GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_Tnp_4 - Helix-turn-helix of DDE superfamily endonuclease
Pfam: PF13613 (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: 53
Sequences: 52523
Seq/Len: 991
HH_delta: 0.006 (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
34_S37_S3.063342.161
20_L28_R2.964082.091
22_F37_S2.785951.965
7_D46_L2.573171.815
23_Q33_Q2.518751.776
20_L24_D2.352741.659
22_F40_F2.351841.659
21_T24_D2.350461.658
6_E39_I2.31381.632
33_Q37_S2.271331.602
4_S7_D1.946161.373
13_L28_R1.814361.280
34_S38_R1.728891.219
14_M25_L1.728291.219
38_R42_E1.722881.215
34_S41_H1.716111.210
13_L20_L1.679311.184
7_D39_I1.664291.174
31_I39_I1.614851.139
32_S35_T1.518181.071
26_A36_V1.510291.065
38_R41_H1.502131.059
22_F33_Q1.482851.046
40_F44_I1.451381.024
15_Y44_I1.448781.022
23_Q27_Y1.43551.012
37_S41_H1.42771.007
35_T39_I1.41660.999
6_E9_L1.416430.999
31_I36_V1.408030.993
8_Q12_T1.374650.970
7_D10_L1.327520.936
35_T38_R1.308570.923
41_H45_P1.287180.908
9_L13_L1.259610.888
5_L9_L1.250620.882
26_A33_Q1.240720.875
7_D42_E1.232640.869
10_L43_W1.191880.841
31_I35_T1.171220.826
10_L39_I1.132060.798
14_M40_F1.07640.759
11_L15_Y1.074860.758
22_F36_V1.063590.750
6_E31_I1.051160.741
24_D27_Y1.031120.727
24_D28_R1.017710.718
27_Y30_G0.963810.680
23_Q37_S0.961420.678
4_S39_I0.91020.642
10_L29_F0.901230.636
32_S38_R0.899210.634
3_L11_L0.880830.621
39_I42_E0.872270.615
25_L29_F0.826460.583
3_L7_D0.826180.583
25_L36_V0.80430.567
42_E46_L0.802710.566
9_L12_T0.799790.564
12_T16_L0.789050.557
3_L8_Q0.745120.526
41_H44_I0.736150.519
5_L8_Q0.735890.519
26_A29_F0.718450.507
10_L13_L0.71790.506
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
3vfzA0.981197.30.006
3vdoA0.981197.30.008
1or7A0.981197.20.014
2lfwA0.981197.20.016
2q1zA0.962397.20.016
1rp3A0.981197.20.021
3hugA0.981197.20.021
3mzyA0.962397.10.038
1s7oA0.981197.10.038
1xsvA0.981197.10.046

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