GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DHDPS - Dihydrodipicolinate synthetase family
Pfam: PF00701 (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: CL0036
Length: 289
Sequences: 4734
Seq/Len: 16.38
HH_delta: -0.013 (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
225_D228_E1.424824.498
14_N18_S1.096343.461
29_D66_A1.049493.313
116_I150_R0.992283.132
93_Q127_D0.964043.043
21_E58_E0.898412.836
77_V89_A0.895772.828
258_L282_K0.892392.817
220_A228_E0.864362.729
25_K66_A0.840292.653
21_E62_I0.836212.640
194_A199_A0.782652.471
25_K62_I0.770522.432
29_D70_R0.733022.314
228_E231_E0.721812.279
57_K91_H0.716132.261
89_A100_V0.690942.181
220_A225_D0.689612.177
25_K65_E0.669712.114
112_Q147_T0.660492.085
219_D223_A0.65822.078
6_F38_G0.641082.024
58_E61_E0.629891.988
113_E117_D0.629631.988
37_D219_D0.628721.985
113_E150_R0.620581.959
142_D169_R0.620221.958
7_P207_A0.61681.947
29_D33_E0.609221.923
120_R124_D0.606561.915
148_L160_I0.604841.909
30_F34_A0.604211.907
124_D154_I0.601561.899
116_I120_R0.601541.899
120_R154_I0.601251.898
82_T118_Y0.596571.883
61_E65_E0.595921.881
131_I159_G0.576171.819
28_I63_V0.573291.810
195_L221_F0.567071.790
20_D23_A0.558451.763
23_A26_R0.546331.725
58_E62_I0.545961.723
34_A212_E0.544551.719
213_L235_R0.544071.717
55_E267_R0.537331.696
282_K286_K0.53471.688
131_I203_I0.531061.676
215_V219_D0.529111.670
231_E235_R0.527891.666
123_A154_I0.527531.665
149_A176_A0.522591.650
64_V73_V0.52011.642
112_Q144_S0.517231.633
279_E282_K0.513211.620
144_S147_T0.511641.615
86_I121_A0.511451.615
102_V122_I0.511171.614
117_D120_R0.503721.590
53_D84_E0.500151.579
12_P24_L0.474111.497
60_L75_A0.473371.494
24_L63_V0.4731.493
254_Y278_K0.471841.489
24_L59_L0.471361.488
151_L157_V0.464851.467
279_E283_E0.463261.462
32_I70_R0.461931.458
90_R94_D0.455131.437
85_A122_I0.448251.415
216_E220_A0.446871.411
6_F40_V0.442991.398
10_I256_L0.442521.397
93_Q126_T0.437951.383
117_D121_A0.437381.381
100_V126_T0.437281.380
32_I71_V0.435561.375
41_V63_V0.431041.361
62_I66_A0.425531.343
62_I65_E0.423081.336
89_A126_T0.420431.327
28_I66_A0.410331.295
28_I67_A0.410321.295
275_D278_K0.406861.284
47_E253_K0.406191.282
57_K61_E0.405841.281
37_D215_V0.397121.254
257_E264_G0.393961.244
257_E262_I0.393081.241
275_D279_E0.392431.239
254_Y258_L0.388761.227
216_E219_D0.388531.226
79_A85_A0.387711.224
54_E58_E0.386191.219
192_L229_A0.385841.218
57_K87_E0.385241.216
283_E287_E0.384861.215
5_I36_V0.383651.211
221_F226_W0.380961.203
53_D91_H0.37871.195
174_L183_V0.376741.189
91_H94_D0.376151.187
74_I131_I0.370681.170
74_I99_A0.369251.166
3_K222_Q0.366671.157
57_K94_D0.366621.157
121_A268_P0.365211.153
23_A263_A0.359911.136
274_S277_E0.357781.129
53_D87_E0.357291.128
18_S83_E0.356691.126
227_E230_R0.35551.122
67_A73_V0.354731.120
86_I90_R0.352861.114
81_S84_E0.349111.102
60_L92_A0.34811.099
40_V101_L0.345611.091
100_V130_I0.342611.082
226_W230_R0.341011.076
280_E283_E0.340131.074
77_V92_A0.339561.072
25_K29_D0.335071.058
30_F261_L0.334261.055
212_E216_E0.33351.053
64_V98_D0.332821.051
77_V100_V0.331771.047
53_D88_L0.330381.043
64_V95_A0.329271.039
228_E232_L0.328291.036
170_L194_A0.327581.034
28_I62_I0.326581.031
21_E25_K0.326271.030
172_Q176_A0.325661.028
123_A156_N0.325321.027
5_I218_Y0.323661.022
7_P36_V0.32081.013
121_A125_A0.320341.011
273_L281_L0.320181.011
42_L59_L0.318851.007
