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4ipu

ID: 1500381467 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 137 (132)
Sequences: 2553 (2073.6)
Seq/Len: 19.341
Nf(neff/√len): 180.5

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: 19.341).

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
28_E32_Q3.4541.00
12_Q16_E2.7201.00
25_A38_I2.5421.00
28_E31_S2.4271.00
117_S125_Q2.3611.00
6_T10_E2.2931.00
37_S87_T2.2491.00
7_E10_E2.1441.00
22_L38_I2.1231.00
39_Q51_S1.9981.00
19_N23_Q1.9371.00
101_T115_V1.9181.00
25_A36_I1.8981.00
11_L104_I1.8741.00
35_A87_T1.8011.00
15_A126_L1.7941.00
21_M50_L1.7631.00
4_P8_R1.7591.00
12_Q114_R1.7501.00
115_V127_E1.7231.00
17_E21_M1.6961.00
46_W49_G1.6541.00
50_L67_H1.5631.00
39_Q53_G1.4771.00
22_L124_I1.4551.00
24_Y64_L1.4291.00
40_A46_W1.3990.99
101_T117_S1.3980.99
7_E107_N1.3880.99
9_N12_Q1.3570.99
11_L15_A1.3510.99
118_I122_G1.3470.99
15_A19_N1.3300.99
21_M52_I1.3290.99
11_L106_Q1.3260.99
19_N116_L1.3040.99
21_M67_H1.2990.99
16_E126_L1.2970.99
8_R12_Q1.2820.99
15_A114_R1.2750.99
39_Q105_C1.2460.98
18_L104_I1.2360.98
24_Y65_R1.2230.98
103_A115_V1.2180.98
21_M24_Y1.2020.98
37_S53_G1.1330.97
30_V92_G1.1200.96
41_L51_S1.1200.96
35_A90_A1.1110.96
2_I6_T1.0940.96
22_L86_L1.0920.96
117_S127_E1.0730.95
19_N124_I1.0730.95
14_A17_E1.0730.95
24_Y28_E1.0720.95
22_L88_F1.0640.95
88_F124_I1.0570.95
32_Q36_I1.0550.95
131_K136_C1.0480.94
57_S61_A1.0470.94
113_G129_S1.0350.94
37_S85_H1.0310.94
6_T9_N1.0270.94
18_L38_I1.0150.93
13_S17_E1.0050.93
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  
4ipuA4199.80.089Contact Map
4dq9A20.868698.30.561Contact Map
2knqA10.905196.90.669Contact Map
1oqwA20.883212.80.875Contact Map
3fyfA20.82483.60.903Contact Map
3qh6A10.56931.70.919Contact Map
3sokA20.8541.60.92Contact Map
4fczB20.19711.40.923Contact Map
1wxpA10.35041.30.924Contact Map
3ld7A30.44531.20.926Contact 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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