GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NDK - Nucleoside diphosphate kinase
Pfam: PF00334 (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: 135
Sequences: 2102
Seq/Len: 15.57
HH_delta: -0.103 (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
41_R45_R1.233643.578
19_E26_E0.907162.631
34_M70_V0.875772.540
73_V126_I0.860782.496
91_D94_E0.852132.471
39_L129_F0.802422.327
23_R103_R0.801292.324
87_C115_G0.797832.314
6_L71_A0.778832.259
118_S121_D0.777452.255
41_R62_D0.727882.111
21_I72_L0.723642.099
24_L83_W0.722062.094
7_I11_A0.718382.083
46_E128_F0.717582.081
85_Q96_A0.708862.056
31_I74_L0.678841.969
78_N81_E0.674811.957
40_T43_E0.672861.951
22_D26_E0.655311.900
80_V119_P0.652441.892
5_A83_W0.651321.889
1_E119_P0.635141.842
50_E124_R0.615321.785
44_A64_M0.597631.733
29_F82_K0.594791.725
29_F79_A0.580351.683
29_F76_G0.580341.683
87_C113_V0.575571.669
46_E49_E0.56991.653
97_P102_A0.567931.647
76_G82_K0.559431.622
17_A70_V0.534141.549
43_E128_F0.50061.452
81_E85_Q0.499191.448
121_D124_R0.497721.443
21_I34_M0.490071.421
37_V71_A0.48941.419
2_R75_E0.487191.413
2_R32_V0.486031.410
27_A86_L0.481551.397
53_G58_D0.480031.392
78_N82_K0.463951.346
45_R52_K0.459311.332
44_A65_S0.458171.329
83_W115_G0.44911.302
58_D62_D0.446491.295
117_D121_D0.44371.287
19_E22_D0.442031.282
77_E107_D0.439031.273
32_V75_E0.439011.273
6_L69_S0.431131.250
61_V65_S0.421971.224
59_A109_I0.41411.201
50_E121_D0.41061.191
91_D108_I0.406991.180
89_P96_A0.403831.171
24_L74_L0.398211.155
11_A20_I0.395481.147
33_A73_V0.394851.145
13_A110_R0.388191.126
122_A126_I0.386241.120
82_K85_Q0.385281.117
21_I70_V0.381481.106
36_M70_V0.37761.095
34_M72_L0.374821.087
127_A132_E0.371071.076
11_A112_A0.369381.071
83_W87_C0.363861.055
123_E127_A0.360691.046
45_R57_F0.359911.044
41_R58_D0.357311.036
39_L44_A0.350251.016
47_F128_F0.348261.010
2_R123_E0.348231.010
45_R61_V0.340690.988
39_L64_M0.336270.975
119_P123_E0.332010.963
80_V121_D0.327480.950
37_V43_E0.32140.932
16_H112_A0.319920.928
106_T110_R0.307710.892
41_R61_V0.306510.889
14_R106_T0.305740.887
107_D110_R0.304940.884
27_A82_K0.302330.877
10_D63_F0.30130.874
12_V36_M0.297670.863
120_E123_E0.293260.850
59_A62_D0.289690.840
14_R112_A0.287330.833
29_F83_W0.286620.831
118_S124_R0.284810.826
12_V17_A0.279990.812
30_E75_E0.278590.808
83_W113_V0.277360.804
43_E133_F0.275680.800
49_E57_F0.275470.799
20_I112_A0.271330.787
82_K86_L0.267730.776
42_E45_R0.265120.769
80_V118_S0.264270.766
16_H19_E0.264050.766
18_G36_M0.262860.762
39_L43_E0.261570.759
124_R128_F0.256290.743
43_E46_E0.256040.743
78_N93_E0.252420.732
39_L69_S0.250940.728
3_T74_L0.250370.726
5_A115_G0.247520.718
7_I20_I0.243670.707
94_E108_I0.241110.699
98_G103_R0.240360.697
44_A61_V0.240280.697
51_H56_F0.239340.694
62_D65_S0.236330.685
48_Y114_H0.235910.684
18_G34_M0.23520.682
21_I31_I0.233430.677
6_L64_M0.232650.675
89_P94_E0.231830.672
38_Q65_S0.231250.671
18_G25_E0.230670.669
3_T83_W0.229790.666
5_A24_L0.227450.660
41_R65_S0.226990.658
45_R53_G0.225160.653
15_G30_E0.223630.649
38_Q42_E0.220770.640
88_G101_R0.219630.637
114_H125_E0.219570.637
5_A72_L0.217860.632
51_H60_L0.217440.631
31_I34_M0.216360.627
55_P59_A0.21590.626
36_M68_P0.21390.620
116_S125_E0.213680.620
49_E52_K0.212780.617
51_H54_K0.210860.612
4_L71_A0.207250.601
24_L87_C0.20720.601
63_F66_S0.206690.599
116_S122_A0.205310.595
13_A66_S0.205090.595
8_K111_N0.204690.594
17_A21_I0.204120.592
31_I36_M0.202940.589
17_A36_M0.201520.584
100_L113_V0.200240.581
17_A22_D0.200220.581
1_E78_N0.199890.580
23_R27_A0.199030.577
117_D125_E0.196950.571
89_P92_P0.19680.571
92_P108_I0.196750.571
79_A106_T0.195490.567
69_S129_F0.195030.566
50_E128_F0.194920.565
10_D106_T0.192050.557
24_L86_L0.191620.556
41_R52_K0.191580.556
42_E133_F0.19010.551
51_H63_F0.189520.550
23_R100_L0.189410.549
43_E47_F0.185790.539
7_I70_V0.185530.538
86_L112_A0.184820.536
66_S110_R0.183160.531
52_K58_D0.182620.530
92_P107_D0.181960.528
93_E106_T0.18170.527
50_E120_E0.181430.526
101_R111_N0.181050.525
46_E132_E0.178620.518
55_P109_I0.176430.512
76_G79_A0.176310.511
22_D25_E0.176180.511
93_E110_R0.174620.506
59_A108_I0.174080.505
3_T79_A0.173370.503
81_E94_E0.172120.499
49_E124_R0.1720.499
92_P105_G0.171130.496
48_Y90_T0.171050.496
74_L83_W0.171040.496
22_D27_A0.170780.495
29_F106_T0.170710.495
35_K131_P0.17040.494
5_A74_L0.170350.494
1_E80_V0.169410.491
102_A112_A0.167160.485
50_E54_K0.166280.482
105_G112_A0.165740.481
13_A106_T0.165120.479
84_R90_T0.164310.477
18_G76_G0.161670.469
78_N91_D0.160070.464
58_D61_V0.160040.464
94_E109_I0.159780.463
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
4hr2A1100-0.103
4fkxA1100-0.089
3l7uA1100-0.087
3q8uA1100-0.087
3fkbA1100-0.084
3r9lA1100-0.083
3evoA1100-0.082
3mpdA1100-0.081
3ztpA1100-0.08
4dz6A1100-0.079

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