216_E228_E0.318251.005
256_L259_R0.317251.001
27_L256_L0.315610.996
93_Q128_L0.315220.995
79_A84_E0.313970.991
273_L277_E0.312440.986
104_P143_L0.312270.986
113_E116_I0.311810.984
54_E87_E0.311040.982
150_R153_K0.310810.981
182_S200_D0.31020.979
145_P176_A0.309970.978
254_Y282_K0.30970.978
132_I148_L0.306830.969
37_D218_Y0.306410.967
146_E176_A0.305750.965
32_I67_A0.305750.965
196_A221_F0.304690.962
100_V128_L0.302160.954
13_F267_R0.301230.951
112_Q150_R0.30120.951
227_E231_E0.299910.947
123_A157_V0.299370.945
117_D271_L0.298730.943
115_L141_N0.296960.937
61_E91_H0.296390.936
245_S280_E0.295790.934
75_A97_A0.295140.932
283_E286_K0.292970.925
206_L240_R0.292880.925
9_L24_L0.291670.921
193_P196_A0.291310.920
172_Q241_E0.29120.919
9_L39_L0.291140.919
14_N20_D0.289350.913
5_I215_V0.287590.908
191_L202_F0.287110.906
134_N142_D0.285680.902
61_E95_A0.283980.896
195_L218_Y0.282790.893
223_A228_E0.282560.892
92_A97_A0.281660.889
91_H95_A0.281570.889
104_P141_N0.279170.881
41_V59_L0.278580.879
7_P31_L0.278440.879
174_L200_D0.278250.878
42_L75_A0.278030.878
97_A128_L0.276990.874
255_A285_L0.276850.874
242_A284_I0.27660.873
22_D26_R0.27630.872
56_R88_L0.274660.867
78_G103_I0.27410.865
121_A124_D0.273640.864
135_N139_T0.273070.862
82_T86_I0.272910.862
9_L31_L0.2720.859
116_I147_T0.271750.858
217_I232_L0.27160.857
73_V97_A0.267520.844
113_E274_S0.266770.842
3_K200_D0.266510.841
13_F51_L0.265090.837
159_G181_F0.26440.835
218_Y222_Q0.264090.834
149_A177_V0.263820.833
120_R153_K0.263230.831
22_D25_K0.262520.829
196_A226_W0.262120.827
96_G128_L0.261270.825
60_L97_A0.260720.823
83_E87_E0.260720.823
5_I202_F0.260410.822
29_D32_I0.258660.817
133_Y161_K0.257590.813
26_R261_L0.257290.812
266_V270_L0.257130.812
204_S207_A0.254860.805
145_P149_A0.254350.803
210_F239_L0.252510.797
276_E279_E0.251480.794
19_I59_L0.250740.792
278_K282_K0.249210.787
32_I66_A0.249060.786
23_A262_I0.249010.786
116_I154_I0.248990.786
257_E278_K0.248320.784
14_N22_D0.248260.784
196_A230_R0.247180.780
20_D262_I0.246570.778
15_A265_P0.246370.778
174_L177_V0.245920.776
224_G227_E0.245690.776
60_L64_V0.244890.773
146_E172_Q0.244520.772
17_G268_P0.244490.772
273_L278_K0.243730.769
170_L183_V0.243330.768
13_F55_E0.242520.766
44_S107_Y0.242160.764
60_L95_A0.241650.763
277_E280_E0.24130.762
254_Y257_E0.241090.761
168_E189_E0.240250.758
24_L28_I0.239860.757
64_V97_A0.239460.756
90_R93_Q0.238620.753
250_A273_L0.238240.752
210_F236_L0.23820.752
2_L99_A0.237660.750
5_I31_L0.237210.749
51_L59_L0.23670.747
117_D268_P0.235050.742
132_I143_L0.234940.742
34_A211_P0.234470.740
28_I39_L0.234060.739
15_A263_A0.233890.738
114_E271_L0.23360.737
162_D170_L0.233250.736
87_E90_R0.231920.732
238_P287_E0.231610.731
212_E259_R0.230390.727
9_L63_V0.230040.726
209_V255_A0.228940.723
123_A130_I0.228320.721
57_K88_L0.228230.720
258_L278_K0.227860.719
192_L226_W0.227830.719
220_A229_A0.22660.715
8_A188_D0.226110.714
172_Q175_R0.225740.713
90_R125_A0.225120.711
131_I158_V0.224890.710
54_E57_K0.224810.710
49_Y108_F0.224740.709
5_I207_A0.224620.709
61_E94_D0.22460.709
36_V211_P0.223920.707
17_G83_E0.22380.706
220_A232_L0.223760.706
85_A89_A0.222890.704
52_T55_E0.222290.702
158_V182_S0.22130.699
193_P197_A0.220010.695
183_V194_A0.219220.692
19_I58_E0.21890.691
85_A102_V0.21880.691
4_G184_F0.218750.691
111_S250_A0.21740.686
87_E91_H0.216390.683
89_A122_I0.216280.683
