GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ACPS - 4-phosphopantetheinyl transferase superfamily
Pfam: PF01648 (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: 115
Sequences: 2244
Seq/Len: 19.51
HH_delta: 0.067 (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
47_L104_I0.813612.998
55_V84_L0.793022.922
51_A102_V0.688732.538
47_L106_H0.667012.458
2_I114_F0.620752.287
4_I114_F0.599252.208
26_T73_E0.579312.135
4_I112_A0.576522.124
89_S93_D0.57322.112
50_T113_A0.567992.093
28_E73_E0.553932.041
21_A30_L0.549472.025
8_K109_D0.54161.996
51_A74_L0.516271.902
60_G63_G0.510721.882
105_S112_A0.507681.871
77_P81_R0.479761.768
6_I110_Y0.473151.743
1_G101_H0.470971.735
75_H83_S0.46611.717
8_K107_D0.436551.609
25_F45_F0.433451.597
55_V59_L0.426221.570
22_E30_L0.407771.502
56_Y67_L0.385211.419
22_E27_P0.384781.418
10_D109_D0.384321.416
53_E57_K0.382041.408
6_I112_A0.380251.401
7_E50_T0.365211.346
24_F49_W0.363691.340
92_F97_I0.363551.340
48_L76_K0.36351.339
86_L100_F0.362181.335
9_I111_A0.362111.334
30_L34_R0.3581.319
33_L44_A0.354891.308
9_I42_L0.354491.306
25_F33_L0.354231.305
56_Y63_G0.3491.286
75_H85_S0.343281.265
28_E31_E0.335471.236
5_D57_K0.324511.196
5_D53_E0.321691.185
33_L45_F0.320551.181
56_Y60_G0.31481.160
30_L45_F0.310551.144
25_F44_A0.302961.116
72_I84_L0.302371.114
43_Q106_H0.297431.096
7_E111_A0.296961.094
77_P83_S0.291481.074
91_I94_G0.290511.070
27_P31_E0.285731.053
7_E12_P0.281371.037
34_R45_F0.278391.026
73_E85_S0.276441.019
55_V72_I0.275651.016
44_A48_L0.275241.014
32_W76_K0.2751.013
20_F24_F0.269670.994
9_I46_T0.266520.982
68_S71_E0.265670.979
4_I103_S0.259260.955
8_K108_E0.25530.941
91_I95_D0.253870.935
51_A104_I0.240590.886
90_W93_D0.238140.877
36_L41_R0.237390.875
55_V100_F0.237110.874
88_A92_F0.233110.859
18_E22_E0.232440.856
55_V86_L0.228790.843
50_T54_A0.223340.823
74_L102_V0.218480.805
21_A33_L0.217020.800
103_S106_H0.214040.789
44_A47_L0.21270.784
7_E107_D0.212540.783
54_A113_A0.21130.779
104_I113_A0.210870.777
82_P102_V0.208910.770
28_E75_H0.207530.765
12_P20_F0.207390.764
21_A34_R0.207330.764
60_G82_P0.206490.761
85_S89_S0.204950.755
59_L67_L0.204110.752
82_P103_S0.201490.742
81_R101_H0.200920.740
4_I105_S0.200570.739
32_W35_S0.200450.739
7_E11_R0.200080.737
46_T50_T0.198680.732
82_P106_H0.197080.726
27_P70_R0.196530.724
77_P80_G0.195180.719
64_S68_S0.192640.710
35_S41_R0.192380.709
18_E30_L0.192150.708
15_R27_P0.191960.707
62_T66_D0.188730.695
3_G57_K0.18870.695
31_E35_S0.184880.681
74_L84_L0.18090.667
56_Y64_S0.180360.665
46_T105_S0.180270.664
67_L72_I0.179060.660
93_D96_K0.178370.657
19_K23_R0.177460.654
88_A91_I0.177180.653
22_E34_R0.176530.650
45_F48_L0.176360.650
86_L92_F0.175930.648
32_W44_A0.175620.647
56_Y62_T0.174870.644
50_T111_A0.173480.639
3_G54_A0.172160.634
65_L95_D0.171550.632
43_Q47_L0.170530.628
31_E34_R0.170220.627
18_E21_A0.169040.623
21_A45_F0.168830.622
11_R23_R0.168560.621
55_V92_F0.168180.620
34_R41_R0.166340.613
84_L100_F0.165820.611
7_E10_D0.16540.609
49_W81_R0.163750.603
25_F32_W0.163120.601
107_D110_Y0.162750.600
21_A25_F0.161450.595
7_E46_T0.161440.595
8_K62_T0.161420.595
94_G97_I0.160280.591
3_G53_E0.159980.589
64_S67_L0.157710.581
26_T70_R0.157250.579
51_A113_A0.155080.571
6_I105_S0.154290.569
101_H114_F0.154240.568
18_E34_R0.153820.567
33_L42_L0.153080.564
47_L107_D0.152860.563
49_W69_F0.152750.563
21_A66_D0.150650.555
26_T71_E0.150130.553
59_L62_T0.149370.550
16_R45_F0.148960.549
10_D15_R0.148410.547
4_I8_K0.148050.546
38_S43_Q0.147910.545
101_H112_A0.146770.541
32_W36_L0.146580.540
20_F23_R0.145860.537
2_I101_H0.145540.536
69_F102_V0.1450.534
10_D108_E0.144530.533
32_W75_H0.144220.531
16_R19_K0.143030.527
89_S98_W0.142710.526
103_S113_A0.142150.524
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
2uv9A0.965299.80.067
2uv8A0.965299.80.074
2bddA0.991399.80.092
3otaA0.973999.80.105
2qg8A0.991399.80.107
3h88A0.973999.80.111
3nfdA0.973999.80.113
2wdsA0.965299.80.121
3hykA0.921799.80.124
3gwmA0.965299.80.128

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