GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TK - Thymidine kinase
Pfam: PF00265 (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: CL0023
Length: 176
Sequences: 3137
Seq/Len: 17.82
HH_delta: 0.063 (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
139_V170_P1.122154.316
144_G168_Y0.876763.372
118_E121_G0.842933.242
145_R171_V0.793493.052
172_C175_C0.68612.639
143_C172_C0.648042.493
147_A169_E0.633482.437
35_F59_I0.61972.384
146_K166_E0.615942.369
142_V174_K0.600152.308
33_L72_I0.587182.258
30_K79_V0.562432.163
85_A96_V0.546742.103
7_T111_L0.543432.090
145_R169_E0.532922.050
140_C143_C0.519481.998
94_Q98_I0.464161.785
143_C175_C0.462591.779
150_T153_I0.444861.711
139_V144_G0.420881.619
55_S58_A0.406521.564
26_E32_V0.39951.537
4_E105_P0.396791.526
59_I72_I0.387111.489
147_A153_I0.37941.459
115_F125_R0.378831.457
147_A167_K0.36411.400
35_F72_I0.362041.393
5_F109_A0.357271.374
8_G12_S0.351651.353
18_L81_G0.350151.347
49_V52_D0.346691.333
88_F94_Q0.333861.284
27_I30_K0.332161.278
22_I81_G0.33031.270
98_I101_N0.32861.264
115_F118_E0.326391.255
80_I99_L0.325621.252
22_I32_V0.321651.237
118_E125_R0.31581.215
146_K168_Y0.308391.186
121_G124_P0.303671.168
149_F167_K0.302051.162
53_G58_A0.300361.155
3_L106_V0.290931.119
140_C172_C0.288331.109
47_K55_S0.283861.092
164_G167_K0.27941.075
125_R128_P0.277621.068
69_I73_L0.276911.065
167_K170_P0.276811.065
5_F85_A0.275481.060
141_E144_G0.275321.059
116_R125_R0.274991.058
116_R119_P0.273681.053
16_T20_R0.273361.051
151_Q171_V0.271131.043
25_Y79_V0.270971.042
8_G11_F0.26741.028
105_P108_C0.26561.022
124_P128_P0.265011.019
97_E101_N0.264841.019
34_V48_I0.263081.012
146_K149_F0.261891.007
115_F123_S0.260031.000
42_R173_R0.259991.000
34_V56_L0.25680.988
96_V108_C0.253740.976
163_G166_E0.253260.974
85_A109_A0.252940.973
118_E122_G0.251830.969
152_R173_R0.242460.933
36_K40_D0.241180.928
42_R168_Y0.239780.922
163_G173_R0.236750.911
77_Y104_I0.235630.906
83_D103_G0.235610.906
31_K75_N0.234350.901
69_I72_I0.233910.900
25_Y108_C0.233270.897
117_G125_R0.232780.895
139_V171_V0.232770.895
96_V100_A0.232230.893
17_E20_R0.231670.891
166_E169_E0.23150.890
166_E173_R0.230090.885
74_E102_K0.230030.885
117_G128_P0.229810.884
149_F154_V0.228450.879
152_R163_G0.228430.879
15_S43_Y0.227740.876
15_S19_I0.227640.876
13_G16_T0.226970.873
33_L41_T0.226130.870
74_E77_Y0.226040.869
25_Y30_K0.225880.869
115_F128_P0.225190.866
148_T154_V0.224980.865
98_I128_P0.224960.865
26_E56_L0.223780.861
123_S133_I0.22310.858
8_G83_D0.221910.854
72_I80_I0.221760.853
11_F83_D0.220880.850
14_K84_E0.220120.847
148_T166_E0.21930.843
119_P125_R0.216310.832
168_Y171_V0.216130.831
42_R88_F0.215060.827
19_I43_Y0.213280.820
73_L76_D0.212730.818
