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VP1 -force run

ID: 1502232372 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 120 (119)
Sequences: 69 (42.6)
Seq/Len: 0.580
Nf(neff/√len): 3.9

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: 0.580).

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
5_V112_S1.9580.87
101_V106_G1.7440.77
35_S38_G1.7160.76
86_G120_I1.6320.70
98_A114_W1.6200.69
108_W119_V1.6170.69
47_A50_R1.5990.68
111_D114_W1.5530.65
46_P50_R1.4940.60
95_N117_D1.4910.60
102_G106_G1.4500.57
63_P120_I1.4240.55
47_A52_N1.3880.52
47_A51_L1.3520.49
34_D38_G1.3350.48
99_D112_S1.3290.47
110_C114_W1.3140.46
109_H114_W1.3130.46
46_P49_K1.2970.45
97_G101_V1.2800.43
15_P21_G1.2640.42
100_G106_G1.2480.41
10_G13_E1.2250.39
58_D119_V1.2170.38
19_A25_P1.2140.38
105_S111_D1.2080.38
98_A111_D1.1950.37
46_P51_L1.1950.37
35_S39_T1.1890.36
101_V104_S1.1880.36
73_A79_G1.1650.35
107_N111_D1.1510.34
29_S64_D1.1430.33
48_R51_L1.1390.33
15_P117_D1.1300.32
16_V30_P1.1280.32
76_S95_N1.1060.30
33_P36_S1.1030.30
7_E105_S1.0940.30
97_G100_G1.0860.29
34_D39_T1.0840.29
40_G43_G1.0800.29
100_G103_N1.0800.29
72_P75_P1.0790.29
33_P38_G1.0780.29
35_S40_G1.0750.28
34_D41_K1.0740.28
32_E98_A1.0670.28
97_G102_G1.0580.27
9_L21_G1.0510.27
91_M117_D1.0460.27
98_A105_S1.0430.26
31_V116_G1.0400.26
95_N120_I1.0360.26
4_R12_V1.0350.26
60_D84_A1.0350.26
4_R17_K1.0330.26
105_S114_W1.0330.26
97_G106_G1.0330.26
62_V104_S1.0310.26
33_P39_T1.0240.25
101_V105_S1.0240.25
14_E59_A1.0240.25
3_K32_E1.0150.25
16_V19_A1.0150.25
10_G114_W1.0120.24
6_L12_V1.0070.24
10_G109_H1.0060.24
19_A112_S1.0050.24
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  
3ng9A100.299.90.396Contact Map
4iovA10.17599.90.445Contact Map
3nttA10.183399.90.456Contact Map
4g0rA10.17599.80.509Contact Map
4qc8A10.17599.50.609Contact Map
1k3vA10.17599.30.644Contact Map
4dpvZ10.399.10.681Contact Map
2pk2A40.25810.883Contact Map
4kblA20.110.90.932Contact Map
1s58A10.16675.20.941Contact 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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