GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VRR_NUC - VRR-NUC domain
Pfam: PF08774 (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: CL0236
Length: 100
Sequences: 589
Seq/Len: 5.89
HH_delta: 0.75 (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
49_P86_L0.425072.785
83_I93_V0.414892.719
83_I87_R0.319122.091
10_I68_V0.29071.905
75_L83_I0.276991.815
86_L91_F0.241931.585
13_W16_K0.240691.577
8_V12_R0.238051.560
6_I98_S0.232021.520
85_K88_E0.224111.468
77_P80_K0.219171.436
11_V15_R0.218111.429
75_L95_V0.216031.416
70_G73_D0.211961.389
55_R58_G0.211331.385
5_D12_R0.206851.355
5_D9_A0.201751.322
46_S78_N0.199631.308
66_I96_C0.19751.294
48_F52_I0.192311.260
75_L80_K0.189871.244
53_L66_I0.189051.239
53_L64_L0.188621.236
75_L93_V0.186491.222
52_I65_F0.185261.214
7_Q51_L0.181951.192
23_V44_V0.181661.190
68_V96_C0.180721.184
54_W91_F0.172541.131
63_F91_F0.171111.121
68_V98_S0.161131.056
11_V51_L0.161121.056
44_V85_K0.16031.050
86_L89_A0.1581.035
84_D87_R0.15681.027
53_L89_A0.155751.021
22_H26_W0.15561.020
72_G97_R0.154081.010
82_W85_K0.153091.003
65_F91_F0.152380.998
15_R59_K0.152320.998
8_V11_V0.151620.993
77_P81_E0.14930.978
53_L94_A0.148370.972
81_E85_K0.145880.956
83_I92_R0.144740.948
73_D76_S0.142220.932
23_V82_W0.141870.930
12_R18_G0.141340.926
54_W63_F0.141130.925
86_L93_V0.140.917
24_K48_F0.139490.914
9_A99_V0.137760.903
16_K57_R0.137670.902
9_A12_R0.137390.900
54_W65_F0.135820.890
7_Q11_V0.135340.887
43_G48_F0.135010.885
64_L94_A0.134830.883
10_I51_L0.134080.879
70_G95_V0.133030.872
68_V73_D0.133010.872
10_I13_W0.132780.870
28_K48_F0.132390.867
46_S88_E0.131660.863
26_W44_V0.131430.861
73_D98_S0.131090.859
81_E84_D0.130920.858
56_P74_R0.130380.854
77_P88_E0.130030.852
83_I95_V0.129490.848
94_A97_R0.128940.845
48_F65_F0.1260.826
25_N28_K0.125920.825
70_G97_R0.1250.819
80_K84_D0.124960.819
6_I10_I0.124810.818
5_D8_V0.123460.809
9_A27_G0.123330.808
5_D17_H0.123040.806
14_L21_F0.121270.795
45_R82_W0.119140.781
80_K95_V0.11890.779
10_I14_L0.118870.779
28_K66_I0.118870.779
5_D15_R0.116010.760
24_K63_F0.115880.759
87_R93_V0.115380.756
55_R89_A0.114790.752
55_R76_S0.113650.745
24_K27_G0.112780.739
74_R80_K0.112740.739
49_P82_W0.112730.739
96_C99_V0.110470.724
23_V26_W0.11040.723
71_P97_R0.109720.719
20_V55_R0.108730.712
14_L53_L0.108230.709
12_R16_K0.108220.709
90_G97_R0.106760.700
64_L98_S0.106070.695
10_I48_F0.105990.695
26_W43_G0.10510.689
80_K88_E0.104960.688
9_A46_S0.104740.686
7_Q28_K0.104050.682
73_D96_C0.103760.680
24_K52_I0.103570.679
7_Q15_R0.103540.678
82_W86_L0.102680.673
12_R15_R0.10240.671
24_K28_K0.102360.671
5_D99_V0.102350.671
18_G49_P0.102330.671
72_G81_E0.102070.669
44_V78_N0.101980.668
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
2wcwA0.8296.80.75
1hh1A0.8396.80.752
2eo0A0.8396.50.761
1ob8A0.8296.40.765
2vldA0.8394.30.798
1gefA0.77920.814
3h1tA0.9591.40.817
2fcoA0.9488.10.829
1zp7A0.9486.30.833
3dnxA0.877.90.847
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