GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Nucleos_tra2_N - Na dependent nucleoside transporter N-terminus
Pfam: PF01773 (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: 75
Sequences: 914
Seq/Len: 12.19
HH_delta: -0.018 (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
16_N19_A0.502662.536
50_E54_D0.500582.525
65_A68_S0.454042.290
48_A51_W0.340931.720
58_A62_Y0.33641.697
42_T45_G0.332431.677
58_A61_D0.332371.677
38_F42_T0.32641.647
44_A48_A0.313151.580
28_G56_F0.302241.525
57_T61_D0.300491.516
11_W20_I0.299351.510
21_K24_T0.297461.501
28_G49_F0.294081.484
11_W17_R0.290081.463
26_I30_G0.285771.442
8_A12_L0.279251.409
23_R27_W0.277551.400
28_G41_K0.27111.368
47_D50_E0.257291.298
42_T46_R0.248931.256
12_L17_R0.248521.254
27_W31_L0.24471.234
45_G63_A0.240641.214
41_K49_F0.237261.197
37_L41_K0.224591.133
38_F45_G0.219251.106
48_A52_I0.218521.102
64_N68_S0.215511.087
4_L8_A0.212241.071
34_V38_F0.212021.070
63_A67_S0.211391.066
46_R50_E0.211061.065
47_D51_W0.206031.039
31_L50_E0.201571.017
15_E73_D0.199831.008
28_G67_S0.191320.965
54_D57_T0.190190.959
8_A34_V0.189930.958
11_W15_E0.18980.957
43_P47_D0.188720.952
36_A59_L0.188470.951
28_G32_Q0.188130.949
6_L59_L0.188050.949
32_Q70_V0.184020.928
8_A14_S0.18390.928
63_A73_D0.182340.920
55_G59_L0.182020.918
50_E57_T0.178690.901
28_G53_S0.177990.898
10_A51_W0.17730.894
39_V70_V0.1770.893
35_L49_F0.173410.875
29_L70_V0.172970.873
8_A47_D0.172460.870
7_L11_W0.171830.867
9_I54_D0.170620.861
2_G39_V0.170460.860
32_Q46_R0.167670.846
53_S63_A0.167540.845
55_G74_L0.166170.838
25_V36_A0.162720.821
3_I29_L0.162560.820
36_A41_K0.162070.818
29_L71_F0.161290.814
19_A48_A0.161060.812
2_G24_T0.159570.805
31_L34_V0.157350.794
32_Q74_L0.15650.789
45_G60_L0.156030.787
6_L22_W0.1560.787
54_D68_S0.154890.781
22_W36_A0.154460.779
9_I18_K0.154460.779
12_L54_D0.154340.779
49_F67_S0.153930.777
37_L49_F0.153040.772
68_S73_D0.152980.772
31_L71_F0.152270.768
43_P46_R0.150640.760
14_S20_I0.150150.757
2_G74_L0.150130.757
51_W55_G0.149830.756
26_I48_A0.149240.753
23_R36_A0.148120.747
18_K26_I0.147320.743
2_G14_S0.146930.741
35_L57_T0.146820.741
8_A26_I0.145870.736
55_G58_A0.145530.734
44_A63_A0.145150.732
1_L5_V0.144830.731
49_F70_V0.143640.725
36_A65_A0.143220.722
8_A50_E0.142390.718
22_W74_L0.141720.715
24_T32_Q0.141670.715
40_L45_G0.141660.715
36_A57_T0.140980.711
51_W57_T0.139980.706
3_I58_A0.138220.697
34_V37_L0.137580.694
11_W22_W0.13630.688
22_W73_D0.134980.681
40_L60_L0.134690.679
62_Y73_D0.13460.679
16_N20_I0.13450.678
3_I21_K0.134130.677
26_I47_D0.13410.676
70_V73_D0.13380.675
61_D71_F0.132940.671
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
3tijA199.9-0.018
4g1uA0.813311.20.895
3ixzA0.926.30.906
2zxeA0.924.70.911
3arcL0.25334.40.912
2jwaA0.324.30.913
2k1kA0.22673.80.915
3b8eG0.243.70.915
2nq2A0.81333.20.918
2l2tA0.322.90.919

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