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TtSpo0J_structureonly

ID: 1515144871 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 230 (210)
Sequences: 5249 (3383.6)
Seq/Len: 24.995
Nf(neff/√len): 233.5

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: 24.995).

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
25_R91_E4.2251.00
32_R71_G3.8561.00
51_A86_M3.0801.00
167_A193_L2.9411.00
74_L81_Y2.9241.00
195_E199_K2.8021.00
31_I74_L2.6011.00
125_R165_L2.5391.00
196_I206_A2.5161.00
59_L84_A2.3611.00
27_P30_S2.3171.00
137_Q152_A2.3071.00
63_L92_V2.2601.00
30_S71_G2.2471.00
100_T103_E2.1921.00
147_A150_T2.1381.00
26_L94_A2.0601.00
65_V94_A2.0541.00
48_K86_M2.0491.00
166_E170_R2.0411.00
121_V165_L2.0351.00
46_S116_E2.0011.00
99_L107_L1.9541.00
48_K52_D1.9531.00
66_R73_E1.9221.00
44_E86_M1.9181.00
47_L86_M1.9181.00
76_A111_E1.8611.00
59_L93_P1.8561.00
201_L209_L1.8431.00
131_L140_V1.8411.00
47_L51_A1.8351.00
84_A89_L1.8231.00
63_L74_L1.8201.00
129_A132_E1.7281.00
26_L65_V1.7221.00
123_E154_A1.7211.00
81_Y85_L1.7071.00
161_P189_R1.6661.00
32_R73_E1.6561.00
38_P108_A1.6461.00
28_L81_Y1.6351.00
139_E142_R1.6111.00
205_Q208_A1.6031.00
66_R104_A1.5721.00
63_L94_A1.5641.00
31_I65_V1.5631.00
168_L178_A1.5401.00
44_E48_K1.5331.00
125_R169_E1.5321.00
84_A87_A1.5321.00
154_A175_A1.5191.00
163_E190_L1.5071.00
27_P91_E1.5001.00
52_D55_R1.4801.00
164_A193_L1.4511.00
54_I59_L1.4411.00
78_E82_R1.4311.00
195_E209_L1.4291.00
177_H203_V1.4281.00
192_G209_L1.4221.00
43_A46_S1.4111.00
119_S169_E1.4030.99
106_E143_R1.3880.99
138_E142_R1.3540.99
34_N104_A1.3150.99
127_Y144_V1.2990.99
66_R101_D1.2950.99
140_V151_V1.2810.99
162_P166_E1.2640.99
54_I84_A1.2610.99
180_A206_A1.2600.99
123_E146_K1.2460.98
149_S152_A1.2430.98
194_K198_E1.2290.98
193_L197_L1.2210.98
34_N108_A1.2110.98
188_D191_W1.1950.98
25_R93_P1.1930.98
34_N73_E1.1680.97
166_E169_E1.1670.97
75_V99_L1.1490.97
53_S110_V1.1480.97
50_L79_R1.1480.97
167_A197_L1.1440.97
167_A172_E1.1310.97
46_S49_E1.1250.97
51_A87_A1.1200.96
57_K103_E1.1180.96
84_A92_V1.1160.96
127_Y140_V1.1120.96
185_E188_D1.1120.96
164_A189_R1.1100.96
162_P165_L1.1060.96
150_T154_A1.1000.96
28_L84_A1.0990.96
48_K51_A1.0980.96
111_E115_R1.0910.96
24_V96_V1.0840.96
60_L64_L1.0720.95
57_K106_E1.0680.95
30_S70_D1.0620.95
42_F78_E1.0520.95
67_P70_D1.0470.94
59_L92_V1.0430.94
63_L81_Y1.0090.93
42_F82_R1.0060.93
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  
1vz0A80.83481000.11Contact Map
4umkA401000.128Contact Map
1r71A40.478399.90.529Contact Map
1vk1A10.821799.80.599Contact Map
1yzsA10.482699.80.61Contact Map
1xw3A10.430499.80.611Contact Map
3mkyB20.465299.50.686Contact Map
1zx4A20.504397.70.832Contact Map
2hwjA60.752297.30.843Contact Map
1u78A10.443592.30.888Contact 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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