GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
peroxidase - Peroxidase
Pfam: PF00141 (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. )
Length: 230
Sequences: 3642
Seq/Len: 15.83
HH_delta: 0.057 (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
221_R225_E0.960013.877
127_L137_A0.705742.850
37_I52_L0.640972.589
219_E222_P0.634692.563
16_A91_C0.617992.496
199_K228_A0.544222.198
31_G112_G0.526922.128
41_S45_D0.520692.103
135_L139_E0.516162.085
202_L225_E0.509662.058
122_S125_Q0.495982.003
183_N208_L0.495732.002
121_D125_Q0.493131.992
20_L88_V0.488341.972
37_I105_G0.482421.948
126_L144_S0.467971.890
21_R25_H0.464881.877
126_L140_M0.440681.780
63_K67_E0.416051.680
189_T196_S0.409471.654
122_S210_S0.404551.634
144_S197_Y0.396971.603
124_D128_A0.389881.575
225_E229_Q0.386381.560
138_E226_R0.385861.558
196_S200_N0.383781.550
42_A45_D0.38181.542
148_T194_D0.377731.525
16_A20_L0.377181.523
74_V79_I0.371581.501
148_T193_F0.363681.469
198_Y224_V0.363081.466
10_K86_D0.359661.453
82_L100_L0.358051.446
203_N228_A0.354841.433
33_C81_A0.3521.422
5_V19_L0.351371.419
88_V93_G0.349811.413
212_Q216_N0.34981.413
23_A81_A0.347151.402
152_A208_L0.343111.386
92_G111_S0.338811.368
7_A11_K0.338131.366
5_V9_F0.335711.356
23_A80_I0.335661.356
215_L221_R0.335321.354
27_C33_C0.335261.354
128_A132_R0.331851.340
6_R86_D0.330091.333
187_L208_L0.328851.328
152_A156_S0.328291.326
196_S199_K0.327291.322
46_A113_A0.326591.319
41_S44_K0.322251.301
39_L60_D0.321911.300
188_D200_N0.321431.298
209_P213_A0.321361.298
6_R90_L0.317921.284
199_K203_N0.31351.266
188_D194_D0.305581.234
189_T192_V0.304991.232
195_N199_K0.303251.225
8_A62_I0.30241.221
63_K76_C0.296461.197
20_L149_I0.293411.185
91_C149_I0.291731.178
18_G53_R0.290861.175
14_T18_G0.290361.173
58_V61_P0.290281.172
105_G109_S0.289711.170
223_I226_R0.288361.165
202_L224_V0.287931.163
223_I227_Y0.285351.152
21_R51_G0.28511.151
40_F50_R0.283731.146
141_V224_V0.283441.145
9_F83_A0.283211.144
115_N133_K0.280431.133
43_E49_N0.278311.124
188_D196_S0.27771.122
26_D36_S0.277451.121
34_D134_G0.277271.120
5_V8_A0.277241.120
9_F16_A0.276511.117
12_D62_I0.275491.113
18_G51_G0.274171.107
138_E223_I0.27321.103
52_L56_F0.27271.101
57_D61_P0.27021.091
59_I83_A0.270121.091
118_S121_D0.270021.090
137_A223_I0.268931.086
93_G111_S0.267031.078
215_L225_E0.266361.076
76_C80_I0.266351.076
198_Y228_A0.266081.075
50_R154_C0.26591.074
214_L224_V0.265811.073
60_D64_A0.265471.072
25_H28_F0.265281.071
200_N205_R0.264881.070
36_S80_I0.263961.066
141_V220_T0.263561.064
63_K79_I0.262951.062
224_V228_A0.261521.056
121_D129_F0.261041.054
36_S76_C0.260821.053
9_F19_L0.25941.048
189_T194_D0.258961.046
138_E227_Y0.257341.039
136_S139_E0.256941.038
144_S214_L0.256621.036
17_P21_R0.255021.030
58_V62_I0.2541.026