36_V215_V0.216180.682
50_S82_T0.215560.680
170_L174_L0.21360.674
149_A153_K0.212860.672
31_L36_V0.212640.671
119_F157_V0.212420.671
74_I101_L0.212340.670
279_E286_K0.211110.666
208_N211_P0.211060.666
154_I157_V0.210720.665
210_F213_L0.210050.663
173_L183_V0.209790.662
258_L286_K0.20970.662
72_P98_D0.209520.661
145_P169_R0.208920.660
265_P272_P0.208750.659
209_V252_I0.20850.658
86_I125_A0.208090.657
276_E280_E0.208090.657
120_R150_R0.207030.654
8_A204_S0.205710.649
35_G215_V0.205170.648
233_Q237_L0.204760.646
41_V73_V0.204250.645
102_V130_I0.204180.645
230_R234_Q0.204040.644
250_A266_V0.203790.643
31_L207_A0.203250.642
191_L217_I0.202830.640
42_L56_R0.202780.640
247_G251_A0.202510.639
146_E149_A0.202330.639
145_P173_L0.200930.634
67_A71_V0.200150.632
27_L31_L0.199980.631
48_F76_G0.199510.630
134_N162_D0.199370.629
275_D282_K0.199210.629
40_V74_I0.199050.628
192_L196_A0.199020.628
99_A158_V0.1990.628
237_L241_E0.198610.627
264_G278_K0.198470.627
6_F74_I0.197830.625
64_V68_A0.19760.624
43_G133_Y0.197340.623
57_K95_A0.197260.623
8_A205_G0.197170.622
153_K178_G0.196930.622
163_S187_D0.196470.620
152_A181_F0.196080.619
39_L67_A0.194580.614
84_E87_E0.194280.613
20_D261_L0.194020.612
257_E263_A0.193870.612
31_L34_A0.193280.610
135_N163_S0.193090.610
192_L233_Q0.192840.609
14_N265_P0.19260.608
44_S133_Y0.191620.605
254_Y266_V0.19090.603
153_K180_D0.190880.603
246_G274_S0.190840.602
57_K92_A0.190760.602
216_E232_L0.190290.601
117_D150_R0.189950.600
67_A70_R0.18990.599
69_G98_D0.188820.596
175_R234_Q0.188730.596
171_I197_A0.187840.593
213_L216_E0.187360.591
247_G250_A0.186790.590
171_I193_P0.186320.588
80_N108_F0.185060.584
171_I233_Q0.184980.584
34_A215_V0.18490.584
19_I24_L0.184890.584
254_Y281_L0.184690.583
145_P172_Q0.184540.583
191_L218_Y0.184220.582
30_F211_P0.183620.580
220_A223_A0.183360.579
217_I221_F0.183010.578
255_A258_L0.182830.577
76_G101_L0.182620.576
167_L190_L0.181310.572
52_T83_E0.181250.572
93_Q125_A0.180420.570
284_I287_E0.180080.568
246_G277_E0.180080.568
186_G203_I0.179990.568
42_L51_L0.179790.568
256_L261_L0.179760.567
75_A92_A0.179640.567
143_L147_T0.178930.565
193_P233_Q0.178820.564
171_I175_R0.177920.562
111_S246_G0.17760.561
209_V256_L0.176790.558
56_R91_H0.17650.557
44_S50_S0.175790.555
142_D166_D0.175720.555
32_I68_A0.175390.554
192_L221_F0.174870.552
127_D156_N0.174770.552
18_S58_E0.174560.551
44_S163_S0.17440.551
10_I262_I0.174140.550
241_E280_E0.173920.549
14_N17_G0.173650.548
19_I62_I0.17340.547
135_N138_R0.173210.547
119_F132_I0.173030.546
244_F248_N0.172820.546
143_L148_L0.17270.545
251_A281_L0.172050.543
142_D164_S0.171750.542
152_A178_G0.170920.540
99_A131_I0.17090.539
184_F201_G0.170430.538
39_L71_V0.17040.538
185_C194_A0.170370.538
280_E284_I0.170280.538
82_T121_A0.169240.534
118_Y121_A0.169120.534
185_C190_L0.1690.533
30_F33_E0.1690.533
164_S190_L0.168490.532
38_G74_I0.168310.531
77_V102_V0.168220.531
147_T150_R0.168070.531
31_L71_V0.167250.528
195_L222_Q0.166510.526
109_K137_A0.16630.525
39_L73_V0.165690.523
178_G181_F0.165670.523
65_E68_A0.165170.521
124_D156_N0.165130.521
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
3si9A1100-0.013
3na8A1100-0.013
3eb2A1100-0.011
3qzeA1100-0.01
3fluA1100-0.006
2ojpA1100-0.003
1xkyA1100-0.002
3takA1100-0.002
3l21A0.9931100-0.002
3vflA0.9965100-0.001

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