GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
APS_kinase - Adenylylsulphate kinase
Pfam: PF01583 (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: 156
Sequences: 5727
Seq/Len: 36.71
HH_delta: 0.188 (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
112_V115_K1.291494.201
130_I134_T1.033193.361
107_D149_V0.91172.966
142_E149_V0.849352.763
108_C113_C0.826082.687
86_R90_E0.809932.635
109_P153_D0.791472.575
21_A25_R0.750742.442
114_R126_R0.749092.437
107_D151_D0.725542.360
21_A24_R0.723072.352
4_V96_I0.695212.261
90_E94_E0.674512.194
109_P112_V0.67182.185
112_V153_D0.627532.041
53_K56_R0.539261.754
19_A35_L0.538081.750
115_K119_K0.532941.734
64_A92_A0.525261.709
108_C152_T0.511011.662
86_R144_L0.501731.632
34_Y72_D0.496781.616
118_P122_Y0.493981.607
7_L19_A0.489371.592
91_W94_E0.482631.570
46_N64_A0.469461.527
10_L113_C0.469421.527
124_K129_E0.434181.412
73_Q76_I0.424321.380
131_K137_D0.412161.341
23_E35_L0.408811.330
110_L114_R0.39981.301
132_N137_D0.397871.294
41_L44_G0.39691.291
6_W103_E0.388091.262
23_E27_F0.38691.259
63_I96_I0.383741.248
130_I133_F0.375821.223
112_V154_K0.369541.202
52_S55_D0.368881.200
58_E61_R0.363061.181
5_I22_L0.360071.171
4_V71_A0.359791.170
151_D154_K0.349571.137
128_G132_N0.347741.131
108_C112_V0.345531.124
71_A96_I0.34521.123
16_T20_R0.34341.117
20_R24_R0.339021.103
60_I63_I0.336521.095
8_T140_Y0.336451.094
27_F33_V0.335021.090
20_R35_L0.332221.081
119_K122_Y0.330611.075
54_E87_E0.328571.069
7_L22_L0.328131.067
132_N136_V0.327881.067
54_E85_Y0.326141.061
90_E93_R0.325421.059
125_A129_E0.325011.057
5_I104_V0.321391.045
65_E68_K0.320391.042
58_E62_R0.319391.039
107_D142_E0.319391.039
40_N43_H0.314531.023
7_L78_I0.312681.017
111_E115_K0.307841.001
102_I148_L0.307110.999
57_E61_R0.30690.998
53_K138_D0.305170.993
94_E98_N0.304030.989
85_Y138_D0.30190.982
106_V152_T0.300440.977
18_L21_A0.296350.964
134_T138_D0.296190.963
59_N62_R0.296190.963
96_I130_I0.29480.959
91_W95_L0.294510.958
135_G139_P0.294340.957
69_L72_D0.293090.953
135_G138_D0.290220.944
56_R59_N0.290010.943
68_K72_D0.288240.938
131_K135_G0.284110.924
105_Y149_V0.281140.915
88_D92_A0.280530.913
63_I81_F0.28020.911
19_A23_E0.277540.903
36_L76_I0.275540.896
20_R23_E0.275510.896
9_G14_G0.275450.896
59_N63_I0.274670.893
8_T103_E0.274530.893
22_L26_L0.274390.893
70_L75_I0.274020.891
9_G15_K0.273950.891
122_Y125_A0.273770.891
74_G77_V0.271690.884
87_E91_W0.270590.880
126_R129_E0.268770.874
19_A37_D0.268610.874
5_I102_I0.268330.873
118_P128_G0.264930.862
66_V70_L0.264890.862
51_F78_I0.263520.857
53_K85_Y0.263380.857
87_E90_E0.262220.853
6_W101_F0.261860.852
73_Q77_V0.256130.833
71_A100_R0.254980.829
86_R137_D0.252590.822
76_I79_V0.252560.822
105_Y142_E0.25190.819
41_L63_I0.250730.816
38_G42_R0.250540.815
116_R152_T0.249040.810
6_W83_S0.246540.802
62_R65_E0.245880.800
104_V148_L0.243470.792
64_A89_R0.241990.787
81_F84_P0.240770.783
64_A95_L0.238890.777
120_G124_K0.238040.774
65_E69_L0.237950.774
57_E60_I0.237270.772
17_T21_A0.233930.761
140_Y143_P0.233250.759
71_A77_V0.232110.755
4_V36_L0.231750.754
12_G107_D0.231660.754
38_G67_A0.229280.746
134_T137_D0.227870.741
18_L106_V0.227020.738
64_A69_L0.226120.736
92_A96_I0.22530.733
57_E87_E0.224640.731
36_L41_L0.224440.730
27_F100_R0.224120.729
37_D80_A0.222410.723
13_S113_C0.221650.721
141_E144_L0.221130.719
16_T39_D0.219990.716
12_G152_T0.219780.715
123_A127_A0.219640.714
85_Y88_D0.219530.714
11_S82_I0.219170.713
121_L128_G0.216410.704
90_E144_L0.215190.700
53_K88_D0.214670.698
97_P100_R0.213270.694
83_S140_Y0.212520.691
64_A67_A0.21250.691
4_V79_V0.212490.691
66_V69_L0.211730.689
121_L125_A0.211290.687
18_L22_L0.211010.686
112_V116_R0.210890.686
57_E91_W0.209830.683
11_S51_F0.209820.683
95_L98_N0.209620.682
52_S81_F0.208330.678
108_C116_R0.207940.676
81_F131_K0.207750.676
40_N65_E0.207730.676
50_G56_R0.207170.674
73_Q121_L0.205590.669
42_R45_L0.205540.669
33_V75_I0.201910.657
61_R91_W0.200810.653
118_P124_K0.19990.650
56_R60_I0.199850.650
49_L52_S0.199590.649
46_N49_L0.199070.648
133_F137_D0.197970.644
4_V101_F0.197810.643
55_D59_N0.197280.642
68_K95_L0.197110.641
54_E57_E0.196770.640
104_V150_I0.196460.639
53_K57_E0.196360.639
125_A128_G0.195950.637
47_A68_K0.195750.637
109_P154_K0.195670.636
13_S43_H0.19480.634
37_D105_Y0.193540.630
96_I100_R0.19330.629
103_E145_N0.192310.626
13_S105_Y0.191950.624
103_E146_P0.190880.621
131_K154_K0.190520.620
50_G59_N0.188820.614
119_K123_A0.187910.611
113_C117_D0.18760.610
46_N69_L0.187190.609
16_T80_A0.186910.608
24_R154_K0.186270.606
114_R117_D0.185870.605
79_V82_I0.185870.605
78_I81_F0.184270.599
16_T42_R0.181540.591
18_L104_V0.178480.581
82_I85_Y0.177850.579
63_I83_S0.177260.577
49_L120_G0.176290.573
64_A68_K0.176110.573
38_G41_L0.174170.567
133_F136_V0.174040.566
111_E114_R0.174020.566
40_N92_A0.174010.566
57_E95_L0.173680.565
18_L137_D0.173440.564
24_R27_F0.172360.561
10_L38_G0.171930.559
97_P145_N0.171790.559
145_N148_L0.170490.555
140_Y145_N0.170460.554
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
1m8pA199.90.188
1x6vB199.90.212
2gksA199.90.235
3uieA199.80.262
3cr8A199.80.28
2yvuA199.80.282
1m7gA199.80.303
2pezA199.70.357
3a4mA0.942399.70.37
1qhxA0.948799.70.374

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