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OPENSEQ.org

dnd132_2001

ID: 1418185085 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 803 (795)
Sequences: 831 (489.6)
Seq/Len: 1.045
Nf(neff/√len): 17.4

HHblits Results: (2013_03)
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: 1.045).

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
120_R404_W5.1771.00
687_V735_A4.8351.00
729_A733_H4.2741.00
47_R92_E4.1971.00
39_G86_M4.0931.00
54_I61_L3.9451.00
462_A465_D3.9281.00
91_R95_G3.7731.00
423_E463_Q3.7551.00
728_A732_E3.5531.00
80_F135_A3.4131.00
501_R539_C3.3231.00
458_E462_A3.2781.00
499_Q503_R3.2201.00
685_V713_D3.1671.00
143_G159_A3.1521.00
458_E503_R3.1101.00
340_V343_E3.0861.00
498_R536_S2.9031.00
452_E455_K2.8701.00
454_L499_Q2.8671.00
598_L623_K2.8311.00
731_E761_R2.8241.00
134_V165_L2.8231.00
24_L46_I2.7561.00
85_A88_A2.7121.00
334_A338_E2.6631.00
70_R128_E2.5981.00
412_V429_C2.5951.00
67_G72_K2.5530.99
104_I130_I2.5290.99
87_T136_G2.5250.99
51_R96_D2.4400.99
371_A397_A2.4060.99
737_L798_A2.3580.99
118_T121_E2.3530.99
130_I159_A2.3440.99
478_A500_C2.2020.98
599_P602_Q2.1920.98
60_I101_A2.1770.98
207_P246_L2.1720.98
103_S228_E2.1700.98
320_I509_T2.1670.98
68_G82_L2.1580.98
528_T560_L2.1520.98
160_R164_D2.1390.97
141_I159_A2.1290.97
508_T538_L2.1060.97
279_A283_K2.0770.97
564_D570_Y2.0600.97
51_R55_E2.0570.97
495_E498_R2.0520.97
776_E780_K2.0460.96
730_A738_I2.0420.96
80_F132_G2.0220.96
275_E278_R1.9990.96
278_R282_D1.9770.95
759_A782_I1.9730.95
24_L49_V1.9700.95
375_P401_A1.9700.95
450_A499_Q1.9680.95
191_M199_I1.9660.95
143_G156_V1.9650.95
729_A732_E1.9640.95
198_L226_F1.8840.94
406_Y410_P1.8700.93
168_A198_L1.8620.93
185_M216_A1.8500.93
369_D372_A1.8460.93
378_V389_L1.8450.93
72_K108_G1.8420.93
480_A512_L1.8380.93
69_S72_K1.8290.92
501_R507_P1.8000.92
130_I162_V1.7940.91
27_R48_A1.7790.91
685_V735_A1.7650.91
51_R93_V1.7260.89
152_A169_I1.7230.89
463_Q466_A1.7220.89
123_V161_L1.7170.89
454_L503_R1.7140.89
358_V411_L1.7090.89
42_E45_V1.7080.88
47_R51_R1.7040.88
84_R88_A1.7010.88
127_K161_L1.6950.88
256_A260_E1.6880.88
198_L265_F1.6850.88
132_G136_G1.6790.87
724_E728_A1.6780.87
188_V222_S1.6570.86
422_M426_G1.6570.86
498_R502_D1.6510.86
423_E466_A1.6460.86
143_G155_V1.6460.86
104_I129_Q1.6410.86
65_T86_M1.6370.85
438_L476_V1.6310.85
132_G135_A1.6300.85
483_V560_L1.6300.85
755_V767_V1.6260.85
596_A778_F1.6160.84
127_K162_V1.6110.84
39_G64_N1.6090.84
157_V428_L1.5980.84
281_R285_G1.5940.83
757_L760_E1.5920.83
717_L729_A1.5870.83
70_R125_I1.5870.83
725_K729_A1.5770.82
512_L538_L1.5760.82
251_F280_L1.5690.82
371_A375_P1.5680.82
596_A779_C1.5600.82
320_I390_A1.5530.81
483_V559_V1.5470.81
47_R96_D1.5400.80
183_S186_T1.5400.80
279_A282_D1.5330.80
104_I159_A1.5260.80
102_A133_C1.5250.79
712_F802_T1.5240.79
156_V196_V1.5220.79
330_K333_T1.5160.79
725_K728_A1.5100.79
619_A623_K1.5070.78
614_V669_R1.5060.78
58_A277_I1.5010.78
389_L406_Y1.5000.78
361_V389_L1.4980.78
60_I140_L1.4950.78
246_L250_P1.4930.77
393_S399_V1.4920.77
82_L86_M1.4910.77
440_P457_I1.4900.77
575_S596_A1.4900.77
188_V221_L1.4900.77
23_L52_D1.4900.77
20_Y49_V1.4890.77
236_L240_G1.4860.77
391_I406_Y1.4850.77
507_P539_C1.4840.77
46_I49_V1.4830.77
391_I399_V1.4820.77
188_V223_T1.4760.76
127_K131_R1.4720.76
685_V733_H1.4670.76
768_I798_A1.4610.75
423_E427_P1.4600.75
723_A754_T1.4590.75
727_V758_V1.4550.75
48_A52_D1.4530.75
497_M508_T1.4530.75
572_D596_A1.4480.74
94_A100_V1.4440.74
558_E563_R1.4430.74
372_A376_E1.4420.74
146_H152_A1.4370.74
712_F799_Q1.4360.73
71_P125_I1.4250.73
160_R167_V1.4240.73
104_I141_I1.4200.72
575_S779_C1.4150.72
40_L82_L1.4140.72
79_P132_G1.4130.72
210_M228_E1.4100.72
441_I695_I1.4080.71
104_I126_F1.3980.71
