GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_26 - CroC1-type HTH DNA-binding domain
Pfam: PF13443 (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: 63
Sequences: 37552
Seq/Len: 596.06
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
6_M31_L3.871362.597
19_K49_A3.452362.316
14_K24_R2.932811.967
5_L8_E2.861641.920
5_L9_R2.733021.833
15_D19_K2.639151.770
24_R28_S2.54761.709
29_R34_K2.360721.584
26_T30_I2.325311.560
28_S32_N2.230271.496
12_T15_D2.208951.482
4_E8_E2.134271.432
14_K18_R2.129241.428
13_Q28_S2.109181.415
11_I15_D2.076771.393
25_S28_S1.978171.327
30_I42_T1.97741.326
22_I42_T1.825891.225
26_T29_R1.801581.208
3_K31_L1.78011.194
53_S56_E1.762661.182
11_I19_K1.757531.179
22_I26_T1.658841.113
11_I49_A1.655091.110
20_T49_A1.653021.109
16_L27_L1.644731.103
42_T45_K1.637621.098
25_S29_R1.634981.097
13_Q31_L1.614921.083
5_L52_C1.606311.077
13_Q24_R1.605421.077
3_K7_A1.566211.051
30_I38_P1.561171.047
44_E48_K1.552571.041
52_C56_E1.472860.988
44_E54_P1.465570.983
16_L50_L1.419030.952
39_S42_T1.409760.946
43_L47_A1.389380.932
3_K13_Q1.385150.929
40_L54_P1.371380.920
20_T46_I1.360070.912
45_K49_A1.346410.903
17_A24_R1.344130.902
17_A27_L1.335850.896
29_R36_S1.282080.860
37_N41_D1.277320.857
23_S26_T1.259460.845
41_D45_K1.234360.828
23_S29_R1.227290.823
15_D18_R1.21820.817
4_E7_A1.199460.805
22_I27_L1.150270.772
46_I50_L1.14670.769
11_I16_L1.119070.751
43_L54_P1.105290.741
47_A54_P1.088590.730
27_L31_L1.0880.730
47_A52_C1.085940.728
40_L43_L1.023860.687
40_L44_E1.016810.682
5_L50_L0.978560.656
26_T42_T0.96910.650
16_L20_T0.96650.648
2_L46_I0.963510.646
5_L56_E0.958360.643
26_T36_S0.937970.629
22_I45_K0.926850.622
21_G45_K0.916480.615
9_R51_N0.916030.614
47_A53_S0.910460.611
38_P42_T0.89050.597
6_M16_L0.887790.596
38_P43_L0.885770.594
13_Q17_A0.833010.559
29_R32_N0.802130.538
16_L46_I0.777340.521
6_M11_I0.774880.520
47_A57_L0.758430.509
44_E55_E0.754060.506
17_A20_T0.753820.506
45_K48_K0.738890.496
29_R33_G0.726240.487
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
4ichA0.984198.7-0.092
3t76A0.968398.7-0.092
3op9A0.984198.6-0.078
3mlfA0.984198.6-0.068
1y9qA0.984198.6-0.067
3ivpA0.984198.6-0.066
3g5gA0.984198.6-0.066
3vk0A0.984198.6-0.06
3omtA0.984198.6-0.058
3qq6A0.984198.6-0.053

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