GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
2-oxoacid_dh - 2-oxoacid dehydrogenases acyltransferase (catalytic domain)
Pfam: PF00198 (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: CL0149
Length: 231
Sequences: 3465
Seq/Len: 15
HH_delta: -0.03 (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
129_D133_R1.006743.481
75_E218_D0.929913.216
118_K126_E0.866642.997
132_E136_E0.817552.827
181_D188_G0.803732.779
185_V190_V0.785022.715
15_A18_K0.783162.708
35_E182_R0.779212.694
126_E129_D0.757832.621
185_V192_V0.723242.501
82_S92_Y0.719422.488
76_H218_D0.709652.454
133_R143_D0.684372.367
5_T93_E0.674372.332
37_D193_R0.659492.280
66_I97_I0.656072.269
69_V149_F0.622632.153
181_D194_P0.62012.144
94_R114_D0.602792.084
36_V198_L0.566551.959
118_K122_E0.555071.919
74_K116_D0.553281.913
29_H201_T0.523631.811
183_P190_V0.514551.779
73_L149_F0.509831.763
70_A95_V0.508311.758
98_G109_V0.507791.756
70_A115_A0.501091.733
7_V91_L0.490221.695
147_G170_Q0.474881.642
42_L61_I0.474121.639
9_L83_W0.465221.609
134_A139_L0.461731.597
69_V219_L0.460291.592
12_M16_I0.456031.577
96_N113_R0.454811.573
218_D221_E0.45391.570
67_K71_L0.441831.528
81_A91_L0.439521.520
164_P175_G0.438181.515
22_E26_T0.436221.508
71_L222_L0.433041.497
15_A19_R0.431011.490
127_L131_A0.428431.481
105_D137_G0.427911.480
65_L176_V0.426111.473
50_E53_E0.423781.465
13_R208_D0.421931.459
66_I127_L0.419651.451
204_H209_G0.412741.427
39_T193_R0.412561.427
78_E211_E0.408841.414
24_L29_H0.405121.401
13_R16_I0.404341.398
119_S122_E0.40331.395
66_I99_V0.401721.389
66_I115_A0.397631.375
21_T25_Q0.396521.371
19_R22_E0.395111.366
6_R90_V0.393521.361
47_E227_E0.392931.359
72_A219_L0.392221.356
220_K224_E0.391521.354
38_V196_M0.391141.353
66_I123_I0.389721.348
198_L219_L0.389431.347
66_I151_I0.388891.345
114_D117_K0.387991.342
41_L64_F0.385711.334
76_H214_R0.383331.326
181_D192_V0.382761.324
78_E91_L0.381531.319
89_I206_V0.379251.311
186_E191_V0.378471.309
27_I166_I0.378291.308
35_E160_E0.377811.306
217_K221_E0.376151.301
49_K58_K0.373371.291
81_A206_V0.36661.268
149_F172_A0.366091.266
38_V41_L0.365531.264
40_A43_A0.363511.257
34_R220_K0.358111.238
33_S161_S0.351031.214
98_G170_Q0.350111.211
32_L202_F0.348321.204
210_A214_R0.34791.203
112_I126_E0.346541.198
218_D222_L0.346051.197
39_T194_P0.345451.195
53_E58_K0.339911.175
94_R116_D0.338721.171
84_D87_G0.338351.170
18_K22_E0.334891.158
6_R87_G0.334741.158
95_V116_D0.332021.148
39_T43_A0.32651.129
149_F174_L0.326021.127
43_A47_E0.324631.123
38_V179_I0.323941.120
131_A135_R0.321411.111
31_T201_T0.316681.095
30_F202_F0.316381.094
183_P192_V0.316231.094
174_L219_L0.309411.070
160_E197_N0.308771.068
186_E189_E0.305351.056
154_L162_F0.304851.054
79_L207_I0.303311.049
96_N111_V0.302811.047
102_D157_F0.302131.045
71_L74_K0.301311.042
99_V127_L0.301261.042
129_D132_E0.300841.040
226_P229_L0.300171.038
176_V196_M0.299051.034
80_N148_T0.298031.031
167_N170_Q0.295711.023
179_I194_P0.295521.022
36_V220_K0.292761.012
6_R84_D0.290231.004
32_L212_A0.287670.995
31_T163_T0.286430.990
63_D123_I0.286040.989
43_A46_K0.283060.979
111_V147_G0.282960.978
37_D186_E0.280530.970
171_V206_V0.279310.966
71_L75_E0.27520.952
114_D118_K0.274610.950
96_N114_D0.274430.949
69_V215_F0.274090.948
66_I112_I0.272640.943
74_K95_V0.27250.942
202_F212_A0.272070.941
11_G14_K0.271860.940
75_E222_L0.268030.927
200_L216_L0.266890.923
200_L212_A0.266590.922
44_L64_F0.264960.916
102_D214_R0.263090.910
84_D90_V0.262020.906
34_R159_V0.261970.906
183_P193_R0.261270.903
65_L223_L0.260460.901
32_L159_V0.260230.900
63_D120_L0.259790.898
46_K49_K0.259350.897
71_L229_L0.258850.895
182_R195_V0.258770.895
186_E193_R0.258540.894
121_A125_K0.258520.894
184_V193_R0.254310.879
42_L194_P0.253990.878
184_V195_V0.253180.875
5_T91_L0.25270.874
83_W206_V0.250440.866
102_D210_A0.249980.864
69_V174_L0.249010.861
46_K50_E0.248320.859
108_V139_L0.247730.857
79_L172_A0.24760.856
35_E180_R0.245990.851
113_R142_E0.245570.849
160_E178_A0.243640.843
133_R140_T0.243150.841
