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elekw

ID: 1518190810 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 300 (270)
Sequences: 1513 (1045.1)
Seq/Len: 5.604
Nf(neff/√len): 63.6

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: 5.604).

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
145_L204_L4.0331.00
92_Y95_R3.4321.00
28_G32_L3.3811.00
92_Y98_D3.0161.00
197_H202_Y2.8281.00
245_F265_Q2.4781.00
125_F129_S2.3561.00
109_G113_V2.2791.00
211_L235_G2.1621.00
68_G113_V2.1621.00
37_F142_A2.1031.00
35_F66_F2.0771.00
118_A128_V2.0581.00
206_L239_F2.0541.00
164_A195_P2.0271.00
140_L232_F2.0271.00
234_I275_G1.9981.00
234_I276_V1.9611.00
234_I272_I1.9561.00
147_N152_E1.9521.00
95_R98_D1.9241.00
104_H264_G1.9101.00
68_G109_G1.8861.00
277_I281_W1.8641.00
239_F243_V1.8461.00
158_D164_A1.8031.00
72_G109_G1.8011.00
199_S243_V1.7741.00
227_A283_Y1.7651.00
64_A68_G1.7631.00
45_R48_R1.7241.00
39_M62_L1.7001.00
230_G275_G1.6871.00
242_I246_F1.6781.00
73_G109_G1.6481.00
154_W196_R1.6471.00
230_G278_M1.6230.99
196_R248_Q1.5860.99
91_L95_R1.5740.99
117_F121_T1.5560.99
82_N85_Q1.5490.99
241_I265_Q1.5400.99
144_R240_R1.5340.99
238_A272_I1.5230.99
75_I93_L1.5220.99
54_T57_E1.5170.99
90_P94_F1.5060.99
18_S23_A1.4960.99
41_L138_F1.4950.99
233_L275_G1.4860.99
85_Q92_Y1.4820.99
87_M90_P1.4710.99
148_F201_L1.4550.98
73_G106_G1.4480.98
116_I120_R1.4310.98
237_G272_I1.4070.98
104_H268_S1.4020.98
30_M33_V1.4000.98
45_R219_I1.3950.98
152_E200_Q1.3820.98
16_I26_W1.3650.97
151_G168_P1.3570.97
147_N153_L1.3530.97
268_S271_M1.3480.97
89_D92_Y1.3290.97
130_D226_G1.3150.97
138_F212_F1.2730.96
36_I40_W1.2710.96
35_F106_G1.2650.96
19_I22_V1.2510.95
129_S136_I1.2460.95
47_N55_K1.2370.95
134_P137_P1.2340.95
61_L128_V1.2330.95
85_Q89_D1.2310.95
38_A139_G1.2200.94
78_V93_L1.2170.94
91_L94_F1.2170.94
61_L65_G1.2050.94
161_F164_A1.2040.94
224_P227_A1.2000.94
64_A113_V1.1860.93
278_M282_A1.1850.93
107_L136_I1.1850.93
53_W131_F1.1800.93
241_I245_F1.1790.93
228_V231_L1.1770.93
157_V194_L1.1750.93
147_N150_N1.1740.93
238_A241_I1.1740.93
57_E123_R1.1710.93
61_L114_M1.1570.92
14_P25_H1.1500.92
199_S262_S1.1490.92
90_P93_L1.1420.91
103_F140_L1.1410.91
74_R99_G1.1370.91
284_R287_P1.1310.91
113_V116_I1.1290.91
208_G211_L1.1260.90
137_P235_G1.1190.90
210_V235_G1.1100.90
104_H237_G1.1100.90
213_I217_L1.1100.90
157_V196_R1.1060.89
102_S153_L1.1050.89
163_F197_H1.0950.89
29_L33_V1.0940.89
115_I125_F1.0900.88
238_A242_I1.0890.88
147_N200_Q1.0880.88
160_N164_A1.0870.88
212_F216_N1.0850.88
212_F215_L1.0850.88
151_G200_Q1.0810.88
26_W149_I1.0740.87
31_Y34_G1.0720.87
27_Y152_E1.0710.87
60_N117_F1.0710.87
46_A58_V1.0700.87
38_A135_L1.0560.86
77_Y80_F1.0520.86
68_G116_I1.0480.86
64_A120_R1.0480.86
76_G102_S1.0460.86
143_G236_Y1.0420.85
74_R101_M1.0360.85
63_Y67_L1.0350.85
17_F26_W1.0270.84
16_I29_L1.0230.84
156_R248_Q1.0210.84
101_M106_G1.0140.83
34_G38_A1.0140.83
16_I25_H1.0110.83
57_E121_T1.0090.83
24_L28_G1.0070.82
27_Y147_N1.0070.82
45_R134_P1.0060.82
41_L135_L1.0020.82
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  
2ls4A10.0840.972Contact Map
2kluA10.173.20.973Contact Map
4us3A10.452.10.975Contact Map
2m20A20.14331.80.976Contact Map
4px7A10.731.80.976Contact Map
2ksfA10.15331.60.977Contact Map
3wu2Y20.09331.50.977Contact Map
2jo1A10.17671.50.977Contact Map
2zxeA10.30671.40.978Contact Map
3ixzA10.30671.40.978Contact 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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