GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PQQ_2 - PQQ-like domain
Pfam: PF13360 (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: CL0186
Length: 238
Sequences: 61170
Seq/Len: 257.02
HH_delta: 0.096 (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
40_Y50_A2.06562.740
126_Y136_A1.996512.649
25_I28_P1.880062.494
41_V51_L1.786842.370
127_V137_L1.723792.287
216_Y226_A1.719372.281
49_Y58_V1.680652.230
80_Y90_A1.647962.186
138_D141_T1.579322.095
52_D55_T1.576862.092
92_D95_T1.573962.088
49_Y61_R1.564682.076
81_V91_L1.553542.061
38_R50_A1.515722.011
135_V147_K1.472671.954
124_R136_A1.459511.936
135_V144_L1.426891.893
189_D192_T1.414581.877
58_V61_R1.405351.864
25_I29_V1.40471.863
168_S171_I1.390051.844
89_Y101_S1.37521.824
214_T226_A1.369241.816
115_S128_G1.365821.812
88_L127_V1.340381.778
78_R90_A1.294461.717
89_Y98_V1.290021.711
48_L81_V1.268321.683
68_I71_A1.248971.657
98_V101_S1.248051.656
73_V76_G1.242791.649
185_V188_V1.229321.631
47_N61_R1.202111.595
144_L147_K1.180231.566
116_S120_V1.158311.537
103_Y106_S1.148321.523
129_T135_V1.103631.464
137_L144_L1.098361.457
217_V227_L1.086591.441
133_K147_K1.081581.435
40_Y79_V1.070631.420
91_L98_V1.062561.410
70_G82_G1.056071.401
29_V32_A1.055311.400
136_A146_W1.054511.399
80_Y125_L1.050831.394
41_V49_Y1.042791.383
51_L58_V1.030761.367
68_I72_P1.028411.364
38_R59_L1.018411.351
87_S101_S1.015541.347
80_Y118_P1.007271.336
178_V188_V0.993741.318
77_G94_K0.934781.240
26_G29_V0.931971.236
214_T217_V0.931361.236
177_Y187_A0.928781.232
73_V77_G0.903611.199
37_G54_K0.900771.195
69_S84_S0.899751.194
209_S213_G0.898381.192
72_P117_S0.896021.189
117_S170_V0.892541.184
90_A100_W0.892361.184
47_N63_D0.889221.180
83_T87_S0.884581.173
123_D140_K0.884411.173
168_S172_S0.883921.173
83_T89_Y0.883571.172
209_S212_G0.881921.170
206_S209_S0.880691.168
206_S210_V0.879771.167
73_V78_R0.879171.166
50_A60_W0.862051.144
43_S47_N0.855451.135
129_T133_K0.852581.131
65_P69_S0.851891.130
195_K198_S0.849931.128
125_L139_P0.848861.126
180_S183_G0.847691.125
126_Y171_I0.843921.120
127_V135_V0.83331.105
124_R145_L0.832321.104
171_I174_G0.828211.099
33_V36_G0.827381.098
106_S127_V0.819051.087
167_G171_I0.817951.085
119_A123_D0.809051.073
119_A124_R0.797441.058
219_S225_Y0.795991.056
133_K149_P0.789451.047
81_V89_Y0.77971.034
208_P211_D0.775811.029
134_L179_S0.773481.026
151_G154_R0.767421.018
106_S129_T0.766791.017
204_I207_L0.76481.015
200_P203_G0.764141.014
219_S223_R0.75661.004
197_W200_P0.745550.989
60_W96_G0.743680.987
75_D78_R0.740480.982
167_G170_V0.731460.970
217_V225_Y0.726690.964
39_V53_A0.721030.957
146_W193_G0.720670.956
65_P68_I0.717270.952
52_D59_L0.716010.950
33_V37_G0.714530.948
179_S183_G0.714190.947
78_R99_L0.713950.947
43_S46_G0.713230.946
118_P125_L0.709810.942
41_V45_D0.709140.941
100_W142_G0.708330.940
43_S49_Y0.701510.931
115_S120_V0.6990.927
190_L193_G0.698640.927
215_L218_T0.695910.923
78_R81_V0.691190.917
27_G42_A0.687780.912
131_S135_V0.686170.910
176_V179_S0.681470.904
136_A148_Y0.677180.898
175_R178_V0.67670.898
74_V77_G0.672060.892
26_G32_A0.67190.891
170_V173_D0.669740.888
64_L89_Y0.669610.888
126_Y177_Y0.664750.882
209_S214_T0.664350.881
52_D57_K0.648590.860
27_G32_A0.647640.859
214_T218_T0.640620.850
150_V154_R0.63970.849
33_V38_R0.638660.847
53_A56_G0.638220.847
213_G230_K0.635230.843
92_D99_L0.63470.842
74_V78_R0.63210.839
119_A171_I0.632020.838
