GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HicB - HicB family
Pfam: PF05534 (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: CL0057
Length: 51
Sequences: 690
Seq/Len: 13.53
HH_delta: 0.336 (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
41_V49_E0.70252.736
25_P28_L0.542772.114
35_A46_W0.49091.912
18_G29_H0.482021.877
16_Y33_A0.440281.715
35_A39_E0.431751.682
29_H43_L0.393951.534
32_L43_L0.368541.435
9_G12_P0.352071.371
29_H33_A0.345841.347
23_R44_N0.335271.306
24_I48_E0.327281.275
22_L47_I0.321951.254
20_F47_I0.311651.214
45_Q48_E0.306361.193
41_V46_W0.300981.172
18_G44_N0.286071.114
31_A35_A0.282461.100
35_A50_A0.280231.091
33_A43_L0.272321.061
10_I48_E0.271521.057
16_Y28_L0.267731.043
8_P12_P0.265641.035
20_F44_N0.265091.032
21_N47_I0.261331.018
30_R34_E0.257641.003
45_Q49_E0.256661.000
17_S26_P0.255080.993
34_E38_A0.254860.993
23_R42_S0.239870.934
46_W50_A0.23630.920
39_E46_W0.232840.907
10_I13_E0.228590.890
18_G26_P0.227050.884
32_L35_A0.224790.875
31_A38_A0.224260.873
13_E30_R0.223440.870
30_R38_A0.221650.863
25_P38_A0.215750.840
20_F24_I0.210360.819
20_F43_L0.209410.816
44_N48_E0.200650.781
16_Y30_R0.191840.747
32_L51_L0.19120.745
19_K44_N0.189330.737
34_E45_Q0.183280.714
37_A40_G0.181890.708
32_L46_W0.180840.704
19_K37_A0.180080.701
25_P48_E0.178830.696
25_P45_Q0.174620.680
36_A42_S0.172820.673
32_L40_G0.171530.668
29_H44_N0.170580.664
8_P11_E0.16970.661
16_Y26_P0.169670.661
17_S29_H0.168770.657
21_N24_I0.168710.657
22_L44_N0.16350.637
34_E39_E0.161390.629
17_S44_N0.161320.628
18_G28_L0.15960.622
24_I51_L0.159380.621
9_G37_A0.158130.616
37_A45_Q0.158050.616
26_P48_E0.155510.606
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
2k9iA0.843198.40.336
2ba3A0.921698.20.375
2kelA0.921697.90.438
1nlaA0.803997.80.453
1bazA0.803997.70.463
1mntA0.745197.70.466
1u9pA0.941297.60.472
3qoqA197.60.473
1p94A0.882497.60.473
2an7A0.686397.40.498

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