GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HRM - Hormone receptor domain
Pfam: PF02793 (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. )
Length: 66
Sequences: 801
Seq/Len: 12.14
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
17_T23_A0.64912.925
9_D13_C0.567262.556
12_L25_Q0.530872.392
6_A16_P0.428611.932
8_W11_W0.399011.798
46_C50_G0.369021.663
22_T45_N0.359621.621
8_W13_C0.357721.612
46_C52_W0.347111.564
7_T44_R0.337291.520
14_W27_C0.328671.481
14_W20_G0.29941.349
4_C14_W0.298191.344
28_P40_G0.277021.248
42_A46_C0.261021.176
24_S41_N0.259841.171
10_G60_Y0.246481.111
24_S43_T0.245661.107
49_N54_E0.245111.105
52_W63_C0.230891.041
59_N62_N0.228761.031
13_C31_F0.226521.021
54_E64_V0.225331.015
46_C63_C0.221080.996
17_T21_E0.219360.989
2_S16_P0.216150.974
21_E24_S0.215460.971
3_Y59_N0.210420.948
8_W47_T0.210130.947
30_G40_G0.205410.926
5_P18_P0.203120.915
15_P25_Q0.201180.907
59_N63_C0.197510.890
24_S28_P0.196740.887
3_Y48_E0.194940.878
16_P61_S0.192890.869
18_P22_T0.192310.867
12_L40_G0.191060.861
13_C27_C0.190960.861
58_P64_V0.190310.858
44_R63_C0.189680.855
50_G63_C0.188730.851
58_P62_N0.188570.850
4_C28_P0.18290.824
4_C9_D0.182750.824
58_P65_S0.182070.820
39_S48_E0.18110.816
41_N47_T0.179550.809
31_F42_A0.178490.804
7_T39_S0.174320.786
2_S18_P0.172720.778
5_P22_T0.170640.769
21_E48_E0.169060.762
45_N53_E0.168670.760
20_G27_C0.168040.757
25_Q49_N0.165990.748
10_G16_P0.165680.747
47_T53_E0.164310.740
44_R60_Y0.162790.734
60_Y63_C0.162350.732
4_C27_C0.162330.732
48_E65_S0.161380.727
18_P41_N0.161270.727
7_T16_P0.160950.725
16_P19_A0.160890.725
40_G64_V0.159710.720
58_P63_C0.159160.717
7_T10_G0.159090.717
15_P26_P0.156590.706
12_L31_F0.156490.705
26_P29_S0.154010.694
6_A13_C0.152540.687
18_P48_E0.150980.680
45_N49_N0.150680.679
42_A58_P0.15010.676
22_T49_N0.148780.670
20_G28_P0.147210.663
14_W28_P0.146910.662
26_P41_N0.143940.649
42_A60_Y0.143250.646
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
3c5tA199.5-0.008
4ersA0.984899.50.007
2qkhA0.969799.50.007
4hj0A0.969799.50.023
3h3gA0.969799.50.033
1u34A0.969799.50.038
2jodA0.984899.50.042
3n94A0.969799.40.052
2l27A0.969799.40.054
2x57A0.969799.40.059

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