May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org

1HCY_A -force run

ID: 1414348344 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 657 (653)
Sequences: 461 (347.6)
Seq/Len: 0.706
Nf(neff/√len): 13.6

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: 0.706).

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
512_V517_E3.4271.00
238_N572_K2.9901.00
307_D311_H2.8350.99
562_C609_C2.6160.99
301_D393_K2.5840.99
69_R112_E2.3950.98
221_F391_F2.3140.97
95_E98_C2.2930.97
505_L570_L2.1990.96
430_Q451_R2.1630.95
37_F46_Y2.1540.95
464_I584_V2.1270.94
86_L90_L2.1100.94
485_I646_V2.0870.94
427_D456_N2.0280.92
233_F483_C2.0230.92
574_K578_M1.9880.91
422_L570_L1.9620.91
513_P517_E1.9590.90
414_N467_S1.9420.90
405_N414_N1.9220.89
505_L649_I1.8770.88
239_W574_K1.8710.88
585_A626_L1.8430.87
639_V642_I1.8350.86
68_Q108_E1.7750.84
413_V586_V1.7620.83
498_A501_F1.7600.83
426_F651_H1.7540.83
86_L106_F1.7300.81
96_W99_F1.7180.81
348_H384_H1.7100.80
395_T627_E1.6970.80
99_F122_S1.6900.79
249_D290_E1.6730.78
487_D491_I1.6680.78
334_S340_Y1.6590.77
3_L8_A1.6360.76
289_L350_M1.6280.76
562_C610_G1.6210.75
478_F586_V1.6160.75
194_H220_F1.6090.74
475_L511_K1.5950.73
347_A383_L1.5830.73
481_F584_V1.5820.73
231_F381_F1.5790.72
190_M568_M1.5660.72
67_E409_S1.5650.71
137_L192_I1.5640.71
305_I327_I1.5610.71
466_M586_V1.5550.71
139_Q154_A1.5510.70
83_A117_Y1.5440.70
408_F476_A1.5420.70
181_V231_F1.5410.70
578_M649_I1.5110.68
305_I323_L1.5020.67
479_R563_G1.5000.67
232_D243_V1.5000.67
296_I328_I1.4920.66
12_Q16_H1.4910.66
4_G8_A1.4830.65
304_Y312_T1.4820.65
479_R569_L1.4720.65
215_R218_E1.4680.64
348_H367_V1.4590.64
194_H348_H1.4450.63
256_F381_F1.4370.62
91_N101_S1.4350.62
580_F649_I1.4340.62
6_G10_K1.4320.61
77_T151_I1.4260.61
479_R587_T1.4250.61
529_T569_L1.4210.61
176_N179_Q1.4050.59
483_C502_C1.4010.59
224_H380_F1.3900.58
254_E382_R1.3560.55
532_D567_R1.3560.55
454_R567_R1.3550.55
226_Q623_G1.3400.54
38_N41_G1.3290.53
528_V608_Q1.3250.53
16_H29_D1.3240.53
621_P629_R1.3230.52
344_H348_H1.3220.52
581_N646_V1.3160.52
216_K326_D1.3160.52
482_L582_L1.3140.52
243_V381_F1.3100.51
417_A463_K1.3090.51
240_L440_G1.3030.51
33_I40_L1.3020.51
97_Y132_I1.2950.50
141_T158_K1.2930.50
194_H344_H1.2920.50
13_D16_H1.2900.50
200_D560_R1.2900.50
34_A37_F1.2870.49
79_Q535_S1.2850.49
432_S572_K1.2840.49
216_K232_D1.2840.49
466_M478_F1.2790.49
293_E386_Y1.2700.48
478_F510_Q1.2690.48
496_D499_R1.2660.48
461_T520_E1.2650.48
295_R339_Y1.2620.47
203_F248_W1.2620.47
95_E516_P1.2580.47
404_D413_V1.2560.47
646_V649_I1.2520.46
66_L82_E1.2430.46
476_A586_V1.2430.46
225_H505_L1.2420.46
341_G563_G1.2420.46
416_V643_K1.2400.45
334_S341_G1.2390.45
194_H224_H1.2370.45
25_T30_L1.2340.45
326_D331_S1.2310.45
48_D52_A1.2280.44
326_D587_T1.2210.44
425_F478_F1.2180.44
583_Y642_I1.2170.44
233_F503_I1.2160.43
40_L43_T1.2160.43
37_F42_D1.2150.43
122_S129_G1.2130.43
214_D616_Y1.2100.43
158_K203_F1.2090.43
228_T385_K1.2080.43
232_D385_K1.2070.43
84_L204_W1.2040.42
17_L103_A1.1950.42
496_D631_P1.1950.42
465_T516_P1.1940.42
4_G7_N1.1920.41
296_I327_I1.1920.41
237_S255_G1.1920.41
93_C126_S1.1880.41
234_E238_N1.1880.41
29_D34_A1.1850.41
99_F207_D1.1850.41
451_R539_L1.1850.41
99_F495_L1.1850.41
140_I405_N1.1820.41
194_H617_P1.1800.41
322_E326_D1.1790.40
37_F53_V1.1750.40
107_R139_Q1.1710.40
413_V584_V1.1710.40
79_Q497_E1.1700.40
437_V579_E1.1700.40
585_A642_I1.1680.40
363_L436_A1.1670.39
299_A305_I1.1660.39
87_F91_N1.1660.39
253_R274_N1.1600.39
