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VCP

ID: 1502224121 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 806 (749)
Sequences: 1242 (761)
Seq/Len: 1.658
Nf(neff/√len): 27.8

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: 1.658).

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_H7.8451.00
657_L687_L7.1281.00
654_V673_E4.3441.00
425_K451_D4.0281.00
650_E677_K3.5391.00
378_L397_E3.1441.00
381_L411_L3.1351.00
654_V672_L3.0011.00
39_V84_M2.9271.00
657_L675_L2.7311.00
701_E734_D2.7281.00
657_L690_I2.5831.00
374_A401_N2.4851.00
475_T533_N2.3201.00
661_L672_L2.3051.00
641_Q693_R2.2640.99
686_D746_S2.1910.99
213_L254_I2.1860.99
664_S731_I2.1700.99
51_L71_V2.1200.99
494_Q498_E2.0980.99
575_F622_A2.0510.99
146_I176_V2.0330.99
491_E700_R1.9960.98
654_V658_K1.9770.98
655_A658_K1.9600.98
388_M415_C1.9500.98
579_L621_G1.9340.98
58_L103_Q1.9290.98
28_V170_P1.9280.98
601_I633_I1.9210.98
738_E741_R1.9120.98
732_R735_H1.9120.98
647_L747_V1.9100.98
690_I740_M1.8780.97
39_V57_V1.8680.97
302_F346_A1.8480.97
206_I253_L1.8380.97
531_I573_V1.8300.97
474_V533_N1.8290.97
671_D674_F1.8000.96
333_D362_R1.7790.96
559_V600_V1.7730.96
674_F733_R1.7650.96
479_I573_V1.7520.96
547_L562_I1.7360.95
547_L576_F1.7240.95
667_A670_V1.6990.95
286_L331_L1.6940.94
661_L666_V1.6800.94
674_F677_K1.6760.94
657_L672_L1.6660.94
479_I526_L1.6590.94
522_C601_I1.6580.94
547_L559_V1.6420.93
561_E564_D1.6300.93
678_M740_M1.6160.92
249_T522_C1.5960.92
378_L382_Q1.5960.92
585_A631_P1.5960.92
546_E560_R1.5780.91
522_C683_S1.5670.91
284_S288_K1.5670.91
464_L572_C1.5660.91
168_T174_C1.5540.90
682_F743_A1.5470.90
542_I562_I1.5400.90
413_A416_S1.5380.90
403_T411_L1.5330.89
28_V35_D1.5220.89
269_I303_I1.5180.89
482_L523_G1.5160.89
554_E557_A1.5150.89
753_R757_M1.5070.88
748_S751_D1.5050.88
664_S691_C1.4860.87
683_S747_V1.4770.87
544_G555_S1.4770.87
305_E348_N1.4700.87
545_P603_Q1.4650.86
511_S535_C1.4640.86
604_I633_I1.4630.86
644_Y647_L1.4630.86
380_I408_G1.4590.86
325_V356_A1.4590.86
668_K730_E1.4560.86
596_A599_R1.4460.85
406_H456_L1.4310.85
57_V84_M1.4110.83
334_G356_A1.4050.83
657_L691_C1.4050.83
733_R737_E1.3980.83
650_E676_A1.3930.82
275_M320_V1.3890.82
752_I755_Y1.3880.82
749_D753_R1.3860.82
531_I620_I1.3800.82
543_K612_S1.3790.82
67_A70_I1.3760.81
378_L396_L1.3760.81
545_P560_R1.3710.81
608_M639_L1.3680.81
747_V751_D1.3580.80
553_G556_E1.3580.80
528_A545_P1.3540.80
664_S695_C1.3430.79
579_L629_I1.3390.79
210_R379_E1.3380.79
67_A71_V1.3380.79
626_P644_Y1.3370.79
507_G664_S1.3320.78
472_P528_A1.3270.78
502_K506_F1.3260.78
403_T456_L1.3220.78
502_K505_K1.3210.78
517_Y626_P1.3150.77
24_N28_V1.3100.77
646_P649_D1.3030.76
678_M737_E1.2960.76
701_E732_R1.2940.75
270_N602_N1.2940.75
693_R696_K1.2880.75
698_A735_H1.2870.75
544_G560_R1.2800.74
751_D754_K1.2790.74
512_K640_D1.2770.74
391_A394_V1.2760.74
667_A730_E1.2640.73
469_V533_N1.2630.73
342_I376_G1.2630.73
42_S79_D1.2550.72
493_V535_C1.2550.72
51_L102_I1.2460.71
674_F678_M1.2440.71
523_G686_D1.2420.71
688_T692_Q1.2310.70
570_A645_I1.2310.70
459_S569_A1.2290.70
520_P575_F1.2280.70
305_E313_R1.2280.70
402_E456_L1.2250.70
471_V533_N1.2220.69
576_F691_C1.2210.69
475_T479_I1.2200.69
329_L334_G1.2200.69
662_R741_R1.2170.69
493_V497_V1.2150.69
223_P230_F1.2140.69
371_I569_A1.2060.68
546_E606_T1.2000.67
313_R356_A1.1990.67
753_R756_E1.1980.67
402_E453_R1.1960.67
454_W457_S1.1960.67
583_A629_I1.1950.67
541_S572_C1.1950.67
26_L170_P1.1940.67
149_G670_V1.1930.67
649_D652_S1.1920.67
325_V329_L1.1890.66
413_A422_A1.1890.66
301_I367_V1.1880.66
