GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_gyraseB - DNA gyrase B
Pfam: PF00204 (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: 173
Sequences: 2991
Seq/Len: 17.29
HH_delta: 0.011 (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
78_D82_K0.699163.020
51_S65_V0.590632.551
128_R132_E0.584372.524
26_E34_E0.5312.294
22_Y36_E0.501372.166
76_I143_L0.496772.146
51_S58_T0.493072.130
59_P120_E0.473172.044
25_G134_A0.470112.031
60_E120_E0.465872.012
37_V105_V0.464342.006
3_K7_K0.461651.994
27_D30_N0.455121.966
81_K91_K0.444671.921
4_D7_K0.442261.910
33_W130_I0.436821.887
14_E43_S0.427461.847
80_A86_L0.424121.832
10_N40_Q0.417241.802
94_P98_R0.411081.776
75_A136_S0.409831.770
146_N149_I0.402211.737
92_I157_A0.401411.734
33_W127_V0.398261.720
109_I127_V0.386871.671
19_E149_I0.377381.630
3_K22_Y0.374511.618
66_D70_D0.370471.600
138_K141_K0.367351.587
53_V109_I0.36161.562
68_F105_V0.352161.521
152_A155_E0.349451.510
39_F101_L0.340521.471
79_Y150_A0.339671.467
139_L143_L0.336811.455
49_I103_A0.333851.442
115_E120_E0.333061.439
166_A170_A0.329421.423
53_V58_T0.32771.416
76_I97_I0.323451.397
73_T94_P0.319991.382
10_N102_T0.319111.378
127_V130_I0.318681.377
68_F103_A0.316771.368
70_D132_E0.314581.359
107_V127_V0.308351.332
80_A154_I0.307941.330
56_I112_P0.29931.293
135_V139_L0.29151.259
163_A167_A0.291281.258
2_F22_Y0.287961.244
78_D136_S0.28611.236
136_S140_E0.283931.227
3_K19_E0.28361.225
7_K19_E0.280641.212
60_E116_G0.280441.211
129_S133_K0.279821.209
24_E36_E0.279161.206
113_Q123_T0.279051.205
20_P38_A0.278411.203
115_E123_T0.277031.197
88_K91_K0.273481.181
143_L150_A0.27311.180
78_D81_K0.269221.163
58_T123_T0.267771.157
142_W146_N0.266331.150
66_D128_R0.2661.149
141_K145_K0.265771.148
53_V114_F0.265571.147
116_G123_T0.264931.144
41_W97_I0.264611.143
23_F37_V0.263871.140
137_E141_K0.263011.136
96_D164_R0.261181.128
116_G120_E0.25891.118
24_E34_E0.257061.110
52_F88_K0.256791.109
35_V130_I0.254931.101
33_W109_I0.25481.101
58_T116_G0.253981.097
159_Q162_K0.252911.093
67_G131_V0.252451.091
80_A92_I0.248861.075
53_V107_V0.248711.074
35_V134_A0.248441.073
163_A170_A0.247191.068
99_E160_A0.243911.054
120_E124_N0.242321.047
17_H41_W0.24131.042
45_Y156_K0.240931.041
124_N129_S0.240741.040
167_A170_A0.24021.038
57_P65_V0.235671.018
8_L11_K0.232191.003
15_P40_Q0.230650.996
21_I39_F0.230510.996
77_N81_K0.226330.978
17_H149_I0.223890.967
60_E121_K0.223530.966
70_D128_R0.221050.955
149_I152_A0.218680.945
155_E159_Q0.21860.944
148_E152_A0.216330.934
74_K132_E0.215630.931
142_W149_I0.21430.926
124_N127_V0.212710.919
18_P149_I0.210680.910
113_Q125_P0.209980.907
46_D50_V0.209070.903
115_E124_N0.208630.901
49_I69_K0.208530.901
58_T113_Q0.20840.900
15_P18_P0.208360.900
37_V68_F0.208330.900
26_E31_D0.207580.897
41_W145_K0.20430.883
26_E30_N0.204280.882
140_E144_E0.203490.879
66_D132_E0.203190.878
19_E146_N0.203110.877
53_V123_T0.202090.873
97_I157_A0.200080.864
83_K151_K0.19970.863
161_A164_R0.198820.859
34_E108_K0.198580.858
23_F135_V0.197290.852
163_A166_A0.197270.852
