1.0520.52
349_R352_S1.0520.52
603_Q606_T1.0490.52
660_N688_T1.0490.52
283_E323_R1.0480.52
293_A298_P1.0480.52
586_R625_R1.0480.52
669_D675_L1.0420.51
737_E740_M1.0410.51
256_R676_A1.0410.51
313_R334_G1.0410.51
146_I149_G1.0410.51
495_Y503_F1.0410.51
385_T388_M1.0400.51
252_T356_A1.0390.51
246_P354_D1.0390.51
542_I629_I1.0390.51
244_Y368_D1.0380.51
399_V449_M1.0370.51
381_L414_L1.0370.51
283_E359_R1.0360.51
305_E329_L1.0360.51
472_P526_L1.0360.51
220_V254_I1.0340.51
534_E545_P1.0340.51
280_G359_R1.0320.50
542_I576_F1.0320.50
575_F580_D1.0300.50
66_E71_V1.0290.50
280_G361_G1.0260.50
552_F557_A1.0250.50
333_D465_R1.0240.49
354_D405_G1.0230.49
406_H414_L1.0230.49
217_K221_E1.0190.49
371_I463_A1.0190.49
748_S755_Y1.0170.49
687_L690_I1.0160.49
755_Y758_F1.0160.49
361_G364_D1.0150.49
80_E690_I1.0150.49
390_L394_V1.0130.48
39_V59_L1.0130.48
20_K23_P1.0120.48
385_T390_L1.0120.48
69_C72_L1.0100.48
575_F578_E1.0100.48
285_N288_K1.0090.48
467_T614_K1.0090.48
271_G287_R1.0080.48
552_F560_R1.0070.48
152_F182_I1.0070.48
91_N150_D1.0070.48
24_N29_D1.0060.48
291_E295_K1.0060.48
224_L363_F1.0030.47
293_A299_A1.0030.47
500_P744_R1.0030.47
223_P238_P1.0020.47
394_V523_G1.0020.47
283_E287_R1.0010.47
562_I651_K1.0000.47
572_C683_S1.0000.47
466_E470_E1.0000.47
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  
3cf2A40.81761000.402Contact Map
3cmuA10.83371000.62Contact Map
3j94A60.56951000.665Contact Map
4ko8A20.56581000.68Contact Map
4cr2J10.45041000.729Contact Map
2x8aA10.28781000.75Contact Map
3cf0A140.34861000.76Contact Map
4cr2L10.43551000.763Contact Map
4cr2M10.43051000.765Contact Map
4cr2K10.44791000.765Contact 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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