GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CDtoxinA - Cytolethal distending toxin AC family
Pfam: PF03498 (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: CL0066
Length: 150
Sequences: 2136
Seq/Len: 14.24
HH_delta: 0.125 (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
107_C127_C1.227214.618
64_C78_C1.077164.053
13_L122_I0.887353.339
109_Q125_T0.658642.478
66_A85_Q0.651552.452
11_A118_I0.607592.286
22_N76_K0.564082.123
72_V108_L0.554092.085
87_F108_L0.531552.000
71_G121_S0.527751.986
125_T136_D0.518241.950
66_A75_Y0.489011.840
106_E126_P0.478821.802
22_N63_T0.477221.796
53_Y102_L0.455651.715
75_Y84_E0.436921.644
67_A124_L0.433951.633
14_T40_K0.424761.598
109_Q136_D0.419421.578
12_V78_C0.418461.575
36_N40_K0.413341.555
111_F123_G0.402321.514
24_L121_S0.402011.513
78_C127_C0.39941.503
14_T41_A0.396621.492
90_I100_K0.396161.491
66_A84_E0.39461.485
24_L71_G0.393251.480
12_V64_C0.385161.449
109_Q137_Q0.380371.431
101_S104_T0.375741.414
98_Q127_C0.370441.394
81_D84_E0.355271.337
5_R142_T0.351261.322
13_L108_L0.341631.286
55_Q78_C0.333681.256
16_W24_L0.329651.240
12_V127_C0.328961.238
63_T76_K0.327621.233
86_V102_L0.314511.184
67_A72_V0.306771.154
39_G42_R0.306681.154
25_D65_L0.304041.144
14_T36_N0.303091.141
6_S139_W0.29991.129
78_C107_C0.297721.120
104_T124_L0.297491.119
5_R12_V0.294091.107
110_T122_I0.294011.106
64_C127_C0.292731.102
61_T74_H0.292051.099
103_S124_L0.287261.081
64_C107_C0.28241.063
22_N75_Y0.280281.055
7_L138_L0.278751.049
4_I99_I0.278551.048
88_S100_K0.278291.047
44_R57_V0.278071.046
87_F101_S0.277211.043
132_E136_D0.273111.028
100_K107_C0.273071.028
7_L135_L0.272971.027
89_I99_I0.27241.025
100_K105_G0.267071.005
4_I13_L0.264990.997
41_A137_Q0.264910.997
42_R59_P0.264280.994
92_T138_L0.256350.965
114_S120_Y0.252770.951
109_Q123_G0.252060.949
113_N123_G0.251980.948
12_V107_C0.25180.948
66_A79_D0.24870.936
6_S9_T0.244580.920
135_L138_L0.239950.903
111_F121_S0.23290.876
125_T132_E0.231140.870
79_D84_E0.230270.867
43_D58_N0.229610.864
106_E124_L0.228630.860
82_N86_V0.223430.841
81_D134_N0.222730.838
57_V64_C0.220460.830
123_G136_D0.215480.811
25_D43_D0.215110.809
68_Y73_F0.213680.804
53_Y88_S0.210220.791
110_T120_Y0.208060.783
18_L40_K0.207220.780
70_N124_L0.201480.758
15_N74_H0.201130.757
90_I98_Q0.200640.755
14_T66_A0.198170.746
15_N25_D0.196340.739
67_A106_E0.194480.732
64_C85_Q0.193630.729
98_Q107_C0.192070.723
55_Q64_C0.191840.722
45_L141_I0.191270.720
45_L56_F0.191210.720
5_R140_F0.191180.719
69_G75_Y0.19110.719
13_L65_L0.189340.712
66_A73_F0.187360.705
80_Q84_E0.186320.701
43_D65_L0.181980.685
53_Y86_V0.1810.681
51_F86_V0.179460.675
75_Y79_D0.179040.674
122_I139_W0.178710.672
23_W74_H0.177830.669
86_V138_L0.176710.665
45_L54_V0.175280.660
92_T98_Q0.17410.655
19_D74_H0.17390.654
90_I93_T0.172280.648
11_A110_T0.171790.646
15_N67_A0.171540.646
15_N110_T0.170580.642
40_K136_D0.167740.631
80_Q86_V0.167680.631
55_Q59_P0.167610.631
99_I108_L0.16730.630
75_Y125_T0.164850.620
113_N120_Y0.163090.614
39_G59_P0.162160.610
110_T114_S0.161510.608
67_A101_S0.159960.602
125_T134_N0.159270.599
113_N136_D0.159190.599
15_N43_D0.15780.594
75_Y81_D0.157680.593
109_Q134_N0.155940.587
45_L89_I0.155030.583
17_A69_G0.15390.579
46_I55_Q0.153450.577
63_T74_H0.153310.577
67_A104_T0.152440.574
72_V124_L0.152260.573
81_D114_S0.151040.568
91_P133_I0.150990.568
40_K84_E0.150820.568
40_K60_K0.149690.563
65_L122_I0.14810.557
65_L74_H0.1480.557
20_P140_F0.147210.554
7_L140_F0.1470.553
15_N60_K0.146730.552
13_L87_F0.146190.550
54_V58_N0.144160.542
60_K74_H0.143930.542
112_N123_G0.143820.541
79_D132_E0.143090.538
111_F114_S0.142650.537
56_F65_L0.142420.536
54_V57_V0.14220.535
38_F134_N0.142060.535
135_L140_F0.141190.531
73_F84_E0.141030.531
57_V78_C0.139610.525
58_N61_T0.13920.524
14_T43_D0.138590.522
67_A70_N0.137950.519
15_N63_T0.137560.518
14_T118_I0.137240.516
89_I103_S0.137190.516
22_N73_F0.136570.514
18_L38_F0.135780.511
39_G69_G0.135160.509
58_N62_G0.134590.506
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
3vsfA0.913399.90.125
3pg0A0.873399.90.173
3ef2A0.9499.90.178
3phzA0.913399.90.188
2dryA0.846799.80.231
4g9mA0.853399.80.234
3aj6A0.8699.80.239
1ybiA0.873399.80.261
1vclA0.866799.80.273
2vseA0.893399.80.274

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