GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bac_DnaA - Bacterial dnaA protein
Pfam: PF00308 (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: 219
Sequences: 32792
Seq/Len: 149.74
HH_delta: 0.082 (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
167_D170_D1.96913.165
187_P190_V1.787662.874
168_D196_R1.568612.521
102_I136_T1.489722.395
172_R192_E1.439122.313
176_Q191_I1.40422.257
139_R144_L1.314182.112
198_F208_A1.304182.096
42_P169_E1.220151.961
53_A57_E1.16171.867
168_D192_E1.139941.832
192_E196_R1.072521.724
50_L163_L1.066621.715
193_Y197_R1.055221.696
140_P143_E1.048281.685
40_Y162_E1.027861.652
191_I195_A1.023171.645
178_K206_E0.997061.603
172_R195_A0.985481.584
53_A56_N0.975741.568
176_Q188_E0.974841.567
172_R176_Q0.966681.554
168_D172_R0.957261.539
77_R112_K0.940991.513
132_Q136_T0.923991.485
48_T121_H0.919891.479
186_L191_I0.913141.468
177_K181_E0.894461.438
48_T104_D0.883431.420
51_L102_I0.874891.406
188_E191_I0.871881.402
177_K206_E0.869691.398
193_Y196_R0.862911.387
172_R191_I0.862161.386
186_L190_V0.861711.385
39_L163_L0.856271.376
190_V194_L0.853951.373
174_I177_K0.840191.351
87_E91_F0.838181.347
50_L165_P0.822991.323
109_L113_Q0.816571.313
108_F139_R0.816371.312
188_E192_E0.8151.310
135_L155_L0.814421.309
131_K135_L0.80951.301
206_E210_N0.801021.288
51_L136_T0.793671.276
192_E195_A0.780321.254
124_N206_E0.776761.249
107_Q137_S0.770011.238
176_Q180_K0.766191.232
73_E117_E0.747011.201
81_D84_R0.746921.201
86_G89_E0.744521.197
117_E120_F0.743421.195
190_V193_Y0.738821.188
121_H124_N0.734321.180
52_Q69_Y0.733951.180
121_H125_R0.732521.177
88_I91_F0.730671.175
87_E90_E0.717111.153
120_F124_N0.716011.151
40_Y164_Q0.712211.145
173_R176_Q0.710891.143
40_Y160_V0.708631.139
110_A113_Q0.703791.131
90_E94_R0.698651.123
175_L205_L0.690441.110
174_I179_A0.687141.105
172_R188_E0.682591.097
71_S74_E0.679841.093
49_H53_A0.67161.080
42_P45_L0.669711.077
40_Y142_S0.669661.076
118_E121_H0.669461.076
79_F83_L0.662861.066
39_L51_L0.661391.063
93_D96_R0.659941.061
107_Q138_D0.659441.060
98_A130_G0.658511.059
75_F78_E0.653571.051
105_D154_R0.653231.050
179_A185_E0.65191.048
69_Y72_A0.650341.045
177_K180_K0.650211.045
79_F82_A0.647621.041
82_A85_D0.645721.038
173_R177_K0.640671.030
171_R195_A0.640211.029
178_K182_R0.639811.028
90_E93_D0.639061.027
168_D195_A0.639011.027
80_A83_L0.635641.022
80_A84_R0.635621.022
175_L209_L0.635531.022
175_L179_A0.62671.007
174_I202_V0.619360.996
171_R205_L0.618930.995
174_I178_K0.618510.994
51_L134_I0.613830.987
65_K68_V0.611220.983
65_K72_A0.608340.978
120_F125_R0.602560.969
166_P171_R0.601220.966
81_D85_D0.598680.962
45_L165_P0.598590.962
169_E172_R0.596120.958
201_D204_E0.594710.956
186_L209_L0.594540.956
166_P174_I0.591890.951
119_L124_N0.589530.948
68_V71_S0.583270.938
170_D173_R0.579610.932
166_P170_D0.57690.927
179_A182_R0.57660.927
124_N127_I0.568660.914
52_Q56_N0.567510.912
197_R204_E0.564360.907
97_S130_G0.562960.905
171_R202_V0.560410.901
153_S203_R0.55940.899
189_E192_E0.556530.895
179_A184_I0.546390.878
106_I135_L0.544050.875
64_G68_V0.537910.865
74_E78_E0.53370.858
