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HORMA

ID: 1517417060 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 233 (202)
Sequences: 1261 (834.7)
Seq/Len: 6.243
Nf(neff/√len): 58.7

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: 6.243).

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 > 50% 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
83_L91_A3.0551.00
194_P197_Y2.9601.00
76_K79_S2.8091.00
80_V85_E1.9721.00
30_E67_K1.9421.00
107_D110_N1.9101.00
17_F28_F1.9001.00
87_G91_A1.8971.00
88_I100_V1.8831.00
185_I191_Q1.8421.00
106_V110_N1.7921.00
193_C197_Y1.7851.00
20_R116_E1.7791.00
106_V109_E1.7551.00
182_F185_I1.7091.00
83_L86_H1.7041.00
186_H189_Y1.6841.00
151_K159_G1.6551.00
198_E204_P1.6341.00
80_V84_L1.6251.00
118_Y167_L1.6241.00
90_D94_K1.5640.99
185_I188_F1.5510.99
88_I91_A1.5210.99
185_I190_T1.5210.99
86_H91_A1.4760.99
80_V83_L1.4590.99
80_V87_G1.4460.99
107_D111_P1.4090.98
183_L190_T1.4060.98
72_G78_D1.3820.98
81_L87_G1.3480.98
197_Y202_F1.3340.98
12_S163_I1.3130.97
13_F102_L1.2930.97
83_L89_F1.2860.97
183_L188_F1.2700.96
64_Q67_K1.2580.96
92_L122_F1.2570.96
222_T231_G1.2500.96
4_F7_I1.2290.96
186_H190_T1.2290.96
152_T155_T1.2260.95
81_L85_E1.2240.95
165_R173_F1.2140.95
81_L86_H1.2130.95
9_L120_F1.2120.95
77_A83_L1.2060.95
181_R189_Y1.1990.95
7_I10_H1.1920.94
14_G23_L1.1870.94
214_R217_N1.1860.94
78_D81_L1.1820.94
14_G71_R1.1790.94
118_Y175_P1.1770.94
17_F23_L1.1750.94
169_T172_T1.1740.94
181_R185_I1.1710.94
7_I11_A1.1700.94
132_L136_L1.1620.93
24_P28_F1.1460.93
156_A164_I1.1420.93
85_E89_F1.1340.92
9_L100_V1.1340.92
91_A118_Y1.1330.92
71_R78_D1.1310.92
81_L97_L1.1300.92
224_S231_G1.1130.91
6_Q93_E1.1120.91
77_A80_V1.1030.91
9_L24_P1.1020.91
65_P71_R1.1000.91
20_R174_L1.0950.91
6_Q84_L1.0910.90
188_F191_Q1.0900.90
132_L135_G1.0900.90
74_N78_D1.0900.90
133_K136_L1.0880.90
213_P217_N1.0860.90
183_L189_Y1.0810.90
19_L172_T1.0790.90
225_C228_M1.0760.89
23_L33_L1.0700.89
7_I33_L1.0700.89
89_F93_E1.0680.89
74_N77_A1.0670.89
79_S86_H1.0580.88
197_Y200_R1.0540.88
20_R28_F1.0520.88
219_K227_I1.0500.88
11_A64_Q1.0490.88
83_L185_I1.0480.88
185_I189_Y1.0460.88
187_L190_T1.0370.87
118_Y166_R1.0280.86
71_R82_N1.0270.86
166_R171_S1.0260.86
167_L175_P1.0190.86
189_Y198_E1.0180.86
134_K138_A1.0130.85
97_L124_Y1.0110.85
66_L167_L1.0100.85
12_S120_F1.0080.85
136_L139_V1.0060.85
69_I73_R1.0020.84
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  
4trkA10.8241000.243Contact Map
4tzmA20.80691000.252Contact Map
3abdA20.73821000.382Contact Map
2vfxA120.75541000.387Contact Map
4aezB30.72961000.402Contact Map
4wzgA1087.40.907Contact Map
4yk8A1081.40.914Contact Map
2qyfB20.673879.70.916Contact Map
4yk8B1059.60.927Contact Map
4j2gA20.622320.20.944Contact 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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