GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CHDNT - CHDNT (NUC034) domain
Pfam: PF08073 (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: CL0114
Length: 55
Sequences: 2214
Seq/Len: 40.25
HH_delta: 0.008 (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
23_V26_L1.217432.685
23_V46_K1.161252.561
20_S43_L1.074032.369
42_L46_K0.927512.046
42_L45_A0.922972.036
19_F50_F0.80321.772
45_A49_E0.800941.767
17_K20_S0.766211.690
40_M44_Q0.689661.521
13_L21_Q0.664531.466
36_M40_M0.653151.441
20_S24_R0.623161.375
13_L17_K0.613161.352
26_L30_A0.597191.317
23_V43_L0.595111.313
46_K49_E0.593461.309
38_K41_M0.593431.309
35_P38_K0.569611.256
25_P29_K0.532611.175
16_Y47_W0.51491.136
41_M44_Q0.497671.098
25_P28_A0.491521.084
20_S40_M0.487531.075
16_Y44_Q0.485911.072
13_L18_A0.448120.988
19_F43_L0.445890.984
44_Q48_R0.433180.955
12_N18_A0.414650.915
27_L39_L0.40820.900
14_T17_K0.406940.898
9_D14_T0.400570.884
17_K36_M0.382760.844
14_T36_M0.379460.837
16_Y20_S0.365960.807
21_Q24_R0.357870.789
26_L29_K0.351860.776
19_F23_V0.351460.775
14_T40_M0.345940.763
14_T18_A0.339650.749
34_A38_K0.336470.742
18_A22_H0.330080.728
22_H26_L0.329050.726
29_K32_P0.324910.717
27_L30_A0.322580.712
27_L43_L0.31240.689
34_A39_L0.308680.681
44_Q47_W0.30150.665
19_F46_K0.295190.651
39_L42_L0.291050.642
17_K40_M0.286530.632
27_L31_N0.286230.631
36_M43_L0.284470.627
11_Q17_K0.281980.622
28_A37_S0.281430.621
15_N36_M0.27950.617
28_A33_K0.278230.614
46_K50_F0.271540.599
14_T20_S0.266140.587
35_P53_H0.261210.576
10_F16_Y0.25890.571
9_D12_N0.252660.557
34_A42_L0.2520.556
37_S41_M0.250520.553
21_Q37_S0.248250.548
41_M45_A0.238280.526
18_A51_Q0.230550.509
31_N42_L0.230030.507
45_A48_R0.229570.506
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
2d7lA0.945599.10.008
1k99A199.10.019
2e6oA199.10.023
1hryA0.927399.10.025
1wgfA199.10.029
2co9A1990.033
3tmmA1990.035
1hmeA0.9636990.039
1j46A0.9273990.04
2lhjA1990.044

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