168_D171_R0.533460.858
72_A103_I0.533460.858
51_L55_A0.533420.857
41_G45_L0.532110.855
156_S211_R0.531680.855
86_G91_F0.528490.850
175_L178_K0.525930.845
116_Q120_F0.524880.844
72_A75_F0.524550.843
174_I206_E0.521120.838
81_D118_E0.517330.832
42_P201_D0.517220.831
84_R87_E0.516390.830
151_L155_L0.516120.830
141_P144_L0.515030.828
64_G67_V0.514780.827
108_F138_D0.514120.826
107_Q139_R0.511180.822
97_S129_S0.509570.819
67_V72_A0.508580.818
66_R69_Y0.507440.816
96_R99_D0.507390.816
150_D153_S0.506870.815
164_Q167_D0.505980.813
189_E193_Y0.505750.813
76_I80_A0.500070.804
55_A58_A0.495660.797
38_F135_L0.493530.793
178_K209_L0.492470.792
181_E210_N0.491020.789
116_Q119_L0.489050.786
163_L166_P0.486920.783
83_L86_G0.48590.781
118_E122_L0.484250.778
55_A67_V0.483670.777
54_I58_A0.479940.771
68_V73_E0.479440.771
47_K104_D0.476160.765
173_R195_A0.474610.763
113_Q118_E0.474220.762
43_S153_S0.474120.762
136_T139_R0.471890.759
202_V205_L0.471040.757
76_I84_R0.469230.754
109_L119_L0.469150.754
79_F84_R0.468780.754
69_Y73_E0.466950.751
132_Q135_L0.466680.750
104_D136_T0.465290.748
143_E146_G0.465230.748
100_L134_I0.464650.747
37_L54_I0.463710.745
106_I109_L0.463450.745
78_E82_A0.462450.743
166_P202_V0.460550.740
83_L88_I0.457510.735
94_R97_S0.456350.734
71_S76_I0.455680.732
44_G203_R0.455480.732
84_R88_I0.455420.732
126_L130_G0.452510.727
117_E121_H0.45080.725
49_H52_Q0.450170.724
73_E76_I0.449860.723
92_K95_L0.44960.723
83_L87_E0.446560.718
107_Q141_P0.446280.717
141_P147_L0.446080.717
87_E92_K0.445830.717
41_G44_G0.440330.708
120_F123_F0.439270.706
78_E81_D0.43830.705
38_F137_S0.433040.696
77_R82_A0.432420.695
38_F155_L0.431460.694
167_D171_R0.428850.689
74_E77_R0.428770.689
126_L129_S0.428250.688
150_D154_R0.427610.687
135_L138_D0.426290.685
176_Q179_A0.425430.684
116_Q124_N0.425390.684
85_D89_E0.424720.683
169_E173_R0.424570.682
67_V73_E0.423850.681
153_S156_S0.423350.681
93_D122_L0.422670.679
41_G47_K0.421790.678
91_F95_L0.421150.677
36_P135_L0.420510.676
100_L132_Q0.420420.676
55_A102_I0.419770.675
145_S152_R0.416880.670
87_E95_L0.415320.668
117_E125_R0.414650.667
88_I95_L0.41340.665
67_V102_I0.413060.664
125_R128_E0.411810.662
164_Q170_D0.41120.661
105_D138_D0.410930.661
123_F133_L0.410430.660
91_F94_R0.408310.656
87_E94_R0.407870.656
89_E93_D0.406260.653
68_V75_F0.405790.652
70_L75_F0.404190.650
180_K183_G0.403190.648
116_Q121_H0.402990.648
204_E208_A0.402150.646
181_E206_E0.401910.646
124_N128_E0.401160.645
207_G211_R0.400020.643
165_P171_R0.3990.641
76_I79_F0.397160.638
121_H127_I0.396440.637
51_L67_V0.394510.634
141_P145_S0.394110.634
80_A85_D0.394080.633
67_V70_L0.393580.633
179_A209_L0.392930.632
39_L161_V0.392120.630
198_F205_L0.391910.630
156_S162_E0.39070.628
48_T69_Y0.390420.628
142_S145_S0.389890.627
36_P126_L0.389260.626
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
2z4sA0.995499.90.082
1l8qA0.981799.90.129
3bosA0.940699.90.216
3uk6A0.954399.90.268
3pfiA0.890499.80.278
3pvsA0.899599.80.283
1hqcA0.89599.80.292
3sylA0.963599.80.302
2v1uA0.96899.80.302
2bjvA0.949899.80.307

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