GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
hisB

ID: 1516928227 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 355 (355)
Sequences: 458 (210)
Seq/Len: 1.290
Nf(neff/√len): 11.1

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: 1.290).

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
135_I145_G4.8381.00
77_M90_V4.5011.00
15_I24_V4.3941.00
14_L80_F3.8211.00
174_N179_Q3.5961.00
27_F75_L2.8741.00
27_F72_P2.8531.00
243_L305_L2.8421.00
66_Q70_D2.8321.00
266_L270_A2.7971.00
95_H101_C2.6251.00
15_I76_M2.5041.00
170_H183_Q2.3400.99
172_V179_Q2.1710.99
89_E113_R2.0870.98
192_S209_A2.0620.98
237_L308_T2.0260.98
127_V137_L1.8960.96
244_K310_G1.8760.96
35_G154_N1.8390.95
322_D325_R1.8380.95
111_V141_M1.8340.95
20_S24_V1.8240.95
198_V292_D1.7810.94
73_H90_V1.7270.92
15_I20_S1.7210.92
19_P24_V1.7200.92
192_S206_D1.7120.92
241_E245_I1.6960.91
37_I79_I1.6920.91
38_P41_L1.6770.91
232_V293_L1.6760.91
298_I326_V1.6580.90
3_Q49_K1.6310.89
72_P75_L1.6200.89
30_L76_M1.6000.88
305_L311_V1.5970.88
52_M90_V1.5890.87
95_H103_C1.5870.87
39_E156_P1.5590.86
49_K88_D1.5370.85
237_L277_P1.5100.84
265_C328_S1.5020.83
279_L299_E1.5020.83
303_R307_Y1.4930.83
155_W158_I1.4660.81
199_G225_Y1.4620.81
80_F85_V1.4490.80
271_L336_T1.4320.79
79_I82_S1.4310.79
210_T351_S1.4290.79
170_H181_D1.4040.77
78_Q81_T1.3820.75
132_A147_R1.3730.75
193_K217_E1.3720.75
264_E274_S1.3640.74
91_L111_V1.3630.74
101_C107_K1.3550.73
136_Q225_Y1.3530.73
45_K159_G1.3520.73
267_A328_S1.3480.73
208_I236_G1.3360.72
148_Y165_R1.3300.71
183_Q217_E1.3290.71
94_P103_C1.3260.71
93_C103_C1.3230.71
15_I22_F1.3060.69
319_G325_R1.3060.69
289_R292_D1.3040.69
91_L109_K1.2950.68
220_V235_T1.2780.67
93_C101_C1.2770.67
24_V220_V1.2710.66
36_V80_F1.2660.66
94_P282_K1.2630.66
315_L329_L1.2620.65
91_L113_R1.2610.65
42_K45_K1.2560.65
208_I271_L1.2550.65
171_V277_P1.2520.65
4_K124_N1.2480.64
108_V111_V1.2470.64
315_L326_V1.2310.63
45_K163_T1.2290.62
159_G163_T1.2280.62
35_G156_P1.2280.62
185_W215_R1.2280.62
75_L97_P1.2250.62
242_A264_E1.2180.61
27_F71_G1.2020.60
208_I265_C1.2000.60
176_K335_R1.1950.59
287_Y296_E1.1940.59
31_A82_S1.1940.59
256_F334_G1.1790.58
267_A311_V1.1750.57
181_D217_E1.1750.57
155_W162_L1.1710.57
158_I162_L1.1700.57
42_K159_G1.1690.57
292_D342_R1.1680.57
91_L110_L1.1670.57
208_I333_F1.1600.56
288_Q294_S1.1590.56
14_L30_L1.1570.56
52_M80_F1.1520.55
62_Q67_A1.1510.55
24_V64_F1.1500.55
228_D294_S1.1470.55
15_I37_I1.1450.54
16_S31_A1.1450.54
190_G206_D1.1380.54
37_I80_F1.1310.53
305_L315_L1.1250.52
19_P22_F1.1180.52
195_N219_N1.1170.52
170_H217_E1.1160.51
179_Q218_I1.1130.51
225_Y237_L1.1110.51
162_L275_G1.1020.50
80_F265_C1.1010.50
184_V243_L1.0980.50
68_D71_G1.0910.49
214_F338_R1.0900.49
37_I76_M1.0890.49
314_H318_K1.0820.48
18_P76_M1.0810.48
41_L44_Q1.0720.47
107_K136_Q1.0660.47
280_E314_H1.0630.46
171_V220_V1.0630.46
15_I79_I1.0580.46
188_R215_R1.0520.45
22_F27_F1.0510.45
293_L298_I1.0510.45
80_F194_I1.0480.45
35_G107_K1.0480.45
62_Q243_L1.0470.45
32_F79_I1.0450.44
21_D29_K1.0410.44
15_I30_L1.0400.44
241_E297_M1.0400.44
180_I242_A1.0350.43
63_S96_L1.0330.43
348_L354_V1.0330.43
64_F68_D1.0290.43
317_T332_A1.0290.43
62_Q145_G1.0290.43
16_S19_P1.0170.42
290_V320_K1.0160.42
52_M64_F1.0070.41
146_L153_L1.0060.41
226_I274_S1.0050.41
115_L118_Q1.0040.40
190_G215_R1.0030.40
336_T348_L1.0030.40
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  
4mu3A10.51271000.52Contact Map
1rhyA20.49011000.522Contact Map
2ae8A60.48451000.524Contact Map
4gquA10.51271000.526Contact Map
2fprA20.45351000.844Contact Map
3l8hA40.501499.90.858Contact Map
2gmwA20.487399.90.873Contact Map
4pnhA12099.90.875Contact Map
2o2xA10.509999.90.876Contact Map
3zvlA10.853599.80.887Contact 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 0.0204 seconds.