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2KVC-Rv0543c

ID: 1515087831 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 103 (97)
Sequences: 243 (182.8)
Seq/Len: 2.505
Nf(neff/√len): 18.6

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: 2.505).

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
30_A34_L2.8301.00
16_R28_S2.2461.00
66_I70_T2.1041.00
30_A33_A1.8510.99
34_L70_T1.7910.98
26_T29_F1.7090.98
29_F32_L1.6110.96
67_T74_P1.4960.94
64_V73_L1.4860.94
14_W27_D1.3930.90
87_A93_L1.3720.89
11_I40_S1.3670.89
36_C81_R1.3290.87
42_D53_R1.3140.87
37_R78_D1.3110.86
27_D39_L1.3070.86
33_A74_P1.3050.86
55_G79_V1.2930.85
53_R69_F1.2900.85
22_G86_L1.2710.84
35_L90_G1.2340.81
63_G71_D1.2150.80
79_V88_A1.2050.79
53_R88_A1.1840.78
87_A92_P1.1810.77
84_A94_D1.1520.75
27_D91_W1.1420.74
62_I66_I1.1410.74
22_G91_W1.1360.73
76_P80_E1.1350.73
30_A70_T1.1250.72
30_A36_C1.1240.72
18_G35_L1.1190.72
29_F81_R1.1070.71
14_W39_L1.1020.70
23_I72_E1.1000.70
45_K89_Q1.0930.69
23_I27_D1.0930.69
63_G95_D1.0900.69
25_P28_S1.0850.68
56_D88_A1.0700.67
60_I64_V1.0600.66
86_L90_G1.0570.65
22_G27_D1.0510.65
46_A49_N1.0440.64
38_R93_L1.0370.63
40_S43_E1.0280.62
71_D79_V1.0260.62
62_I94_D1.0230.62
90_G93_L1.0230.62
33_A70_T1.0180.61
77_E87_A1.0180.61
5_N68_H1.0040.60
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  
2kvcA111000.025Contact Map
2lkyA111000.032Contact Map
2m0nA111000.061Contact Map
3ol3A20.91261000.075Contact Map
4giuA20.737976.60.881Contact Map
3h5qA10.796172.80.884Contact Map
1uouA10.7087720.885Contact Map
4ga6A20.990370.80.886Contact Map
1brwA20.76768.40.888Contact Map
4eadA10.776767.30.889Contact 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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