GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bac_transf - Bacterial sugar transferase
Pfam: PF02397 (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: 187
Sequences: 3784
Seq/Len: 20.24
HH_delta: 0.956 (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
2_R6_I1.351473.630
23_I88_L1.154093.100
41_E49_P1.153063.097
160_Y164_N1.099022.952
39_R51_R1.094892.941
30_E78_P1.049792.819
26_L79_V1.03482.779
41_E51_R1.021182.743
97_V136_I0.963482.588
57_T83_L0.926862.489
82_F86_T0.894612.403
13_L95_W0.794122.133
139_L143_N0.79162.126
153_E156_E0.778022.090
105_V137_T0.747232.007
4_F8_L0.735051.974
172_K176_K0.732091.966
10_L98_L0.705111.894
24_A36_V0.681391.830
44_G134_P0.677391.819
28_K34_G0.671181.803
23_I83_L0.65031.747
139_L160_Y0.646231.736
39_R53_Y0.640311.720
53_Y96_N0.634211.703
9_A13_L0.627611.686
28_K36_V0.626311.682
5_D103_S0.625131.679
22_I26_L0.60711.631
23_I55_F0.602351.618
37_F53_Y0.600381.612
176_K180_A0.599741.611
132_V162_I0.583461.567
61_N65_D0.57941.556
49_P112_P0.56561.519
110_E114_E0.558471.500
105_V174_I0.557191.496
35_P60_V0.543621.460
20_F55_F0.539361.449
95_W99_K0.537941.445
8_L104_L0.535841.439
16_L20_F0.523211.405
59_R65_D0.511641.374
79_V83_L0.510881.372
179_R183_K0.504411.355
9_A98_L0.502721.350
27_I30_E0.501811.348
1_K5_D0.495891.332
43_V49_P0.493691.326
160_Y169_L0.493151.324
1_K170_D0.489881.316
6_I10_L0.489711.315
138_G141_Q0.487171.308
14_I17_S0.481551.293
12_L16_L0.479031.287
104_L174_I0.477471.282
27_I31_S0.457841.230
12_L104_L0.454811.221
25_I29_L0.447511.202
167_L171_L0.4451.195
139_L173_I0.441791.187
138_G154_K0.440241.182
114_E118_Y0.434541.167
87_S145_R0.433811.165
6_I9_A0.42821.150
112_P116_E0.426311.145
12_L94_L0.422711.135
13_L17_S0.421591.132
143_N176_K0.420271.129
94_L104_L0.42021.129
45_K133_K0.41981.127
43_V115_V0.415231.115
161_Y170_D0.414561.113
146_S150_D0.411451.105
174_I178_I0.410391.102
139_L169_L0.408381.097
83_L86_T0.406531.092
1_K165_W0.398971.072
144_G148_L0.397171.067
127_R163_E0.395161.061
111_V114_E0.395041.061
145_R148_L0.394351.059
10_L14_I0.393441.057
40_Q52_I0.392891.055
72_N81_R0.390551.049
38_F63_D0.387481.041
8_L12_L0.38741.040
91_L94_L0.384381.032
110_E115_V0.381731.025
140_A154_K0.378451.016
6_I98_L0.376061.010
28_K31_S0.375851.009
35_P56_R0.375091.007
47_G130_L0.374651.006
2_R9_A0.374461.006
110_E154_K0.37321.002
127_R131_S0.372961.002
111_V118_Y0.370460.995
175_L179_R0.367620.987
181_V185_G0.365780.982
27_I36_V0.365360.981
18_P21_L0.361560.971
53_Y99_K0.36130.970
96_N101_D0.359120.965
110_E151_F0.358350.962
139_L157_L0.355420.955
1_K103_S0.352310.946
137_T177_T0.352140.946
53_Y95_W0.349180.938
141_Q158_D0.348640.936
36_V55_F0.346360.930
31_S34_G0.345980.929
59_R62_A0.345630.928
23_I26_L0.344330.925
150_D153_E0.340770.915
110_E118_Y0.339150.911
125_Y130_L0.335780.902
76_I81_R0.333680.896
87_S154_K0.333680.896
17_S20_F0.331650.891
78_P81_R0.33040.887
145_R151_F0.329480.885
113_E118_Y0.328310.882
30_E79_V0.328130.881
83_L88_L0.32290.867
20_F91_L0.319460.858
24_A27_I0.316510.850
61_N64_D0.316170.849
59_R74_P0.315030.846
17_S21_L0.314830.846
138_G155_L0.312110.838
151_F154_K0.311740.837
18_P22_I0.308090.827
38_F111_V0.307650.826
119_S125_Y0.307630.826
118_Y151_F0.307550.826
