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stalk helix with L1NS

ID: 1499722593 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 710 (679)
Sequences: 1340 (773)
Seq/Len: 1.973
Nf(neff/√len): 29.7

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: 1.973).

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
91_G107_I5.6071.00
29_V179_S4.4391.00
312_A691_L4.1871.00
204_D207_G2.2941.00
318_L683_R2.2671.00
189_T193_T2.2611.00
263_R267_A2.2221.00
486_L640_V2.2041.00
483_V640_V2.1070.99
212_A237_V2.0730.99
433_E480_N2.0480.99
52_P59_T2.0110.99
257_S260_D1.9720.99
242_I288_T1.9700.99
256_K264_D1.9350.99
188_N219_L1.9240.99
163_E167_R1.9200.98
35_S39_S1.8770.98
207_G210_T1.8610.98
407_F413_F1.8510.98
45_L286_A1.8370.98
306_T310_V1.8000.97
249_Q252_I1.7780.97
496_T638_D1.7740.97
279_R288_T1.7620.97
482_M485_N1.7280.96
26_P32_G1.7260.96
490_E635_N1.6840.96
316_Q695_Q1.6760.96
99_K106_E1.6490.95
136_S139_V1.6310.95
217_L243_G1.6270.95
43_E53_R1.6220.95
503_D507_L1.6060.94
248_S251_D1.5950.94
266_Y270_Q1.5880.94
500_D634_K1.5870.94
32_G37_G1.5740.93
200_S204_D1.5730.93
340_F443_I1.5670.93
32_G38_K1.5440.92
425_E484_H1.5200.92
32_G35_S1.5130.91
173_F180_I1.5100.91
146_D149_G1.4980.91
228_D233_R1.4820.90
30_V43_E1.4700.90
30_V42_L1.4500.89
251_D264_D1.4400.88
676_E684_R1.4290.88
210_T216_K1.4250.88
34_Q39_S1.4250.88
667_S670_L1.4140.87
428_S636_I1.4140.87
222_A250_L1.4120.87
24_Q176_N1.4110.87
266_Y283_K1.4060.87
52_P60_R1.4050.87
99_K257_S1.4000.86
486_L636_I1.3900.86
329_K671_D1.3890.86
35_S40_S1.3870.86
441_R640_V1.3790.85
57_I60_R1.3780.85
562_N589_A1.3780.85
114_E117_R1.3770.85
309_N698_S1.3730.85
264_D271_K1.3670.85
56_G60_R1.3620.84
187_A214_I1.3560.84
590_S593_K1.3550.84
265_E269_L1.3540.84
520_L523_E1.3450.83
30_V34_Q1.3440.83
640_V649_V1.3440.83
171_L202_E1.3430.83
59_T62_P1.3410.83
631_I634_K1.3230.82
487_V636_I1.3230.82
193_T490_E1.3220.82
692_K696_G1.3210.82
389_T622_E1.3190.82
38_K43_E1.3160.81
186_A189_T1.3160.81
167_R171_L1.3070.81
167_R195_E1.3070.81
35_S38_K1.3070.81
125_V166_I1.3060.81
30_V35_S1.3000.80
104_F230_L1.2980.80
28_I213_V1.2940.80
221_D249_Q1.2930.80
111_I120_G1.2910.80
65_L144_L1.2890.80
279_R490_E1.2880.80
53_R56_G1.2880.80
127_P172_R1.2860.79
181_I204_D1.2850.79
409_P433_E1.2830.79
40_S43_E1.2810.79
152_K195_E1.2810.79
457_F460_L1.2800.79
204_D210_T1.2770.79
54_G58_V1.2730.78
407_F624_L1.2720.78
8_I12_Q1.2710.78
240_G281_G1.2700.78
183_A239_L1.2660.78
