GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-RVT - zinc-binding in reverse transcriptase
Pfam: PF13966 (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: 86
Sequences: 985
Seq/Len: 11.45
HH_delta: 0.887 (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
60_P69_E0.359062.350
62_C74_H0.296741.942
48_K51_L0.289611.895
39_R46_P0.28381.857
51_L56_I0.273771.792
15_S18_V0.253921.662
47_T50_N0.247311.618
73_E78_H0.244921.603
40_A76_F0.234221.533
46_P50_N0.227061.486
43_N72_I0.217261.422
73_E76_F0.206031.348
52_Q60_P0.203611.332
29_V33_V0.202961.328
73_E77_F0.190421.246
12_R15_S0.187741.229
74_H79_C0.187381.226
35_F47_T0.183931.204
9_N17_S0.182631.195
49_D71_T0.177821.164
4_V8_Y0.177421.161
80_P83_R0.173971.139
4_V33_V0.173141.133
32_K38_W0.172831.131
30_P33_V0.16931.108
44_R47_T0.167311.095
74_H86_W0.166481.089
29_V32_K0.16481.078
62_C65_C0.164591.077
65_C82_A0.164411.076
13_S18_V0.163611.071
25_W30_P0.162741.065
38_W44_R0.162721.065
46_P77_F0.162711.065
59_D78_H0.162631.064
40_A43_N0.162041.060
4_V12_R0.161421.056
8_Y54_R0.161371.056
48_K77_F0.161231.055
4_V10_L0.160171.048
10_L17_S0.159991.047
65_C79_C0.158191.035
70_E74_H0.156021.021
22_K26_K0.154961.014
15_S19_D0.154241.009
62_C70_E0.152160.996
6_S26_K0.150570.985
10_L14_S0.150070.982
11_L14_S0.149160.976
45_L72_I0.148930.975
46_P56_I0.147710.967
28_K34_K0.145660.953
26_K34_K0.144870.948
39_R42_H0.144730.947
64_L82_A0.143070.936
31_P48_K0.14250.933
33_V36_F0.1420.929
30_P36_F0.141310.925
63_P70_E0.14080.921
26_K31_P0.140160.917
29_V85_L0.139870.915
48_K63_P0.139810.915
13_S16_S0.139460.913
9_N13_S0.139050.910
34_K63_P0.137780.902
35_F39_R0.137610.901
67_N80_P0.136750.895
52_Q58_V0.135810.889
61_I69_E0.13530.885
30_P39_R0.13430.879
13_S29_V0.134230.878
31_P45_L0.134020.877
36_F70_E0.133270.872
43_N50_N0.133080.871
4_V11_L0.131690.862
63_P85_L0.131130.858
41_L69_E0.130910.857
40_A48_K0.130670.855
9_N15_S0.129840.850
50_N54_R0.129590.848
20_W23_I0.129550.848
38_W54_R0.128730.842
59_D69_E0.128460.841
27_S34_K0.12760.835
37_L42_H0.127430.834
27_S37_L0.126920.831
35_F42_H0.125680.822
52_Q59_D0.125560.822
27_S57_Q0.12540.821
10_L13_S0.1250.818
6_S11_L0.124960.818
41_L46_P0.12390.811
46_P63_P0.123640.809
7_A12_R0.123360.807
39_R44_R0.123310.807
5_K20_W0.122650.803
61_I68_E0.122490.802
5_K9_N0.121720.797
41_L44_R0.120750.790
7_A14_S0.120250.787
36_F76_F0.120050.786
12_R16_S0.119440.782
28_K39_R0.119350.781
18_V80_P0.119220.780
23_I41_L0.118360.775
35_F52_Q0.118070.773
53_R83_R0.117860.771
25_W32_K0.117460.769
30_P45_L0.117430.768
7_A15_S0.117280.768
8_Y12_R0.117240.767
40_A72_I0.116990.766
37_L41_L0.115840.758
53_R58_V0.115470.756
7_A11_L0.114770.751
35_F48_K0.114760.751
79_C86_W0.114260.748
9_N18_V0.114050.746
61_I80_P0.113970.746
46_P82_A0.113530.743
60_P78_H0.113430.742
7_A10_L0.11130.728
31_P75_L0.11120.728
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
3qwlA0.930214.30.887
3rj2X0.372111.20.892
2aklA0.60475.30.906
2qkdA0.44194.70.908
2xb1A0.33723.30.914
2jneA0.56983.10.916
3o70A0.48843.10.916
2cs3A0.46512.80.917
4e2xA0.4072.40.92
2d8yA0.44192.20.922
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