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T0836 30-204 -force run

ID: 1405445853 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 175 (167)
Sequences: 115 (75.8)
Seq/Len: 0.689
Nf(neff/√len): 5.9

Jackhmmer Results: (2014_04_16)
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: 0.689).

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
147_K151_L2.4110.98
31_F58_A2.2790.96
70_W114_T2.2760.96
138_D141_A2.0350.92
64_W67_L1.9910.91
117_F122_V1.9080.88
20_F72_M1.8280.85
107_G111_W1.8140.85
118_F122_V1.7180.80
130_I137_A1.6080.74
118_F123_F1.5930.73
18_V168_A1.5800.72
18_V166_T1.5770.72
30_Y33_F1.5100.67
129_K135_V1.4940.66
55_A132_L1.4860.65
31_F59_L1.4740.64
31_F127_N1.4680.64
158_L165_A1.4550.63
52_K133_G1.4440.62
52_K55_A1.3730.56
83_L88_T1.3630.55
147_K158_L1.3620.55
30_Y35_Q1.3430.53
75_L79_N1.3400.53
77_A110_M1.3320.52
42_I49_A1.3300.52
31_F148_T1.3140.51
130_I145_A1.3020.50
74_V79_N1.3010.50
16_L72_M1.2740.48
115_V159_L1.2720.47
66_A69_T1.2480.45
58_A127_N1.2470.45
28_L163_M1.2370.45
108_T166_T1.2300.44
18_V76_L1.2200.43
36_I131_A1.2150.43
76_L148_T1.2130.43
60_F70_W1.1920.41
21_G120_V1.1850.40
12_I161_I1.1840.40
82_Y110_M1.1760.40
86_A111_W1.1720.39
32_N35_Q1.1680.39
113_A140_D1.1680.39
124_I149_A1.1610.38
64_W157_T1.1600.38
13_F75_L1.1580.38
28_L149_A1.1410.37
113_A155_T1.1400.37
40_P46_L1.1400.37
86_A107_G1.1380.37
43_P146_A1.1330.36
144_K148_T1.1320.36
133_G142_K1.1200.35
149_A163_M1.1200.35
38_V54_I1.1140.35
120_V124_I1.1050.34
31_F149_A1.0990.34
40_P110_M1.0970.33
59_L149_A1.0860.33
81_G157_T1.0780.32
48_P52_K1.0740.32
39_M54_I1.0710.31
33_F106_I1.0650.31
147_K150_M1.0640.31
28_L124_I1.0630.31
165_A168_A1.0600.31
58_A124_I1.0580.31
33_F157_T1.0560.30
32_N163_M1.0520.30
70_W117_F1.0510.30
131_A152_V1.0500.30
123_F152_V1.0490.30
58_A145_A1.0460.30
36_I150_M1.0440.30
34_V163_M1.0440.30
31_F56_P1.0420.29
124_I163_M1.0410.29
57_E169_M1.0310.29
30_Y55_A1.0210.28
67_L130_I1.0190.28
22_I108_T1.0150.28
42_I48_P1.0130.27
14_R142_K1.0030.27
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: (12Jul14)
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  
1hx2A10.11431.50.977Contact Map
2kluA10.36571.40.977Contact Map
2k1kA20.21141.30.978Contact Map
2fhoA10.09141.20.978Contact Map
1eaiC20.121.10.979Contact Map
2jv4A10.26291.10.979Contact Map
1e0lA10.18861.10.979Contact Map
4gd3A20.662910.979Contact Map
3kw2A20.291410.979Contact Map
2r5vA20.2810.979Contact 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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