GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TUDOR - Tudor domain
Pfam: PF00567 (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: CL0049
Length: 121
Sequences: 1344
Seq/Len: 11.11
HH_delta: 0.064 (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
18_E116_K0.39712.560
86_L93_E0.379242.444
40_Y107_F0.373612.408
8_V21_V0.35042.259
19_F117_C0.349112.250
86_L91_N0.342962.211
110_L113_Q0.338662.183
37_L41_Y0.335412.162
36_E106_E0.308871.991
16_P19_F0.306551.976
69_Y89_Y0.303941.959
60_C71_A0.300271.935
21_V117_C0.299081.928
82_Y100_L0.296031.908
68_W101_R0.295781.907
41_Y104_P0.28911.863
55_G58_C0.284161.832
57_G60_C0.283881.830
65_D69_Y0.282561.821
87_I112_P0.280311.807
69_Y91_N0.265421.711
58_C71_A0.255991.650
103_L108_A0.24311.567
41_Y107_F0.239951.547
30_Y89_Y0.235591.519
33_L107_F0.235161.516
14_D18_E0.230481.486
52_S55_G0.222531.434
32_K36_E0.219941.418
58_C62_V0.219721.416
57_G62_V0.216761.397
58_C61_V0.211351.362
55_G61_V0.207351.337
81_Q94_K0.202581.306
82_Y97_A0.193841.249
15_S18_E0.193561.248
22_Q30_Y0.190621.229
62_V86_L0.189231.220
59_L103_L0.181131.168
11_T22_Q0.17911.154
37_L59_L0.175381.130
11_T90_G0.169071.090
23_P26_A0.164631.061
52_S56_E0.164631.061
66_G99_D0.16411.058
30_Y34_Q0.162891.050
62_V91_N0.162011.044
63_S93_E0.161521.041
96_S99_D0.160071.032
108_A112_P0.159351.027
55_G60_C0.154560.996
37_L107_F0.153720.991
29_A36_E0.151790.978
83_K94_K0.150920.973
35_E39_D0.145750.939
20_Y85_F0.144290.930
111_P115_I0.143970.928
16_P115_I0.143810.927
60_C95_V0.14370.926
28_K32_K0.141770.914
52_S57_G0.141770.914
82_Y96_S0.14150.912
68_W102_P0.139740.901
37_L103_L0.139720.901
60_C63_S0.139140.897
16_P41_Y0.138680.894
55_G62_V0.13710.884
40_Y104_P0.13630.879
57_G61_V0.135470.873
33_L110_L0.133890.863
60_C86_L0.133820.863
26_A30_Y0.132330.853
5_T10_I0.13090.844
41_Y59_L0.130480.841
85_F114_A0.129980.838
71_A101_R0.128960.831
83_K92_T0.128580.829
10_I13_V0.128450.828
6_F19_F0.12830.827
12_H20_Y0.128150.826
30_Y110_L0.126430.815
34_Q69_Y0.125830.811
71_A84_V0.125420.808
62_V65_D0.124540.803
105_P108_A0.124330.801
63_S86_L0.124330.801
37_L40_Y0.12430.801
100_L104_P0.124130.800
32_K39_D0.124060.800
14_D20_Y0.121860.785
62_V71_A0.12180.785
44_N51_E0.121010.780
40_Y116_K0.1210.780
38_Q42_E0.120750.778
60_C65_D0.120480.777
99_D105_P0.120110.774
57_G87_I0.12010.774
46_K106_E0.119550.771
105_P109_S0.119540.771
75_V80_N0.11930.769
72_V118_K0.119210.768
6_F20_Y0.1190.767
22_Q89_Y0.118280.762
22_Q69_Y0.11790.760
30_Y69_Y0.115710.746
95_V99_D0.115360.744
65_D91_N0.115230.743
5_T17_G0.115060.742
86_L89_Y0.114860.740
55_G59_L0.114820.740
12_H91_N0.114670.739
76_D102_P0.114490.738
65_D86_L0.113450.731
34_Q89_Y0.113140.729
20_Y116_K0.113130.729
9_Y27_D0.113020.728
84_V95_V0.112740.727
84_V88_D0.112350.724
108_A113_Q0.11220.723
6_F39_D0.111180.717
81_Q96_S0.110080.710
78_D97_A0.109860.708
82_Y85_F0.109830.708
87_I93_E0.109760.707
17_G26_A0.109430.705
24_D94_K0.109160.704
76_D95_V0.1090.703
76_D110_L0.108920.702
41_Y101_R0.108680.701
37_L104_P0.108590.700
31_E34_Q0.107760.695
13_V24_D0.107080.690
27_D30_Y0.106380.686
38_Q67_R0.105810.682
33_L113_Q0.105440.680
5_T89_Y0.105380.679
9_Y37_L0.105210.678
44_N103_L0.104580.674
11_T21_V0.104580.674
7_E24_D0.104410.673
75_V79_E0.104030.671
71_A96_S0.103850.669
52_S61_V0.103380.666
12_H112_P0.103020.664
13_V85_F0.1030.664
49_S100_L0.102980.664
23_P27_D0.102650.662
61_V93_E0.101580.655
6_F68_W0.101510.654
7_E21_V0.101440.654
108_A116_K0.101080.652
14_D87_I0.101070.651
75_V120_A0.100550.648
48_P100_L0.100280.646
75_V83_K0.100270.646
81_Q84_V0.100080.645
20_Y90_G0.09940.641
20_Y66_G0.099190.639
38_Q44_N0.099020.638
8_V117_C0.098830.637
73_I78_D0.098670.636
70_R88_D0.098530.635
14_D118_K0.098360.634
31_E77_I0.098240.633
17_G29_A0.098030.632
60_C64_E0.098010.632
33_L37_L0.0980.632
103_L117_C0.097320.627
33_L36_E0.096950.625
43_N109_S0.096920.625
42_E78_D0.096880.624
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
4b9xA0.991799.90.064
4b9wA0.991799.90.066
3bdlA0.991799.90.088
2hqxA0.991799.90.105
3ntkA0.950499.90.11
2wacA0.983599.90.12
2diqA0.84399.70.253
3fdrA0.776999.70.267
2eqkA0.702599.30.451
1g5vA0.6612990.537

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