39_P46_Y1.1570.39
265_G385_K1.1570.39
646_V652_H1.1570.39
411_M495_L1.1540.38
82_E96_W1.1520.38
194_H388_D1.1510.38
224_H344_H1.1500.38
563_G569_L1.1480.38
435_N451_R1.1470.38
579_E648_K1.1470.38
151_I624_Y1.1460.38
81_K450_A1.1430.38
5_T8_A1.1420.37
242_P488_N1.1360.37
193_H388_D1.1360.37
295_R301_D1.1270.36
75_F198_H1.1270.36
320_G341_G1.1270.36
248_W293_E1.1210.36
295_R320_G1.1210.36
368_M562_C1.1210.36
67_E70_H1.1200.36
412_V471_D1.1190.36
23_E26_K1.1190.36
201_F375_T1.1190.36
237_S578_M1.1180.36
348_H368_M1.1180.36
481_F507_K1.1130.35
107_R521_R1.1130.35
610_G616_Y1.1130.35
132_I576_E1.1130.35
75_F348_H1.1080.35
86_L178_E1.1080.35
527_S607_A1.1050.35
189_G572_K1.1050.35
434_I502_C1.1040.34
329_E344_H1.1020.34
219_L562_C1.1000.34
207_D387_M1.1000.34
232_D501_F1.0980.34
232_D241_D1.0970.34
331_S433_L1.0970.34
405_N624_Y1.0960.34
220_F344_H1.0950.34
617_P622_L1.0940.34
151_I372_E1.0940.34
483_C652_H1.0930.34
563_G623_G1.0920.34
137_L145_F1.0920.34
171_T398_F1.0870.33
194_H197_W1.0870.33
479_R499_R1.0860.33
193_H198_H1.0860.33
72_Y83_A1.0840.33
125_H512_V1.0840.33
437_V505_L1.0830.33
112_E149_E1.0800.33
324_L624_Y1.0760.32
220_F348_H1.0750.32
170_F430_Q1.0750.32
464_I572_K1.0740.32
118_A303_G1.0720.32
231_F235_R1.0710.32
640_S651_H1.0700.32
272_P275_I1.0700.32
588_D591_K1.0700.32
347_A375_T1.0680.32
93_C128_L1.0670.32
444_E481_F1.0670.32
215_R609_C1.0650.32
69_R110_M1.0640.32
232_D588_D1.0640.32
153_K156_S1.0630.31
344_H384_H1.0620.31
384_H588_D1.0610.31
231_F386_Y1.0590.31
123_V281_D1.0580.31
60_L98_C1.0560.31
324_L328_I1.0550.31
410_G470_N1.0550.31
363_L651_H1.0540.31
215_R610_G1.0520.31
363_L426_F1.0510.31
348_H388_D1.0480.30
194_H384_H1.0470.30
150_V252_I1.0460.30
388_D617_P1.0460.30
188_I193_H1.0460.30
147_N172_G1.0450.30
134_L236_L1.0450.30
459_E570_L1.0430.30
64_R82_E1.0430.30
231_F301_D1.0420.30
390_I405_N1.0420.30
170_F228_T1.0420.30
545_N550_G1.0410.30
478_F512_V1.0400.30
598_G601_D1.0400.30
67_E258_P1.0340.29
88_A206_E1.0340.29
345_N367_V1.0330.29
328_I415_G1.0320.29
337_V467_S1.0320.29
78_R465_T1.0300.29
206_E277_F1.0290.29
339_Y358_H1.0280.29
330_S337_V1.0260.29
411_M512_V1.0250.29
623_G628_R1.0240.29
32_D54_E1.0220.29
41_G47_N1.0220.29
46_Y227_L1.0210.28
295_R340_Y1.0210.28
122_S126_S1.0200.28
222_W504_E1.0200.28
504_E618_D1.0200.28
73_S272_P1.0190.28
118_A134_L1.0190.28
495_L630_I1.0190.28
99_F236_L1.0170.28
79_Q83_A1.0170.28
145_F298_E1.0160.28
496_D630_I1.0160.28
311_H514_S1.0150.28
224_H341_G1.0150.28
198_H215_R1.0150.28
144_M372_E1.0150.28
64_R450_A1.0150.28
103_A118_A1.0150.28
117_Y125_H1.0130.28
23_E466_M1.0130.28
300_I328_I1.0130.28
175_K296_I1.0130.28
87_F209_Y1.0130.28
185_G195_V1.0120.28
95_E145_F1.0110.28
215_R321_I1.0110.28
214_D610_G1.0110.28
618_D627_E1.0110.28
236_L425_F1.0090.28
482_L601_D1.0080.28
409_S414_N1.0070.27
496_D629_R1.0050.27
132_I636_I1.0050.27
342_S505_L1.0040.27
408_F588_D1.0040.27
365_P435_N1.0040.27
450_A589_G1.0040.27
184_F190_M1.0020.27
107_R182_A1.0010.27
220_F329_E1.0000.27
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  
1hc1A60.9651000.056Contact Map
4l37A10.95891000.087Contact Map
3gwjA60.95891000.093Contact Map
3ixvA120.92851000.107Contact Map
1llaA10.8951000.109Contact Map
3hhsB10.93911000.118Contact Map
3wkyA20.90411000.13Contact Map
3hhsA10.93151000.134Contact Map
1bt3A10.441497.20.971Contact Map
2p3xA10.450597.10.971Contact 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.

Page generated in 1.1554 seconds.