GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
APH - Phosphotransferase enzyme family
Pfam: PF01636 (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: CL0016
Length: 239
Sequences: 11169
Seq/Len: 46.73
HH_delta: 0.204 (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
15_R22_R1.164463.604
56_R75_E1.08173.348
169_I198_G1.07153.316
179_L190_I1.046283.238
58_L75_E1.041843.225
15_R76_Y0.981083.037
48_A56_R0.902542.793
24_V76_Y0.800122.476
17_T22_R0.798922.473
25_L73_L0.772442.391
181_D184_D0.764422.366
172_D191_D0.753122.331
13_V24_V0.712362.205
97_Q100_R0.692922.145
173_L189_I0.686982.126
167_V200_P0.664672.057
77_I188_G0.652692.020
172_D177_N0.64481.996
98_L178_I0.641771.986
41_A57_V0.637071.972
101_A189_I0.617961.913
23_Y58_L0.615461.905
18_T23_Y0.600241.858
102_L106_H0.598891.854
102_L173_L0.582281.802
181_D186_R0.57741.787
97_Q186_R0.570861.767
99_G103_A0.545081.687
101_A104_Q0.541421.676
98_L173_L0.538861.668
22_R76_Y0.528471.636
96_R99_G0.511281.582
169_I196_G0.497331.539
198_G203_D0.494781.531
177_N191_D0.4921.523
155_E159_L0.481971.492
97_Q101_A0.472761.463
40_E44_L0.468091.449
38_R42_A0.466331.443
16_V25_L0.461821.429
41_A45_R0.456231.412
16_V23_Y0.441771.367
94_L180_V0.438671.358
45_R49_E0.437681.355
99_G106_H0.431431.335
11_N26_K0.424781.315
103_A107_Q0.419491.298
22_R78_P0.418591.296
92_P96_R0.41391.281
146_E150_E0.413271.279
96_R100_R0.412921.278
150_E154_Q0.411581.274
26_K40_E0.410821.272
34_A38_R0.404031.251
40_E193_E0.398741.234
44_L57_V0.398431.233
154_Q158_A0.389131.204
126_L130_E0.389011.204
154_Q157_E0.388661.203
152_L156_L0.38691.198
46_Q49_E0.386531.196
95_L99_G0.383371.187
23_Y73_L0.378211.171
11_N193_E0.375991.164
39_R42_A0.37471.160
100_R103_A0.373251.155
42_A45_R0.370811.148
91_R94_L0.370761.148
18_T21_G0.369921.145
93_E96_R0.368541.141
50_H108_V0.367351.137
168_L195_A0.36071.116
106_H203_D0.358071.108
98_L207_L0.356331.103
170_H173_L0.354231.096
41_A60_F0.350871.086
43_V192_F0.341241.056
139_S142_F0.336231.041
168_L197_W0.331751.027
178_I189_I0.329571.020
125_F129_L0.328711.017
77_I179_L0.328541.017
14_Y27_F0.327031.012
27_F71_Y0.325051.006
173_L178_I0.324281.004
46_Q50_H0.324041.003
35_E38_R0.322810.999
93_E97_Q0.319960.990
124_E127_R0.319650.989
100_R104_Q0.316510.980
125_F130_E0.315950.978
13_V26_K0.310150.960
147_E150_E0.310060.960
52_I104_Q0.306670.949
171_G194_D0.304470.942
9_F174_H0.303750.940
165_P200_P0.303370.939
38_R60_F0.303050.938
81_P179_L0.302570.936
79_G82_L0.302320.936
170_H203_D0.300580.930
75_E188_G0.30.929
115_F118_W0.30.929
21_G75_E0.295270.914
123_L127_R0.293820.909
171_G198_G0.29320.907
156_L159_L0.29280.906
171_G196_G0.29190.903
125_F128_Q0.290740.900
79_G179_L0.290610.899
127_R131_S0.290380.899
48_A57_V0.284440.880
78_P181_D0.284130.879
181_D188_G0.283750.878
41_A72_L0.283380.877
103_A106_H0.283040.876
45_R48_A0.282210.873
47_L51_G0.279580.865
44_L192_F0.27920.864
192_F196_G0.278260.861
166_P199_D0.27810.861
97_Q187_I0.277070.858
45_R56_R0.276580.856
169_I203_D0.276220.855
112_F115_F0.275320.852
65_E68_G0.274820.851
174_H194_D0.273310.846
166_P197_W0.273270.846
48_A54_V0.272150.842
24_V190_I0.271060.839
10_S193_E0.268430.831
43_V195_A0.267980.829
42_A46_Q0.265560.822
171_G203_D0.265190.821
57_V75_E0.264620.819
25_L71_Y0.264430.818
47_L52_I0.264270.818
23_Y75_E0.263820.817
17_T20_D0.263530.816
27_F69_F0.262120.811
202_Y206_R0.260970.808
94_L97_Q0.260820.807
