GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_Tnp_ISL3 - Helix-turn-helix domain of transposase family ISL3
Pfam: PF13542 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0123
Length: 52
Sequences: 32120
Seq/Len: 617.69
HH_delta: 0.092 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

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] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
30_F45_R2.869612.219
28_R36_E2.64712.047
30_F48_F2.437281.885
31_K41_W2.25031.740
42_S45_R2.205891.706
28_R32_D2.20561.705
34_A44_V2.068321.599
41_W45_R1.997141.544
29_S32_D1.897891.467
13_T16_L1.734381.341
45_R49_D1.724441.333
23_L33_V1.703891.317
39_V47_I1.666131.288
30_F41_W1.618191.251
12_I16_L1.549241.198
42_S46_R1.506021.164
24_L48_F1.483411.147
23_L36_E1.441141.114
40_S43_T1.428241.104
14_K18_Q1.421531.099
31_K35_R1.370631.060
46_R50_R1.362551.054
15_R47_I1.352241.046
43_T47_I1.342241.038
46_R49_D1.329681.028
43_T46_R1.275970.987
33_V44_V1.268040.980
17_E21_L1.262960.977
34_A41_W1.245730.963
21_L25_R1.240860.959
18_Q22_K1.237610.957
20_I24_L1.209710.935
15_R19_Y1.165540.901
16_L47_I1.140590.882
23_L28_R1.120120.866
39_V43_T1.020080.789
32_D36_E1.000040.773
23_L37_L0.996780.771
19_Y47_I0.964120.745
24_L27_S0.928050.718
30_F44_V0.9280.718
42_S49_D0.913040.706
22_K26_E0.905730.700
40_S46_R0.900780.696
32_D35_R0.876280.678
20_I37_L0.874260.676
19_Y23_L0.870120.673
15_R18_Q0.83720.647
39_V44_V0.83660.647
47_I50_R0.800770.619
31_K34_A0.787010.609
13_T17_E0.742730.574
12_I17_E0.742390.574
22_K36_E0.739880.572
16_L50_R0.732190.566
22_K25_R0.716220.554
19_Y22_K0.703450.544
23_L26_E0.692150.535
16_L19_Y0.682530.528
18_Q21_L0.628610.486
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
2jn6A0.884697.20.092
1u78A0.903897.20.101
2rn7A0.903897.10.116
2gloA0.884696.90.141
2k27A196.90.143
1tc3C0.884696.80.155
1k78A196.80.167
2elhA196.70.171
4dyqA196.70.172
2lvsA0.826996.50.193

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