136_L153_I0.210650.810
16_T41_T0.210520.810
55_S89_D0.208720.803
85_A108_C0.206760.795
8_G14_K0.205830.792
163_G174_K0.204870.788
70_I73_L0.204620.787
3_L98_I0.204470.786
50_S98_I0.203790.784
42_R163_G0.202980.781
10_M104_I0.202560.779
24_R28_A0.201130.774
145_R148_T0.199880.769
15_S41_T0.19980.768
25_Y32_V0.199170.766
88_F163_G0.197590.760
115_F119_P0.197090.758
151_Q163_G0.19690.757
57_E89_D0.196570.756
23_H138_A0.196460.756
42_R95_L0.196050.754
119_P122_G0.195930.754
69_I95_L0.195750.753
140_C175_C0.195020.750
77_Y80_I0.19490.750
7_T116_R0.194520.748
139_V168_Y0.19450.748
3_L100_A0.193860.746
50_S53_G0.193310.744
129_L132_K0.192980.742
85_A92_I0.19180.738
26_E29_G0.191530.737
72_I82_I0.190960.734
42_R94_Q0.190710.734
38_A74_E0.190220.732
4_E21_R0.189460.729
147_A152_R0.189290.728
121_G125_R0.188930.727
77_Y102_K0.188740.726
57_E71_D0.187990.723
152_R164_G0.187040.719
80_I104_I0.186980.719
50_S173_R0.186960.719
116_R120_F0.186830.719
24_R42_R0.185990.715
93_V125_R0.185680.714
54_I71_D0.185680.714
153_I167_K0.185630.714
74_E103_G0.185190.712
70_I102_K0.184350.709
15_S124_P0.184230.709
116_R122_G0.184050.708
20_R24_R0.183940.707
24_R173_R0.183270.705
151_Q154_V0.183170.705
73_L99_L0.18290.703
152_R168_Y0.181890.700
115_F120_F0.181740.699
148_T171_V0.181310.697
119_P128_P0.181290.697
44_G127_L0.180930.696
73_L77_Y0.180850.696
21_R88_F0.180430.694
31_K76_D0.18020.693
8_G103_G0.180130.693
115_F122_G0.179660.691
47_K57_E0.179510.690
83_D86_Q0.179370.690
146_K164_G0.17890.688
88_F152_R0.177380.682
24_R27_I0.177370.682
48_I52_D0.177240.682
70_I98_I0.177140.681
26_E45_E0.177130.681
8_G13_G0.176670.680
71_D75_N0.176230.678
145_R174_K0.175830.676
51_H164_G0.17580.676
163_G171_V0.175620.675
82_I96_V0.175250.674
86_Q110_G0.174420.671
98_I102_K0.174360.671
76_D103_G0.174360.671
42_R98_I0.17340.667
122_G125_R0.173370.667
153_I169_E0.173170.666
150_T164_G0.172630.664
116_R121_G0.172580.664
142_V173_R0.17230.663
10_M86_Q0.171680.660
26_E30_K0.171530.660
10_M14_K0.170630.656
9_P56_L0.170560.656
23_H29_G0.170280.655
70_I74_E0.169950.654
144_G166_E0.169930.654
50_S147_A0.169910.654
163_G168_Y0.169880.653
77_Y103_G0.169330.651
51_H147_A0.169290.651
123_S127_L0.168880.650
127_L173_R0.16870.649
15_S94_Q0.16860.648
3_L122_G0.168520.648
42_R46_D0.168490.648
35_F42_R0.168230.647
118_E128_P0.168220.647
120_F152_R0.167330.644
21_R42_R0.166940.642
20_R129_L0.16590.638
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
3e2iA0.98861000.063
1w4rA0.97161000.088
2j9rA0.98861000.108
2orvA0.97161000.114
1xx6A0.98861000.149
2b8tA0.9831000.2
2orwA0.98861000.216
1p9rA0.903499.80.568
4ihqA0.937599.70.589
3jvvA0.909199.50.649

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