GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CPT - Chloramphenicol phosphotransferase-like protein
Pfam: PF07931 (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: 174
Sequences: 13264
Seq/Len: 76.23
HH_delta: 0.214 (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
122_I125_R1.837093.673
24_R170_L1.509333.018
161_S164_E1.485012.969
20_A166_A1.442042.883
117_R154_E1.277852.555
119_P158_S1.215552.430
118_C123_L1.175442.350
20_A23_E1.163432.326
124_E128_R1.059652.119
119_P122_I1.027812.055
112_L153_L0.985511.970
118_C157_T0.983141.966
6_L18_A0.97271.945
24_R166_A0.945121.890
37_F40_M0.924261.848
155_V165_C0.903371.806
17_I169_I0.892191.784
117_R156_D0.862281.724
116_V157_T0.861021.721
17_I165_C0.85811.716
17_I166_A0.846121.692
118_C122_I0.840511.680
20_A24_R0.838521.677
122_I158_S0.823551.647
100_D104_R0.817571.635
168_E171_A0.815371.630
24_R167_R0.806591.613
71_A74_A0.800221.600
167_R171_A0.787361.574
11_S127_E0.787141.574
125_R129_A0.774851.549
75_A78_A0.761031.522
114_V153_L0.750011.500
162_P166_A0.740811.481
73_H77_A0.717511.435
159_A168_E0.716941.433
12_S118_C0.71031.420
64_L68_L0.708181.416
19_R23_E0.676671.353
36_T39_D0.674211.348
74_A78_A0.670571.341
20_A163_E0.667171.334
25_L170_L0.665291.330
64_L67_R0.656641.313
115_G154_E0.651381.302
77_A81_R0.64791.295
142_A146_H0.6421.284
22_Q26_P0.631281.262
166_A170_L0.631231.262
19_R22_Q0.631131.262
120_L124_E0.628951.258
159_A164_E0.627581.255
123_L127_E0.626261.252
71_A75_A0.618971.238
164_E167_R0.617891.235
9_P123_L0.613231.226
165_C168_E0.587021.174
120_L139_A0.579371.158
17_I116_V0.57791.155
23_E166_A0.56811.136
92_F95_P0.559821.119
16_S162_P0.557811.115
34_V38_V0.554341.108
79_M84_N0.55261.105
6_L21_L0.551481.103
139_A143_E0.545291.090
121_E125_R0.544361.088
128_R135_I0.543581.087
91_V94_G0.541521.083
63_P66_R0.531911.063
65_F68_L0.53171.063
157_T165_C0.527671.055
79_M82_A0.526311.052
78_A82_A0.523891.047
75_A79_M0.509011.018
21_L169_I0.505771.011
3_I106_L0.501791.003
20_A170_L0.498680.997
5_I113_F0.495910.992
67_R71_A0.486960.974
18_A22_Q0.48550.971
63_P67_R0.485260.970
103_R150_R0.485020.970
34_V72_M0.48180.963
139_A142_A0.480940.962
134_P137_L0.479520.959
8_G12_S0.479220.958
140_W144_H0.478540.957
49_G52_L0.476110.952
70_A74_A0.473770.947
3_I80_A0.47230.944
17_I20_A0.470380.940
164_E168_E0.47010.940
101_C104_R0.469870.939
36_T40_M0.469860.939
167_R170_L0.466380.932
16_S20_A0.462660.925
95_P150_R0.460290.920
22_Q31_H0.457040.914
67_R70_A0.457040.914
24_R163_E0.455590.911
51_G55_A0.450840.901
7_N151_Y0.446410.893
37_F72_M0.44410.888
20_A162_P0.441880.883
156_D159_A0.439820.879
18_A87_I0.438620.877
4_I114_V0.43750.875
4_I112_L0.437430.875
3_I88_V0.436870.873
85_N88_V0.433050.866
141_Q144_H0.432450.865
39_D42_P0.430390.861
69_Y73_H0.429910.860
148_G151_Y0.42780.855
18_A29_W0.426460.853