52_P62_P1.2650.78
53_R59_T1.2630.78
425_E488_A1.2590.77
53_R60_R1.2550.77
679_D694_L1.2550.77
15_F18_V1.2540.77
30_V40_S1.2540.77
12_Q64_I1.2470.76
174_I203_V1.2460.76
37_G40_S1.2450.76
457_F691_L1.2450.76
221_D225_D1.2440.76
40_S59_T1.2430.76
215_T218_D1.2400.76
170_I625_I1.2360.76
220_M225_D1.2310.75
628_Y638_D1.2290.75
486_L639_S1.2290.75
237_V241_I1.2240.75
531_D537_S1.2190.74
246_N265_E1.2190.74
106_E109_Q1.2160.74
8_I11_L1.2150.74
39_S60_R1.2070.73
34_Q37_G1.2070.73
216_K240_G1.2050.73
431_C636_I1.2040.73
318_L322_Y1.2030.73
57_I166_I1.2020.73
55_T58_V1.1990.72
241_I617_D1.1990.72
226_A243_G1.1970.72
311_L315_Y1.1940.72
51_L63_L1.1930.72
171_L203_V1.1930.72
533_L536_D1.1930.72
627_S631_I1.1910.72
34_Q59_T1.1860.71
260_D263_R1.1850.71
224_T249_Q1.1840.71
34_Q56_G1.1830.71
400_T403_R1.1830.71
26_P34_Q1.1830.71
689_D692_K1.1800.71
34_Q40_S1.1780.70
35_S59_T1.1770.70
4_L56_G1.1740.70
32_G40_S1.1720.70
32_G39_S1.1680.70
46_V49_D1.1680.70
248_S661_V1.1620.69
14_V19_G1.1610.69
498_H634_K1.1590.69
14_V17_T1.1570.68
279_R292_L1.1530.68
193_T269_L1.1520.68
104_F213_V1.1510.68
94_L131_H1.1500.68
30_V37_G1.1500.68
27_Q176_N1.1490.68
29_V174_I1.1490.68
187_A401_G1.1480.68
1_M14_V1.1480.68
12_Q139_V1.1470.67
495_N642_K1.1470.67
15_F19_G1.1470.67
51_L66_Q1.1460.67
485_N647_F1.1440.67
183_A204_D1.1390.67
248_S252_I1.1390.67
217_L403_R1.1370.67
489_I647_F1.1360.66
16_N19_G1.1310.66
477_P481_E1.1310.66
293_L297_I1.1290.66
53_R190_D1.1280.66
200_S205_P1.1270.66
217_L245_V1.1270.66
488_A654_D1.1270.66
521_A524_L1.1260.65
36_S143_T1.1260.65
464_I654_D1.1260.65
293_L304_L1.1240.65
28_I43_E1.1210.65
221_D224_T1.1200.65
371_H431_C1.1200.65
25_L28_I1.1190.65
632_V635_N1.1190.65
243_G273_Y1.1170.64
425_E429_L1.1160.64
638_D641_P1.1150.64
34_Q43_E1.1140.64
281_G285_L1.1110.64
683_R686_E1.1110.64
486_L643_A1.1110.64
265_E285_L1.1100.64
531_D536_D1.1080.64
92_K98_N1.1060.63
52_P56_G1.1050.63
9_N12_Q1.1030.63
632_V638_D1.1030.63
27_Q457_F1.1000.63
677_S686_E1.0980.63
62_P199_I1.0980.63
418_K421_I1.0960.62
169_L211_L1.0960.62
34_Q58_V1.0950.62
53_R273_Y1.0950.62
116_E166_I1.0940.62
502_A506_G1.0940.62
637_Q648_L1.0940.62
436_H476_L1.0910.62
532_K536_D1.0900.62
26_P40_S1.0880.61
191_M229_V1.0880.61
316_Q691_L1.0870.61
220_M226_A1.0860.61
62_P169_L1.0840.61
685_K689_D1.0830.61
111_I115_T1.0830.61
26_P30_V1.0820.61
98_N559_T1.0820.61
634_K638_D1.0820.61
53_R57_I1.0770.60
51_L56_G1.0760.60
159_P162_I1.0750.60
