GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Nuc_deoxyrib_tr - Nucleoside 2-deoxyribosyltransferase
Pfam: PF05014 (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: CL0498
Length: 113
Sequences: 1228
Seq/Len: 10.87
HH_delta: 0.135 (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_R88_L0.517692.898
60_R84_Y0.440812.468
8_F75_D0.394332.208
5_G78_T0.344131.927
21_E25_K0.342391.917
65_V85_A0.338151.893
14_A18_R0.33691.886
49_R53_E0.333621.868
83_G87_A0.33191.858
1_I28_F0.318071.781
31_Y58_G0.299941.679
23_L30_V0.294391.648
57_E61_E0.290971.629
2_Y33_P0.286731.605
59_I84_Y0.275671.543
67_A82_L0.27171.521
52_F86_Y0.26151.464
5_G16_V0.259071.450
65_V92_V0.257571.442
3_L30_V0.253791.421
59_I85_A0.251781.410
2_Y77_G0.247011.383
77_G81_E0.238821.337
59_I90_K0.236161.322
69_L94_L0.229891.287
16_V32_S0.228621.280
74_P79_A0.224081.254
64_I93_I0.221321.239
19_L22_A0.219741.230
18_R21_E0.218311.222
6_P77_G0.21551.206
55_D77_G0.212881.192
7_F16_V0.206381.155
84_Y88_L0.205481.150
24_E35_D0.201991.131
57_E60_R0.20051.122
56_L80_F0.200431.122
27_G30_V0.20031.121
55_D78_T0.19791.108
8_F78_T0.193191.082
51_I55_D0.191791.074
79_A83_G0.187531.050
16_V34_Q0.184651.034
20_R35_D0.183551.028
56_L59_I0.181581.017
76_S79_A0.17410.975
56_L84_Y0.1740.974
47_W50_E0.172340.965
1_I64_I0.172040.963
22_A26_N0.168280.942
17_E24_E0.166580.933
83_G86_Y0.166450.932
78_T82_L0.165920.929
21_E49_R0.165350.926
65_V90_K0.162380.909
31_Y36_N0.162120.908
80_F83_G0.161970.907
67_A78_T0.159760.894
80_F84_Y0.159410.892
2_Y55_D0.159010.890
64_I91_P0.157460.882
22_A25_K0.156950.879
7_F15_R0.156370.875
6_P75_D0.15590.873
24_E29_E0.155830.872
8_F68_N0.155650.871
4_A78_T0.154810.867
82_L92_V0.15340.859
35_D38_E0.152760.855
47_W51_I0.152510.854
48_A51_I0.151110.846
21_E24_E0.150840.844
49_R61_E0.150740.844
23_L32_S0.150120.840
24_E62_C0.150040.840
85_A92_V0.148480.831
3_L16_V0.148150.829
45_Q49_R0.147090.823
85_A90_K0.145910.817
8_F55_D0.145730.816
60_R89_G0.145660.815
58_G61_E0.145390.814
74_P82_L0.142720.799
7_F77_G0.1410.789
14_A17_E0.140780.788
2_Y75_D0.140650.787
18_R22_A0.140080.784
69_L82_L0.139450.781
17_E88_L0.139030.778
56_L60_R0.139010.778
53_E57_E0.137340.769
31_Y62_C0.136950.767
9_S70_D0.136890.766
51_I77_G0.136620.765
20_R24_E0.136220.763
14_A24_E0.136110.762
19_L95_L0.133840.749
77_G82_L0.133510.747
71_G96_T0.132560.742
3_L85_A0.132470.742
15_R18_R0.13210.740
43_D58_G0.132070.739
8_F76_S0.132050.739
24_E50_E0.131260.735
1_I39_N0.13080.732
25_K28_F0.129560.725
4_A55_D0.129170.723
32_S35_D0.127110.712
69_L74_P0.126960.711
37_D65_V0.125980.705
51_I68_N0.125420.702
7_F75_D0.125290.701
18_R84_Y0.124990.700
65_V86_Y0.124550.697
68_N79_A0.124380.696
39_N54_R0.124170.695
84_Y87_A0.123730.693
65_V82_L0.122650.687
39_N43_D0.122070.683
26_N53_E0.119840.671
53_E88_L0.119150.667
66_I94_L0.118720.665
43_D92_V0.118140.661
23_L66_I0.118060.661
36_N39_N0.117370.657
5_G68_N0.117190.656
68_N94_L0.116850.654
25_K29_E0.116810.654
7_F97_E0.116460.652
50_E91_P0.11610.650
6_P55_D0.115430.646
39_N86_Y0.115280.645
10_E46_E0.115150.645
13_K25_K0.114590.642
67_A85_A0.114370.640
26_N91_P0.114160.639
11_E71_G0.1140.638
3_L45_Q0.113730.637
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
3ehdA199.80.135
1f8yA0.955899.80.143
1s2dA0.955899.80.144
2f62A0.938199.80.149
2khzA0.920499.70.248
4fykA0.920499.70.293
1t1jA0.911599.20.464
1eiwA0.699198.10.649
3hynA0.9912970.738
1rcuA0.911596.50.754

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