531_I537_A1.1850.66
495_Y511_S1.1830.66
254_I459_S1.1830.66
592_D595_G1.1810.66
675_L691_C1.1790.65
587_G598_D1.1760.65
574_L670_V1.1730.65
274_I286_L1.1720.65
543_K550_M1.1720.65
351_N378_L1.1720.65
235_V423_I1.1720.65
68_V71_V1.1670.64
315_K570_A1.1610.64
60_K103_Q1.1600.63
543_K555_S1.1590.63
559_V582_I1.1550.63
560_R606_T1.1550.63
247_P334_G1.1550.63
557_A658_K1.1530.63
450_D643_I1.1530.63
476_W533_N1.1490.62
450_D453_R1.1450.62
751_D758_F1.1400.62
325_V334_G1.1370.61
543_K614_K1.1330.61
689_E693_R1.1330.61
24_N27_I1.1320.61
227_P230_F1.1310.61
603_Q608_M1.1300.60
82_I102_I1.1290.60
398_Q449_M1.1290.60
245_G248_G1.1280.60
485_V643_I1.1280.60
547_L558_N1.1250.60
617_V647_L1.1250.60
320_V324_I1.1240.60
208_G456_L1.1230.60
59_L92_L1.1180.59
636_P685_A1.1180.59
111_G114_I1.1170.59
528_A573_V1.1170.59
750_N753_R1.1170.59
329_L348_N1.1160.59
507_G731_I1.1140.59
549_T557_A1.1120.59
348_N356_A1.1080.58
493_V631_P1.1060.58
203_Y221_E1.1050.58
493_V561_E1.1050.58
146_I149_G1.1050.58
629_I704_E1.1030.58
255_A344_M1.1010.58
661_L736_F1.0980.57
111_G174_C1.0960.57
450_D454_W1.0950.57
406_H536_Q1.0950.57
482_L686_D1.0930.57
756_E760_Q1.0920.57
610_G632_A1.0910.56
422_A451_D1.0910.56
542_I576_F1.0900.56
277_K603_Q1.0900.56
406_H414_L1.0890.56
207_G408_G1.0880.56
488_E742_F1.0860.56
520_P622_A1.0840.56
575_F609_D1.0840.56
583_A604_I1.0840.56
372_P380_I1.0810.55
492_L511_S1.0810.55
289_A301_I1.0800.55
259_A300_I1.0790.55
59_L100_I1.0790.55
325_V332_M1.0780.55
329_L356_A1.0760.55
252_T356_A1.0760.55
473_Q533_N1.0750.55
39_V82_I1.0740.55
348_N359_R1.0730.55
349_R352_S1.0730.55
254_I460_N1.0710.54
209_C212_Q1.0690.54
538_N554_E1.0690.54
460_N567_R1.0670.54
280_G283_E1.0670.54
283_E361_G1.0670.54
359_R362_R1.0660.54
581_S686_D1.0660.54
650_E654_V1.0650.54
669_D675_L1.0640.54
293_A298_P1.0630.54
495_Y499_H1.0630.54
244_Y368_D1.0620.53
69_C72_L1.0620.53
165_V168_T1.0610.53
24_N29_D1.0610.53
608_M611_M1.0610.53
385_T388_M1.0610.53
28_V34_E1.0600.53
381_L414_L1.0570.53
545_P552_F1.0560.53
102_I587_G1.0540.53
220_V254_I1.0510.52
291_E295_K1.0470.52
45_K48_E1.0440.52
495_Y503_F1.0440.52
135_L182_I1.0420.51
98_D102_I1.0410.51
390_L394_V1.0390.51
691_C736_F1.0380.51
57_V114_I1.0350.51
256_R676_A1.0340.50
224_L363_F1.0330.50
431_D437_I1.0320.50
51_L57_V1.0310.50
304_D307_D1.0310.50
293_A299_A1.0300.50
586_R625_R1.0300.50
66_E71_V1.0300.50
176_V517_Y1.0290.50
65_R150_D1.0280.50
752_I756_E1.0270.50
283_E323_R1.0270.50
246_P354_D1.0260.50
575_F580_D1.0250.49
550_M557_A1.0240.49
660_N688_T1.0230.49
737_E740_M1.0200.49
412_A416_S1.0190.49
50_Q102_I1.0190.49
257_A261_E1.0160.49
27_I30_E1.0160.49
647_L683_S1.0160.49
280_G361_G1.0150.48
661_L690_I1.0140.48
20_K23_P1.0130.48
313_R334_G1.0130.48
552_F560_R1.0130.48
361_G364_D1.0120.48
552_F557_A1.0120.48
666_V672_L1.0120.48
333_D465_R1.0090.48
217_K221_E1.0090.48
283_E287_R1.0070.48
575_F578_E1.0060.47
702_S729_P1.0050.47
371_I463_A1.0050.47
542_I558_N1.0050.47
603_Q606_T1.0030.47
248_G251_K1.0030.47
80_E690_I1.0020.47
39_V59_L1.0010.47
280_G359_R1.0000.47
247_P287_R1.0000.47
415_C691_C1.0000.47
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
3cmuA10.82261000.62Contact Map
3j94A60.56951000.665Contact Map
4ko8A20.56581000.681Contact Map
4cr2J10.45041000.729Contact Map
2x8aA10.28781000.751Contact Map
3cf0A140.34861000.76Contact Map
4cr2L10.43181000.764Contact Map
4cr2M10.4331000.765Contact Map
4cr2K10.44791000.766Contact 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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