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tspo-pfam

ID: 1516638099 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 169 (155)
Sequences: 2902 (2240.4)
Seq/Len: 18.723
Nf(neff/√len): 180.0

Jackhmmer Results: (2016_04)
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: 18.723).

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
116_S145_A3.9331.00
98_I111_D3.4731.00
119_A144_L3.1461.00
66_I130_S3.1081.00
42_W149_V2.9041.00
47_W51_P2.7831.00
106_G155_W2.6541.00
109_L152_Y2.3551.00
91_L118_V2.3211.00
16_S58_S2.2541.00
18_G93_W2.1051.00
122_T137_L2.0001.00
123_T134_A1.9581.00
127_H134_A1.8781.00
84_L125_A1.8581.00
135_R138_Y1.7751.00
63_G137_L1.7691.00
109_L151_N1.7381.00
152_Y156_R1.7261.00
153_Y156_R1.6821.00
153_Y157_D1.6731.00
116_S148_T1.6481.00
33_W105_M1.5841.00
122_T126_W1.5581.00
116_S144_L1.5401.00
112_L148_T1.5071.00
39_K43_H1.4931.00
71_L78_A1.4781.00
98_I108_A1.4771.00
57_Y92_N1.4311.00
127_H135_R1.4261.00
84_L121_A1.4251.00
8_A65_Y1.4070.99
38_Q157_D1.4030.99
33_W103_R1.4030.99
42_W153_Y1.3700.99
15_P85_Y1.3510.99
64_S82_L1.3410.99
16_S19_G1.3380.99
11_L64_S1.3340.99
67_V126_W1.3180.99
149_V153_Y1.2860.99
112_L151_N1.2860.99
34_Y43_H1.2830.99
108_A111_D1.2820.99
121_A125_A1.2790.99
70_E130_S1.2770.99
15_P61_G1.2570.99
123_T141_L1.2440.98
64_S85_Y1.2380.98
39_K154_V1.1880.98
123_T137_L1.1760.98
63_G133_A1.1510.97
90_A94_A1.1480.97
91_L111_D1.0930.96
80_V125_A1.0920.96
81_P126_W1.0900.96
109_L148_T1.0830.96
127_H131_P1.0640.95
94_A111_D1.0620.95
116_S119_A1.0570.95
11_L15_P1.0440.94
41_S153_Y1.0390.94
104_Q107_W1.0300.94
116_S141_L1.0220.93
63_G122_T1.0220.93
10_G14_V1.0190.93
65_Y69_K1.0170.93
120_T141_L1.0160.93
67_V81_P1.0090.93
54_G58_S1.0090.93
142_A146_F1.0080.93
30_G46_R1.0010.92
60_M64_S1.0010.92
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  
2mgyA111000.165Contact Map
4uc1A30.9291000.226Contact Map
4ryoA101000.242Contact Map
1yewC30.52076.60.948Contact Map
4phzK30.71015.20.951Contact Map
2a65A10.4324.70.952Contact Map
3w4tA10.75154.40.953Contact Map
4xp4A104.10.953Contact Map
3zuxA10.84621.90.96Contact Map
3orgA40.4261.90.96Contact 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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