332_L344_A1.3980.71
610_K613_V1.3860.70
463_Q467_L1.3840.69
575_S778_F1.3810.69
87_T133_C1.3810.69
15_Y284_V1.3780.69
625_M629_E1.3720.69
686_V798_A1.3680.68
331_Q343_E1.3650.68
610_K665_T1.3550.67
15_Y281_R1.3530.67
688_M704_C1.3480.67
256_A287_A1.3470.66
740_L754_T1.3410.66
497_M538_L1.3400.66
130_I141_I1.3300.65
27_R45_V1.3260.65
512_L541_F1.3220.64
628_M674_L1.3180.64
368_V373_L1.3180.64
572_D778_F1.3170.64
101_A140_L1.3130.64
83_N129_Q1.3100.63
236_L239_E1.3090.63
16_F265_F1.3030.63
798_A802_T1.2940.62
47_R93_V1.2940.62
129_Q228_E1.2920.62
54_I94_A1.2850.61
515_I525_L1.2820.61
482_T515_I1.2810.61
359_L389_L1.2800.61
509_T540_S1.2690.60
7_I12_R1.2640.59
717_L721_V1.2610.59
619_A622_D1.2600.59
80_F131_R1.2540.58
645_K650_E1.2510.58
16_F60_I1.2500.58
749_V752_E1.2460.58
423_E467_L1.2390.57
629_E674_L1.2380.57
143_G160_R1.2330.56
333_T337_Q1.2310.56
156_V167_V1.2300.56
103_S129_Q1.2230.55
134_V162_V1.2230.55
421_K425_L1.2210.55
742_A747_T1.2200.55
629_E633_D1.2130.55
171_M201_T1.2120.54
437_I538_L1.2100.54
54_I98_A1.2060.54
38_W41_K1.1980.53
499_Q502_D1.1910.52
211_R760_E1.1890.52
483_V490_A1.1870.52
235_E245_R1.1850.52
715_V729_A1.1820.52
210_M221_L1.1820.52
778_F781_A1.1780.51
450_A492_H1.1770.51
73_L77_V1.1770.51
390_A437_I1.1750.51
556_A778_F1.1750.51
470_P505_G1.1720.51
689_A726_I1.1720.51
156_V191_M1.1670.50
259_V287_A1.1660.50
215_R753_D1.1650.50
48_A51_R1.1640.50
201_T210_M1.1630.50
256_A283_K1.1590.49
186_T308_S1.1580.49
327_T365_A1.1520.49
364_G446_L1.1500.49
143_G152_A1.1470.48
484_S559_V1.1450.48
352_A387_T1.1440.48
499_Q504_W1.1430.48
712_F798_A1.1400.48
68_G85_A1.1380.47
226_F265_F1.1350.47
617_V666_A1.1310.47
572_D575_S1.1290.47
5_R164_D1.1240.46
266_I284_V1.1230.46
146_H169_I1.1230.46
454_L504_W1.1200.46
618_E621_L1.1100.45
403_L434_A1.1100.45
246_L251_F1.1100.45
71_P117_M1.1080.45
111_V596_A1.1040.44
68_G86_M1.0960.44
731_E734_D1.0940.43
728_A761_R1.0920.43
451_A455_K1.0910.43
62_T228_E1.0880.43
318_V357_P1.0860.43
494_M533_S1.0860.43
450_A454_L1.0830.42
458_E465_D1.0800.42
374_L398_A1.0770.42
730_A735_A1.0760.42
493_S510_I1.0760.42
108_G539_C1.0740.42
592_P778_F1.0730.41
641_I644_D1.0720.41
255_A266_I1.0710.41
400_E432_F1.0680.41
256_A286_D1.0670.41
16_F228_E1.0660.41
538_L541_F1.0650.41
88_A92_E1.0640.41
23_L26_S1.0630.41
491_R562_D1.0630.41
480_A538_L1.0590.40
124_D712_F1.0560.40
342_S732_E1.0520.40
788_S797_L1.0510.39
317_G416_S1.0490.39
420_G424_R1.0470.39
576_G596_A1.0470.39
84_R135_A1.0450.39
12_R59_D1.0430.39
90_A100_V1.0420.39
15_Y49_V1.0410.39
358_V390_A1.0410.39
438_L460_L1.0410.39
259_V284_V1.0390.38
123_V157_V1.0370.38
364_G370_E1.0360.38
449_T455_K1.0320.38
225_T265_F1.0310.38
334_A343_E1.0290.38
430_K470_P1.0280.37
461_L506_L1.0260.37
259_V283_K1.0250.37
29_L50_H1.0250.37
93_V96_D1.0250.37
156_V194_M1.0240.37
67_G108_G1.0230.37
450_A453_R1.0220.37
592_P776_E1.0190.37
344_A377_L1.0140.36
441_I657_L1.0130.36
331_Q685_V1.0120.36
702_I745_T1.0120.36
188_V220_R1.0120.36
29_L32_G1.0110.36
435_P473_L1.0110.36
706_M709_N1.0100.36
750_R753_D1.0080.36
704_C716_D1.0070.36
727_V763_L1.0060.36
19_G22_T1.0020.35
130_I134_V1.0010.35
104_I191_M1.0000.35
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: (06Sep14)
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  
4cczA10.68121000.529Contact Map
1q7zA20.68621000.543Contact Map
4m3pA40.42961000.748Contact Map
3k13A30.33131000.826Contact Map
1f6yA20.31881000.826Contact Map
2yciX10.3351000.827Contact Map
3bulA10.2641000.842Contact Map
3ezxA10.25781000.864Contact Map
1y80A10.15321000.865Contact Map
4jgiA20.25161000.867Contact 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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