121_D124_R0.628050.833
40_Y93_A0.627610.833
115_S118_P0.627190.832
204_I209_S0.625870.830
37_G52_D0.625620.830
119_A122_G0.620870.824
26_G44_G0.613530.814
50_A62_F0.612160.812
139_P142_G0.61170.811
69_S72_P0.609510.809
78_R92_D0.607080.805
187_A195_K0.606380.804
205_Y208_P0.598660.794
134_L178_V0.598430.794
93_A96_G0.597990.793
118_P139_P0.594860.789
38_R41_V0.593250.787
186_V217_V0.592750.786
178_V181_G0.592520.786
50_A59_L0.590870.784
116_S119_A0.59030.783
45_D49_Y0.58880.781
205_Y218_T0.587850.780
207_L211_D0.587730.780
138_D145_L0.582490.773
151_G178_V0.580270.770
138_D143_K0.577760.766
221_D225_Y0.576510.765
29_V72_P0.574650.762
29_V33_V0.574430.762
187_A198_S0.573740.761
28_P32_A0.573520.761
201_I217_V0.572780.760
32_A39_V0.571070.758
189_D193_G0.5710.757
90_A99_L0.569080.755
210_V214_T0.56870.754
32_A35_D0.568120.754
35_D38_R0.566470.751
175_R187_A0.561960.745
37_G53_A0.561810.745
19_Y51_L0.560820.744
189_D196_L0.557970.740
81_V85_D0.557590.740
178_V186_V0.557290.739
209_S216_Y0.555940.738
34_P37_G0.553510.734
210_V213_G0.551350.731
117_S169_P0.550090.730
204_I208_P0.5490.728
169_P172_S0.548880.728
207_L210_V0.54770.727
84_S130_S0.543180.721
33_V40_Y0.542460.720
67_P70_G0.542030.719
79_V82_G0.539560.716
42_A71_A0.539190.715
124_R127_V0.538290.714
48_L79_V0.533240.707
92_D97_K0.532250.706
114_S130_S0.528440.701
64_L91_L0.524330.696
213_G228_D0.524020.695
44_G84_S0.521640.692
126_Y190_L0.519580.689
80_Y139_P0.51770.687
25_I32_A0.517120.686
203_G206_S0.516850.686
77_G93_A0.515470.684
116_S127_V0.515470.684
180_S186_V0.515040.683
124_R138_D0.514950.683
114_S118_P0.511430.678
126_Y176_V0.511110.678
211_D214_T0.511110.678
123_D138_D0.5110.678
210_V216_Y0.510530.677
124_R190_L0.509520.676
183_G187_A0.507420.673
74_V122_G0.507340.673
125_L137_L0.502390.666
38_R52_D0.502280.666
100_W103_Y0.501910.666
38_R42_A0.499710.663
77_G92_D0.497690.660
206_S218_T0.494810.656
126_Y170_V0.494130.656
172_S208_P0.492540.653
205_Y210_V0.486890.646
189_D194_E0.486830.646
65_P71_A0.485110.644
70_G115_S0.484590.643
80_Y116_S0.48420.642
175_R179_S0.477370.633
73_V118_P0.47660.632
129_T132_G0.47350.628
204_I220_S0.472670.627
175_R191_A0.472340.627
192_T195_K0.469590.623
75_D122_G0.467630.620
79_V93_A0.467120.620
172_S175_R0.466960.619
140_K191_A0.466690.619
215_L229_L0.465450.617
74_V79_V0.464920.617
134_L148_Y0.464250.616
169_P173_D0.46420.616
73_V79_V0.462740.614
117_S120_V0.461020.612
168_S179_S0.460920.611
78_R139_P0.460420.611
82_G116_S0.460220.611
180_S184_R0.45720.607
98_V144_L0.454990.604
218_T224_L0.454890.603
115_S119_A0.453060.601
183_G188_V0.452740.601
171_I175_R0.450640.598
214_T228_D0.450550.598
199_K227_L0.449270.596
136_A145_L0.448680.595
42_A46_G0.446690.593
181_G184_R0.445530.591
177_Y208_P0.444510.590
60_W63_D0.443020.588
90_A118_P0.44280.587
181_G185_V0.440450.584
168_S173_D0.437470.580
100_W146_W0.437340.580
95_T98_V0.437140.580
205_Y209_S0.435760.578
58_V98_V0.435540.578
192_T196_L0.434760.577
32_A36_G0.429060.569
67_P84_S0.42890.569
175_R196_L0.428130.568
96_G99_L0.426690.566
188_V195_K0.426380.566
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
1vyhC0.928699.90.096
2ynnA0.93799.90.126
3sfzA0.920299.90.128
4gqbB0.93799.90.128
3dm0A0.903499.90.132
1gotB0.928699.90.132
3v7dB0.928699.90.132
4j73A0.93799.90.135
3frxA0.907699.90.137
3ow8A0.928699.90.138

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