54_G252_I1.0730.60
241_I269_L1.0730.60
213_V366_I1.0720.60
57_I66_Q1.0710.60
432_V483_V1.0710.60
8_I297_I1.0700.60
56_G59_T1.0670.59
175_S473_R1.0670.59
483_V644_V1.0660.59
531_D535_Q1.0650.59
237_V269_L1.0630.59
30_V38_K1.0620.59
142_L289_L1.0620.59
474_K659_E1.0620.59
417_V421_I1.0600.58
53_R58_V1.0580.58
532_K535_Q1.0580.58
688_A703_E1.0570.58
26_P38_K1.0560.58
196_A460_L1.0560.58
521_A536_D1.0550.58
532_K537_S1.0550.58
478_V481_E1.0540.58
335_Q656_L1.0530.58
323_G614_E1.0530.58
167_R199_I1.0520.58
140_V290_N1.0510.58
498_H501_F1.0510.58
126_S137_P1.0500.57
636_I639_S1.0490.57
23_I263_R1.0480.57
125_V194_S1.0480.57
310_V474_K1.0480.57
265_E268_F1.0470.57
396_I409_P1.0470.57
631_I638_D1.0460.57
89_E137_P1.0460.57
177_P340_F1.0450.57
10_K649_V1.0440.57
1_M28_I1.0440.57
26_P37_G1.0440.57
125_V151_T1.0440.57
31_V34_Q1.0440.57
520_L524_L1.0420.57
46_V194_S1.0420.57
521_A537_S1.0420.57
36_S39_S1.0400.56
52_P58_V1.0400.56
200_S207_G1.0400.56
656_L661_V1.0390.56
132_L186_A1.0380.56
310_V314_Q1.0370.56
36_S380_S1.0370.56
39_S43_E1.0360.56
193_T301_L1.0350.56
201_R235_I1.0350.56
232_G472_L1.0350.56
33_T648_L1.0340.56
496_T628_Y1.0330.56
10_K700_I1.0320.55
29_V32_G1.0310.55
104_F108_R1.0310.55
498_H504_A1.0300.55
267_A321_S1.0280.55
374_F464_I1.0280.55
62_P147_L1.0260.55
237_V240_G1.0250.55
336_L405_A1.0250.55
43_E182_L1.0250.55
314_Q433_E1.0240.55
105_D388_N1.0220.54
30_V39_S1.0220.54
39_S149_G1.0200.54
367_C645_M1.0190.54
208_R299_D1.0190.54
180_I196_A1.0180.54
37_G42_L1.0170.54
51_L54_G1.0170.54
39_S58_V1.0150.54
91_G102_T1.0150.54
34_Q52_P1.0150.54
684_R694_L1.0140.53
220_M273_Y1.0140.53
621_I632_V1.0130.53
30_V182_L1.0110.53
167_R198_K1.0110.53
311_L690_M1.0110.53
313_A317_S1.0110.53
34_Q38_K1.0100.53
41_V246_N1.0100.53
24_Q193_T1.0080.53
12_Q33_T1.0080.53
563_W567_L1.0070.53
500_D504_A1.0060.53
27_Q31_V1.0050.52
445_H685_K1.0050.52
14_V18_V1.0050.52
77_K174_I1.0030.52
28_I42_L1.0020.52
212_A269_L1.0010.52
38_K59_T1.0010.52
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  
4uudA40.47041000.334Contact Map
4bejA40.80421000.346Contact Map
3szrA10.76061000.442Contact Map
4whjA20.77041000.446Contact Map
3zvrA10.87751000.457Contact Map
3w6pA20.47891000.594Contact Map
4p4uA10.45491000.658Contact Map
3t34A20.46761000.673Contact Map
2x2eA20.46761000.681Contact Map
1jwyB10.3931000.741Contact 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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