118_K129_D0.24140.835
160_E180_R0.240290.831
101_V135_R0.239760.829
17_A83_W0.236140.817
23_S168_P0.23590.816
27_I168_P0.234030.809
149_F215_F0.233470.807
12_M103_T0.233240.807
150_T170_Q0.231280.800
24_L27_I0.231040.799
53_E56_G0.230950.799
31_T199_S0.230330.796
21_T27_I0.23020.796
8_P87_G0.229670.794
69_V172_A0.228310.789
24_L28_P0.227840.788
140_T143_D0.227030.785
174_L200_L0.225850.781
217_K220_K0.222960.771
51_A228_R0.220940.764
98_G147_G0.217950.754
221_E228_R0.217890.753
139_L144_L0.216210.748
112_I127_L0.214760.743
96_N143_D0.214660.742
122_E125_K0.213370.738
62_T156_M0.212950.736
32_L216_L0.212280.734
79_L211_E0.211550.732
108_V144_L0.21060.728
14_K86_D0.209310.724
181_D187_D0.208660.722
176_V198_L0.208580.721
9_L89_I0.206470.714
79_L215_F0.205110.709
24_L201_T0.204410.707
67_K123_I0.204080.706
16_I20_M0.203920.705
49_K53_E0.202160.699
14_K18_K0.201330.696
185_V193_R0.198280.686
35_E195_V0.196960.681
125_K128_R0.196790.680
19_R168_P0.195860.677
20_M109_V0.195860.677
32_L177_G0.195680.677
29_H166_I0.195070.675
215_F219_L0.193580.669
161_S197_N0.193510.669
97_I123_I0.193160.668
32_L154_L0.19310.668
21_T24_L0.192880.667
78_E214_R0.192870.667
47_E225_N0.192570.666
141_P145_Q0.192460.666
36_V223_L0.192280.665
126_E133_R0.191690.663
33_S163_T0.191680.663
24_L31_T0.191480.662
65_L151_I0.190060.657
166_I172_A0.189890.657
7_V10_S0.189860.657
38_V194_P0.189780.656
133_R138_K0.189740.656
112_I118_K0.189440.655
6_R93_E0.188680.652
172_A200_L0.188460.652
79_L171_V0.188030.650
122_E126_E0.18790.650
133_R139_L0.18740.648
113_R126_E0.187270.648
37_D40_A0.186920.646
111_V146_G0.186670.646
127_L130_L0.186080.643
177_G213_A0.1860.643
34_R216_L0.185940.643
12_M105_D0.185880.643
128_R132_E0.185730.642
181_D185_V0.184980.640
40_A227_E0.184850.639
198_L216_L0.184310.637
33_S197_N0.18350.635
111_V150_T0.182540.631
100_A107_L0.181820.629
23_S29_H0.181310.627
117_K122_E0.180720.625
62_T65_L0.179510.621
48_L59_I0.178950.619
76_H211_E0.178720.618
61_I179_I0.17810.616
62_T99_V0.175990.609
37_D184_V0.17550.607
115_A122_E0.175130.606
40_A193_R0.175020.605
149_F200_L0.174550.604
73_L79_L0.174430.603
97_I149_F0.173460.600
154_L159_V0.172940.598
140_T145_Q0.171840.594
42_L46_K0.171280.592
181_D189_E0.171060.592
67_K70_A0.170940.591
60_S124_A0.170930.591
42_L179_I0.170880.591
154_L175_G0.170270.589
96_N147_G0.170230.589
68_A223_L0.169150.585
23_S166_I0.168540.583
111_V144_L0.168230.582
63_D127_L0.168220.582
109_V170_Q0.168050.581
204_H208_D0.167980.581
59_I63_D0.16780.580
41_L45_R0.167030.578
39_T181_D0.166330.575
219_L223_L0.166160.575
202_F207_I0.165870.574
70_A97_I0.165850.574
160_E182_R0.165650.573
111_V170_Q0.165630.573
123_I130_L0.165440.572
40_A225_N0.165140.571
161_S164_P0.165020.571
109_V173_I0.164780.570
99_V131_A0.16470.570
57_G125_K0.164640.569
164_P201_T0.164630.569
71_L218_D0.164040.567
99_V151_I0.16350.565
109_V148_T0.16310.564
35_E197_N0.162760.563
31_T164_P0.162390.562
185_V191_V0.161960.560
49_K52_G0.161660.559
166_I169_P0.161430.558
59_I64_F0.161120.557
44_L47_E0.160930.556
5_T8_P0.160850.556
69_V72_A0.160490.555
52_G56_G0.160480.555
7_V78_E0.160230.554
160_E195_V0.160180.554
225_N228_R0.159610.552
13_R17_A0.159480.551
154_L177_G0.159210.551
65_L196_M0.157810.546
126_E130_L0.15780.546
214_R217_K0.15770.545
43_A194_P0.157170.543
147_G167_N0.156810.542
9_L17_A0.156590.541
26_T168_P0.156380.541
171_V207_I0.155920.539
19_R167_N0.15580.539
53_E117_K0.155670.538
72_A76_H0.155350.537
23_S27_I0.155210.537
71_L95_V0.155080.536
182_R197_N0.154840.535
211_E214_R0.154630.535
92_Y148_T0.153770.532
39_T184_V0.153710.532
172_A207_I0.153710.532
159_V162_F0.153530.531
11_G15_A0.153480.531
63_D124_A0.152960.529
163_T202_F0.152590.528
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
3dvaI0.9957100-0.03
3maeA0.9957100-0.013
1sczA0.9957100-0.01
1dpbA1100-0.008
2ii3A0.9957100-0.002
3l60A0.97841000
3b8kA0.99131000.003
3rqcA0.94371000.034
2xt6A0.91771000.087
1q23A0.90041000.253

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