GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
dNK - Deoxynucleoside kinase
Pfam: PF01712 (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: 146
Sequences: 3141
Seq/Len: 21.51
HH_delta: 0.274 (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
74_L126_A1.032723.420
80_T83_E0.914273.028
128_N137_D0.909143.011
75_D110_E0.881512.919
130_D133_E0.788852.612
77_S127_D0.690232.286
11_E15_E0.68652.273
75_D105_H0.673272.230
105_H110_E0.667242.210
38_M108_A0.610582.022
29_Y120_P0.610332.021
124_I134_N0.595311.971
111_D115_K0.566721.877
128_N133_E0.564581.870
135_P139_E0.513851.702
73_Y123_V0.509931.689
110_E123_V0.503941.669
122_L141_V0.499581.654
78_P98_L0.495911.642
73_Y121_V0.47731.581
135_P138_I0.470611.558
72_I141_V0.469041.553
76_A80_T0.465091.540
107_E111_D0.463661.535
73_Y113_L0.459141.521
75_D123_V0.455181.507
76_A81_C0.451951.497
98_L102_E0.449811.490
99_E102_E0.449441.488
102_E107_E0.431051.427
85_I88_R0.422731.400
28_I61_I0.422221.398
80_T127_D0.41151.363
70_L122_L0.410561.360
137_D140_Q0.399351.323
73_Y110_E0.393531.303
10_F14_K0.392531.300
81_C85_I0.382551.267
8_S12_Q0.381111.262
12_Q24_M0.376621.247
125_D128_N0.371911.232
136_E140_Q0.369561.224
82_L98_L0.369411.223
72_I122_L0.368171.219
6_L28_I0.367961.219
78_P105_H0.36751.217
111_D114_K0.365271.210
72_I124_I0.362731.201
81_C101_L0.359791.191
34_V38_M0.357671.184
113_L123_V0.357571.184
29_Y71_I0.355161.176
83_E87_K0.347071.149
55_K58_D0.346391.147
6_L32_D0.344451.141
80_T84_R0.343991.139
112_W121_V0.331751.099
124_I141_V0.33171.098
49_E52_L0.331171.097
134_N137_D0.329871.092
74_L138_I0.329341.091
16_L19_K0.328611.088
79_E83_E0.326221.080
99_E103_R0.323391.071
57_F60_L0.320081.060
116_Y121_V0.315771.046
79_E102_E0.310421.028
49_E53_Y0.308721.022
76_A126_A0.307461.018
10_F13_Y0.301160.997
6_L57_F0.300960.997
137_D141_V0.295150.977
58_D66_K0.292840.970
100_Y104_L0.292190.968
113_L121_V0.290240.961
66_K116_Y0.282310.935
90_R93_E0.282150.934
34_V108_A0.279240.925
32_D36_A0.278970.924
26_R30_S0.275030.911
54_D58_D0.269410.892
133_E136_E0.266860.884
29_Y121_V0.265960.881
136_E139_E0.264480.876
26_R35_F0.261810.867
70_L141_V0.26180.867
82_L85_I0.261260.865
30_S109_Y0.260290.862
131_F135_P0.259520.859
96_I100_Y0.258010.854
84_R126_A0.257980.854
78_P81_C0.257840.854
30_S35_F0.257480.853
77_S80_T0.256720.850
110_E113_L0.255740.847
51_D55_K0.254550.843
83_E86_K0.251540.833
139_E142_I0.251250.832
50_Y54_D0.245960.815
5_F92_E0.245580.813
103_R107_E0.242450.803
6_L60_L0.239570.793
16_L22_V0.238580.790
5_F101_L0.237650.787
5_F9_R0.231990.768
78_P102_E0.230020.762
22_V26_R0.22990.761
114_K123_V0.228170.756
32_D53_Y0.2270.752
79_E98_L0.222230.736
52_L59_E0.222230.736
133_E137_D0.221950.735
96_I101_L0.218980.725
45_L49_E0.218890.725
108_A111_D0.21810.722
75_D125_D0.218010.722
45_L48_E0.217260.719
47_K51_D0.213910.708
72_I138_I0.212990.705
116_Y120_P0.21260.704
73_Y105_H0.210610.697
36_A45_L0.210460.697
37_K108_A0.208160.689
54_D115_K0.207520.687
61_I65_P0.206670.684
81_C98_L0.205680.681
25_E68_P0.205620.681
5_F8_S0.204830.678
134_N138_I0.201450.667
13_Y60_L0.19650.651
138_I142_I0.196080.649
78_P82_L0.196060.649
8_S27_S0.194320.644
9_R32_D0.193390.640
6_L61_I0.193030.639
4_Y11_E0.192510.638
22_V25_E0.191470.634
34_V104_L0.191360.634
60_L63_E0.190320.630
23_I26_R0.190280.630
28_I32_D0.190160.630
6_L56_L0.188030.623
33_F57_F0.187590.621
36_A92_E0.185910.616
133_E140_Q0.185590.615
124_I138_I0.185430.614
13_Y65_P0.184570.611
71_I121_V0.184260.610
97_P101_L0.18330.607
9_R30_S0.183190.607
51_D54_D0.182970.606
109_Y112_W0.182420.604
135_P142_I0.181370.601
27_S61_I0.179640.595
72_I134_N0.175410.581
8_S32_D0.175150.580
120_P123_V0.174890.579
128_N140_Q0.173690.575
53_Y57_F0.17350.575
33_F54_D0.173030.573
33_F61_I0.172560.571
66_K120_P0.172510.571
33_F112_W0.172270.570
46_S117_D0.170860.566
57_F96_I0.17020.564
6_L101_L0.169620.562
45_L104_L0.169090.560
50_Y53_Y0.168610.558
124_I127_D0.167290.554
24_M27_S0.166830.552
17_N136_E0.166650.552
48_E52_L0.166450.551
131_F138_I0.166130.550
22_V63_E0.165880.549
9_R68_P0.163760.542
27_S32_D0.162950.540
56_L59_E0.162690.539
23_I30_S0.162320.538
91_E95_N0.161830.536
86_K98_L0.161740.536
71_I120_P0.161210.534
46_S49_E0.160850.533
11_E85_I0.160770.532
93_E101_L0.160410.531
17_N20_Q0.159520.528
77_S102_E0.159520.528
55_K140_Q0.158410.525
82_L111_D0.156650.519
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
4hlcA0.917899.80.274
3ld9A0.883699.80.282
3v9pA0.904199.80.292
3tmkA0.897399.80.299
4tmkA0.904199.80.307
4edhA0.91199.80.311
3lv8A0.904199.80.323
3hjnA0.890499.70.368
1p6xA0.945299.70.385
2ocpA0.938499.70.395

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