4_F167_L0.302780.813
26_L30_E0.301890.811
115_V118_Y0.301820.811
50_F102_M0.297670.799
30_E77_T0.295410.793
87_S181_V0.295250.793
19_L23_I0.294590.791
95_W101_D0.29260.786
14_I18_P0.290570.780
143_N157_L0.287520.772
97_V104_L0.284730.765
46_N131_S0.284730.765
179_R184_K0.284040.763
30_E33_P0.279910.752
164_N169_L0.278630.748
166_S169_L0.278390.748
168_W172_K0.277680.746
124_E156_E0.277520.745
13_L98_L0.277490.745
4_F104_L0.276130.742
16_L19_L0.27410.736
43_V112_P0.272350.731
8_L11_L0.27050.726
115_V130_L0.270090.725
114_E117_L0.26940.724
3_A6_I0.266480.716
69_T140_A0.266230.715
2_R5_D0.266060.715
152_E156_E0.266010.714
128_R159_L0.26510.712
72_N75_R0.264680.711
94_L136_I0.264650.711
144_G150_D0.264140.709
85_K93_Q0.263160.707
20_F23_I0.262820.706
110_E155_L0.260030.698
7_V11_L0.25910.696
16_L94_L0.257150.691
171_L175_L0.256690.689
43_V130_L0.255820.687
24_A28_K0.254980.685
21_L25_I0.254460.683
147_E150_D0.252780.679
179_R182_L0.251530.676
142_V176_K0.250220.672
138_G158_D0.250040.672
43_V111_V0.249710.671
169_L172_K0.249560.670
18_P94_L0.248570.668
16_L23_I0.248420.667
139_L164_N0.248290.667
20_F37_F0.247520.665
114_E140_A0.247440.665
165_W169_L0.246830.663
111_V151_F0.246510.662
52_I93_Q0.246010.661
119_S126_R0.245970.661
21_L24_A0.245770.660
39_R52_I0.245730.660
155_L159_L0.245670.660
20_F95_W0.24470.657
13_L20_F0.24370.655
125_Y128_R0.243010.653
30_E83_L0.242570.651
74_P140_A0.242160.650
61_N74_P0.241760.649
54_K90_E0.240060.645
66_G70_L0.239310.643
27_I83_L0.238830.641
12_L174_I0.238640.641
26_L29_L0.238580.641
95_W98_L0.237880.639
67_K70_L0.237250.637
142_V180_A0.235280.632
128_R158_D0.235170.632
140_A143_N0.234040.629
4_F171_L0.233830.628
9_A104_L0.231340.621
178_I181_V0.231180.621
6_I13_L0.230840.620
27_I56_R0.230210.618
159_L162_I0.22880.614
9_A14_I0.228470.614
9_A16_L0.228250.613
65_D68_Q0.228140.613
176_K179_R0.227770.612
34_G60_V0.225170.605
28_K35_P0.225090.605
9_A17_S0.224390.603
11_L14_I0.223520.600
79_V82_F0.222530.598
180_A184_K0.222210.597
147_E185_G0.220150.591
148_L154_K0.218440.587
78_P82_F0.217470.584
110_E140_A0.216630.582
131_S163_E0.216110.580
126_R130_L0.216090.580
16_L55_F0.216020.580
66_G113_E0.215220.578
87_S144_G0.214620.576
144_G147_E0.214470.576
110_E128_R0.213970.575
178_I182_L0.211760.569
19_L22_I0.210970.567
54_K58_M0.210690.566
112_P115_V0.21020.565
105_V165_W0.209240.562
22_I25_I0.208520.560
31_S79_V0.20820.559
90_E93_Q0.207470.557
107_P132_V0.207230.557
68_Q118_Y0.206570.555
173_I177_T0.205250.551
33_P60_V0.203810.547
8_L94_L0.20340.546
47_G126_R0.202490.544
2_R133_K0.202430.544
168_W175_L0.202230.543
111_V115_V0.202190.543
27_I79_V0.201960.542
139_L176_K0.200730.539
29_L33_P0.200490.538
43_V114_E0.200370.538
124_E128_R0.200150.538
128_R163_E0.199740.536
58_M75_R0.199490.536
40_Q110_E0.198930.534
114_E151_F0.198060.532
84_R90_E0.196880.529
27_I35_P0.196650.528
41_E112_P0.194730.523
59_R76_I0.194370.522
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
3cwbI0.278138.40.956
3floA0.588214.50.964
2clyA0.406413.30.964
2bzwB0.14446.50.969
4hytG0.27276.20.969
2k44A0.14444.60.971
1hywA0.30484.60.971
3c1xA0.44924.30.971
4iabA0.33164.10.971
2jp3A0.22463.80.972
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