GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_25 - Helix-turn-helix domain
Pfam: PF13413 (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: 62
Sequences: 38714
Seq/Len: 624.42
HH_delta: -0.043 (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
6_R31_E3.981822.599
19_E54_F3.819082.493
14_E24_V3.213032.097
5_A8_A2.987671.950
5_A9_K2.756951.800
29_A34_D2.648361.729
26_Y30_I2.529331.651
24_V28_E2.441881.594
15_D19_E2.425881.583
28_E32_N2.286171.492
12_S15_D2.239361.462
14_E18_E2.169921.416
13_L28_E2.145821.401
4_E8_A2.049841.338
25_S28_E1.98941.299
26_Y29_A1.909431.246
30_I47_Y1.885631.231
13_L24_V1.882351.229
11_L15_D1.87891.226
16_V27_L1.862521.216
20_T51_Y1.861941.215
29_A35_F1.860451.214
11_L19_E1.718081.121
5_A57_L1.705391.113
22_I47_Y1.685361.100
16_V55_L1.636241.068
50_K54_F1.626451.062
11_L54_F1.616451.055
20_T54_F1.596011.042
22_I26_Y1.580321.032
25_S29_A1.551361.013
49_R53_R1.528560.998
3_R31_E1.503830.982
3_R7_E1.480010.966
49_R59_P1.410880.921
47_Y50_K1.402360.915
51_Y55_L1.400870.914
52_A57_L1.377620.899
46_G50_K1.338190.873
13_L31_E1.311230.856
15_D18_E1.29940.848
48_L59_P1.269750.829
22_I27_L1.267740.827
16_V51_Y1.26230.824
3_R13_L1.252580.818
23_S26_Y1.220190.796
17_A24_V1.208390.789
9_K56_G1.205740.787
52_A59_P1.198510.782
4_E7_E1.180220.770
17_A27_L1.102270.719
48_L52_A1.082070.706
21_K50_K1.064470.695
39_P46_G1.041130.680
5_A55_L1.024490.669
26_Y35_F1.009380.659
11_L16_V1.000610.653
26_Y47_Y0.982010.641
23_S29_A0.959290.626
16_V20_T0.923110.603
22_I50_K0.915030.597
6_R13_L0.859350.561
6_R16_V0.851070.556
40_S47_Y0.848460.554
40_S46_G0.811210.530
50_K53_R0.808750.528
47_Y51_Y0.808140.527
27_L30_I0.805030.525
49_R52_A0.799390.522
17_A20_T0.795050.519
20_T30_I0.787530.514
13_L32_N0.74810.488
20_T27_L0.747350.488
29_A32_N0.739050.482
52_A58_D0.730050.477
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
3fymA198.6-0.043
4ichA0.903298.6-0.041
2wusR198.6-0.037
3op9A0.903298.5-0.019
3ivpA0.903298.5-0.012
1y9qA0.903298.5-0.009
3mlfA0.903298.5-0.008
3t76A0.887198.5-0.005
2bnmA0.903298.5-0.004
3omtA0.903298.50

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