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T0808 1-100 -force run

ID: 1404889634 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 100 (96)
Sequences: 58 (54.3)
Seq/Len: 0.604
Nf(neff/√len): 5.5

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: 0.604).

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
34_T58_S2.2670.95
25_V57_V1.9820.89
34_T47_V1.9550.88
32_Y58_S1.7930.81
31_G69_A1.6280.71
73_L94_L1.5800.68
58_S61_F1.4410.57
75_A92_V1.4300.57
43_T81_I1.3860.53
51_T83_V1.3810.53
25_V63_L1.3760.52
31_G66_P1.3640.51
25_V82_K1.3560.51
28_S36_Q1.3440.50
39_G51_T1.3360.49
40_A77_G1.3150.47
52_N94_L1.3070.47
63_L94_L1.2900.45
39_G56_I1.2860.45
62_Y79_S1.2650.43
34_T55_S1.2460.42
28_S75_A1.2360.41
60_Y71_L1.2180.40
24_V83_V1.2090.39
82_K89_G1.2040.38
30_N61_F1.2020.38
51_T64_H1.1920.38
54_K72_S1.1500.34
52_N60_Y1.1450.34
75_A94_L1.1390.34
27_V30_N1.1390.34
38_D42_I1.1350.33
42_I57_V1.1340.33
31_G59_I1.1330.33
19_Q82_K1.1160.32
45_R49_H1.1150.32
45_R48_T1.1100.32
29_G61_F1.1010.31
64_H85_Y1.0970.31
70_D84_S1.0890.30
41_R76_K1.0870.30
19_Q72_S1.0870.30
26_G90_F1.0790.29
25_V58_S1.0770.29
12_L21_Q1.0770.29
84_S99_F1.0770.29
43_T88_K1.0730.29
9_A60_Y1.0730.29
83_V92_V1.0720.29
44_Q78_H1.0690.29
56_I81_I1.0520.28
27_V36_Q1.0460.27
61_F78_H1.0400.27
22_Q25_V1.0370.27
25_V66_P1.0310.26
22_Q71_L1.0200.26
30_N59_I1.0000.24
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: (05Jul14)
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  
3uw0A10.652.70.886Contact Map
2x3cA10.7937.40.896Contact Map
2w9xA20.6236.60.897Contact Map
2bgoA10.6936.40.897Contact Map
4enzA10.835.20.898Contact Map
1dbgA10.6832.10.9Contact Map
2a2uA40.8128.50.902Contact Map
1y0gA40.6722.90.907Contact Map
4c91A20.81210.908Contact Map
3cbcA30.7819.90.909Contact 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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