134_A138_A0.260230.805
135_R139_S0.258920.801
145_L149_E0.258760.801
12_R27_F0.257680.798
44_L54_V0.257290.796
171_G206_R0.256630.794
136_L139_S0.256540.794
55_P75_E0.254760.789
145_L148_L0.254450.788
54_V57_V0.254250.787
156_L160_L0.253570.785
106_H169_I0.253220.784
124_E128_Q0.252690.782
9_F13_V0.252680.782
198_G202_Y0.251370.778
192_F195_A0.24960.773
39_R43_V0.248460.769
104_Q108_V0.247490.766
82_L178_I0.24670.764
102_L203_D0.246360.763
90_Q93_E0.246080.762
15_R24_V0.246070.762
174_H177_N0.244350.756
196_G202_Y0.242870.752
28_Y37_L0.241270.747
164_L199_D0.239580.742
122_R125_F0.239430.741
53_P101_A0.237420.735
11_N28_Y0.237190.734
26_K193_E0.237160.734
23_Y26_K0.236940.733
170_H190_I0.236890.733
51_G104_Q0.236670.733
170_H178_I0.23430.725
109_P167_V0.233940.724
104_Q107_Q0.233330.722
105_L192_F0.233290.722
204_L207_L0.233070.721
192_F199_D0.232740.720
109_P197_W0.232570.720
204_L208_L0.230190.712
193_E198_G0.229270.710
128_Q131_S0.228920.709
155_E158_A0.228750.708
135_R142_F0.228060.706
57_V60_F0.227750.705
179_L188_G0.226610.701
59_A73_L0.226240.700
9_F12_R0.225350.697
24_V179_L0.225070.697
105_L189_I0.225020.696
129_L133_T0.224660.695
11_N88_P0.224650.695
152_L155_E0.223160.691
148_L153_L0.22210.687
201_A204_L0.221870.687
95_L175_P0.220770.683
132_W135_R0.219310.679
12_R29_R0.219280.679
53_P75_E0.219160.678
171_G202_Y0.218510.676
110_P197_W0.21810.675
130_E134_A0.217080.672
44_L74_M0.216980.672
64_D67_N0.216930.671
10_S194_D0.215870.668
99_G204_L0.215230.666
36_R193_E0.214990.665
173_L206_R0.214930.665
31_P34_A0.214190.663
168_L192_F0.213630.661
178_I190_I0.213440.661
113_S117_D0.21320.660
130_E133_T0.212860.659
89_E92_P0.212630.658
99_G207_L0.212420.657
194_D206_R0.211520.655
129_L134_A0.211160.654
189_I192_F0.211110.653
169_I202_Y0.211070.653
16_V73_L0.210640.652
64_D70_P0.210520.652
46_Q111_P0.209520.648
121_W125_F0.208740.646
157_E160_L0.208610.646
83_D176_G0.208320.645
34_A37_L0.206670.640
80_R181_D0.205520.636
148_L152_L0.204990.634
128_Q132_W0.204860.634
137_R141_L0.204380.633
118_W122_R0.203640.630
178_I207_L0.202730.627
99_G208_L0.201830.625
110_P168_L0.201660.624
149_E154_Q0.201560.624
170_H189_I0.200960.622
126_L129_L0.200650.621
26_K72_L0.199850.619
52_I105_L0.199790.618
175_P208_L0.199220.617
126_L132_W0.198460.614
44_L55_P0.198350.614
116_A119_P0.197180.610
79_G188_G0.196690.609
112_F116_A0.194180.601
153_L157_E0.194010.600
101_A106_H0.193250.598
90_Q94_L0.193150.598
88_P92_P0.192680.596
125_F134_A0.191850.594
141_L145_L0.191180.592
166_P198_G0.191070.591
116_A126_L0.191050.591
40_E74_M0.190580.590
94_L185_G0.190330.589
59_A64_D0.190230.589
123_L128_Q0.189670.587
46_Q168_L0.18960.587
176_G206_R0.189510.587
114_P117_D0.189310.586
122_R128_Q0.188560.584
98_L189_I0.188530.584
152_L160_L0.188480.583
47_L50_H0.188350.583
124_E130_E0.187390.580
74_M79_G0.187160.579
89_E93_E0.18630.577
11_N14_Y0.186110.576
9_F206_R0.185860.575
46_Q112_F0.185780.575
76_Y79_G0.185120.573
113_S116_A0.183770.569
34_A70_P0.183510.568
55_P188_G0.182610.565
143_D147_E0.182370.564
152_L157_E0.182240.564
118_W121_W0.18220.564
68_G71_Y0.18220.564
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
3dxpA0.991699.90.204
3atsA0.983399.90.224
4gkhA0.966599.90.225
1nd4A0.95499.90.23
2ppqA0.95499.90.244
3ovcA0.95499.90.245
3tm0A0.970799.90.245
3sg8A0.974999.90.248
3i1aA0.962399.90.255
3r70A0.949899.90.257

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