9_P12_S0.426450.853
116_V169_I0.422050.844
143_E146_H0.419810.839
141_Q145_V0.417160.834
138_A141_Q0.416230.832
73_H102_L0.415910.832
147_E150_R0.413390.827
12_S123_L0.412650.825
38_V41_M0.409610.819
100_D103_R0.40720.814
50_D53_E0.405710.811
8_G14_K0.405370.810
7_N113_F0.404510.809
21_L25_L0.402560.805
8_G13_G0.399010.798
93_L96_R0.397970.796
146_H149_G0.396450.793
22_Q87_I0.396330.792
162_P165_C0.39470.789
74_A77_A0.393390.787
118_C126_R0.391920.784
144_H148_G0.390270.780
115_G152_D0.386840.773
12_S115_G0.384350.768
52_L55_A0.37790.756
15_S19_R0.371940.744
133_R136_G0.371070.742
121_E124_E0.370610.741
166_A169_I0.369060.738
5_I111_V0.369020.738
18_A31_H0.368890.738
155_V169_I0.368120.736
15_S89_D0.36540.731
66_R69_Y0.363990.728
120_L123_L0.360290.720
5_I93_L0.359110.718
144_H147_E0.358480.717
117_R148_G0.35670.713
116_V165_C0.356540.713
72_M75_A0.355310.710
35_D84_N0.354760.709
65_F69_Y0.352290.704
85_N89_D0.349070.698
5_I88_V0.345110.690
35_D38_V0.345080.690
124_E127_E0.344480.689
163_E166_A0.343770.687
13_G126_R0.341930.684
63_P68_L0.341630.683
35_D39_D0.340110.680
7_N115_G0.337670.675
124_E130_R0.337350.674
70_A101_C0.337110.674
21_L170_L0.335990.672
86_V89_D0.335260.670
8_G15_S0.328320.656
129_A132_D0.328030.656
16_S126_R0.319510.639
10_S123_L0.318130.636
95_P100_D0.3180.636
51_G54_P0.317740.635
48_P52_L0.316760.633
45_R49_G0.316160.632
68_L71_A0.316060.632
78_A81_R0.316040.632
122_I126_R0.31590.632
18_A89_D0.315250.630
69_Y72_M0.3150.630
96_R100_D0.308870.618
46_Y49_G0.308640.617
6_L87_I0.308450.617
151_Y154_E0.30820.616
64_L69_Y0.305050.610
37_F75_A0.303280.606
112_L152_D0.301580.603
118_C165_C0.300420.601
38_V42_P0.299850.600
124_E139_A0.299220.598
115_G151_Y0.296770.593
21_L166_A0.295240.590
19_R31_H0.292350.585
142_A145_V0.292330.584
15_S18_A0.288950.578
141_Q146_H0.286280.572
9_P115_G0.286180.572
99_Q102_L0.285650.571
50_D74_A0.284220.568
133_R137_L0.284130.568
53_E64_L0.283470.567
45_R48_P0.282330.564
126_R157_T0.282170.564
146_H150_R0.281480.563
38_V68_L0.281440.563
125_R128_R0.281310.562
156_D168_E0.279960.560
12_S157_T0.279780.559
143_E147_E0.279250.558
76_I80_A0.27730.554
80_A86_V0.275320.550
34_V37_F0.275130.550
114_V155_V0.274170.548
24_R27_E0.27290.546
68_L72_M0.272630.545
79_M86_V0.2720.544
80_A109_L0.27180.543
41_M44_G0.270930.542
73_H105_L0.270590.541
23_E27_E0.270240.540
137_L142_A0.26840.537
3_I110_P0.26620.532
28_P84_N0.265940.532
70_A73_H0.264690.529
127_E130_R0.264620.529
20_A169_I0.263760.527
10_S130_R0.263140.526
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
1qhxA199.90.214
1x6vB0.913899.70.361
3t61A0.902399.70.371
1m8pA0.919599.70.374
2gksA0.919599.70.379
3uieA0.913899.60.381
4eunA0.919599.60.381
3a4mA0.896699.60.383
2cdnA0.942599.60.392
3lw7A0.93199.60.394

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