23_F138_K0.197150.852
78_D140_E0.196510.849
60_E115_E0.194950.842
150_A154_I0.193650.837
68_F135_V0.19070.824
75_A139_L0.190370.822
107_V131_V0.190130.821
81_K90_D0.190110.821
111_N124_N0.189570.819
78_D133_K0.189440.818
16_L24_E0.189120.817
97_I161_A0.188960.816
114_F119_K0.188350.814
147_P150_A0.187890.812
74_K78_D0.187470.810
37_V101_L0.186070.804
85_K154_I0.184440.797
58_T115_E0.183660.793
86_L90_D0.182620.789
84_N87_K0.182210.787
158_L161_A0.180660.780
63_T125_P0.180570.780
85_K157_A0.176860.764
41_W120_E0.176140.761
71_A135_V0.175830.760
27_D31_D0.173970.752
27_D133_K0.173860.751
100_G156_K0.173520.750
11_K151_K0.173080.748
113_Q116_G0.173050.748
165_E169_K0.172780.746
84_N88_K0.171430.741
165_E168_K0.169860.734
4_D65_V0.169830.734
134_A137_E0.169120.731
65_V75_A0.168910.730
113_Q124_N0.168420.728
115_E121_K0.168230.727
151_K155_E0.167970.726
15_P20_P0.167910.725
31_D110_P0.167860.725
50_V57_P0.167720.725
81_K86_L0.167350.723
51_S116_G0.166620.720
41_W57_P0.166090.717
10_N42_T0.165980.717
74_K136_S0.165680.716
8_L12_D0.165040.713
87_K90_D0.164290.710
81_K88_K0.163110.705
2_F86_L0.16310.705
22_Y105_V0.162090.700
51_S113_Q0.160750.694
84_N154_I0.160580.694
86_L91_K0.159430.689
23_F134_A0.159040.687
58_T64_H0.158780.686
134_A138_K0.158010.683
132_E136_S0.157010.678
17_H168_K0.15680.677
86_L89_K0.155040.670
12_D15_P0.154530.668
83_K154_I0.154510.667
49_I89_K0.154250.666
10_N13_K0.154210.666
53_V116_G0.152740.660
54_N119_K0.151710.655
66_D125_P0.151660.655
52_F77_N0.151220.653
75_A140_E0.151170.653
73_T77_N0.151110.653
14_E18_P0.150710.651
47_E98_R0.150710.651
95_E112_P0.150580.650
4_D8_L0.149810.647
142_W162_K0.149350.645
67_G71_A0.149250.645
33_W110_P0.148980.644
100_G103_A0.148510.642
5_Y66_D0.14810.640
17_H20_P0.147930.639
51_S123_T0.147640.638
4_D97_I0.147520.637
148_E151_K0.147380.637
156_K160_A0.14730.636
31_D138_K0.14620.632
94_P100_G0.146020.631
45_Y159_Q0.14580.630
162_K169_K0.144790.625
6_V104_V0.144530.624
20_P23_F0.144340.624
3_K20_P0.144190.623
145_K160_A0.144080.622
85_K155_E0.142820.617
17_H40_Q0.142670.616
54_N62_G0.142450.615
47_E69_K0.142140.614
7_K20_P0.141650.612
71_A75_A0.141440.611
17_H21_I0.14130.610
107_V147_P0.141290.610
101_L153_I0.140920.609
9_L102_T0.140890.609
11_K165_E0.140610.607
10_N17_H0.140590.607
52_F57_P0.140550.607
92_I154_I0.140250.606
163_A168_K0.139660.603
80_A84_N0.139630.603
56_I80_A0.139390.602
141_K144_E0.139370.602
109_I115_E0.139010.600
27_D130_I0.1390.600
67_G113_Q0.138490.598
27_D42_T0.138440.598
5_Y165_E0.138360.598
99_E156_K0.13830.597
49_I101_L0.137920.596
154_I157_A0.137890.596
22_Y37_V0.137870.596
58_T122_L0.137550.594
109_I130_I0.137530.594
110_P130_I0.137330.593
72_I101_L0.13720.593
59_P104_V0.136950.592
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
3lnuA0.97111000.011
1ei1A0.98271000.022
1s16A0.98271000.043
1kijA0.98271000.044
4hy1A0.98271000.135
1zxmA0.93641000.139
1pvgA0.8961000.18
3cwvA0.92491000.184
4gfhA0.9481000.25
2q2eB0.81599.50.657

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