44_K56_F0.252781.021
35_G105_G0.252021.018
8_A65_K0.251071.014
140_M220_T0.248131.002
151_R191_T0.243390.983
123_V210_S0.242860.981
224_V227_Y0.241490.975
226_R230_D0.240720.972
81_A98_V0.239680.968
222_P226_R0.239120.966
183_N206_G0.237390.959
26_D80_I0.237350.959
19_L83_A0.233920.945
57_D60_D0.231550.935
40_F218_P0.231360.934
122_S213_A0.231340.934
107_V111_S0.230760.932
23_A26_D0.228720.924
5_V79_I0.227240.918
195_N228_A0.227160.917
145_G198_Y0.224650.907
210_S214_L0.224220.906
44_K60_D0.223030.901
115_N132_R0.222090.897
123_V220_T0.221710.895
202_L221_R0.218710.883
15_L18_G0.217680.879
48_P51_G0.217170.877
150_G191_T0.215850.872
77_A104_D0.215750.871
152_A206_G0.215310.870
137_A219_E0.214330.866
150_G190_P0.214110.865
10_K90_L0.213760.863
85_R88_V0.213710.863
64_A68_A0.213070.860
26_D81_A0.21280.859
150_G155_S0.212530.858
53_R57_D0.212130.857
63_K74_V0.211930.856
12_D185_V0.210740.851
172_Y185_V0.21040.850
94_P188_D0.207790.839
21_R151_R0.207220.837
61_P65_K0.20680.835
138_E142_A0.204760.827
105_G108_S0.204630.826
111_S114_S0.202720.819
16_A149_I0.201950.816
22_L38_L0.201950.816
37_I56_F0.200490.810
202_L229_Q0.200170.808
23_A96_I0.199910.807
142_A227_Y0.199660.806
89_E95_R0.198130.800
109_S112_G0.197860.799
127_L140_M0.197440.797
18_G55_G0.1970.796
126_L210_S0.1970.796
23_A84_A0.196880.795
123_V217_D0.196720.794
87_A149_I0.196530.794
19_L80_I0.196330.793
84_A87_A0.196230.792
38_L80_I0.195820.791
56_F80_I0.195370.789
144_S210_S0.195340.789
121_D124_D0.194790.787
59_I80_I0.194690.786
17_P151_R0.193480.781
148_T185_V0.19340.781
152_A207_L0.192530.778
150_G154_C0.192360.777
21_R50_R0.192290.777
137_A140_M0.192170.776
226_R229_Q0.191750.774
26_D33_C0.190750.770
202_L215_L0.190370.769
227_Y230_D0.189970.767
156_S174_G0.188860.763
137_A220_T0.18760.758
88_V193_F0.187460.757
39_L76_C0.186930.755
188_D199_K0.186640.754
200_N204_G0.186460.753
147_H150_G0.185040.747
21_R148_T0.183570.741
196_S204_G0.18320.740
76_C79_I0.182960.739
118_S156_S0.182880.739
26_D38_L0.182270.736
197_Y214_L0.180680.730
45_D110_P0.179860.726
83_A87_A0.179670.726
52_L80_I0.179310.724
126_L214_L0.17890.722
16_A90_L0.178790.722
136_S140_M0.178580.721
105_G110_P0.177650.717
6_R10_K0.176490.713
129_F133_K0.17570.710
34_D37_I0.175660.709
140_M144_S0.173170.699
53_R58_V0.173080.699
206_G212_Q0.172930.698
139_E223_I0.172690.697
74_V83_A0.172240.696
124_D219_E0.172040.695
141_V198_Y0.170770.690
9_F86_D0.170070.687
127_L217_D0.170050.687
216_N221_R0.169530.685
31_G107_V0.168110.679
50_R153_H0.167630.677
184_G187_L0.167530.677
65_K68_A0.166920.674
150_G153_H0.166920.674
8_A11_K0.166870.674
197_Y201_L0.166830.674
68_A74_V0.166360.672
225_E228_A0.165960.670
52_L55_G0.16540.668
62_I83_A0.165060.667
41_S110_P0.164620.665
26_D29_V0.164470.664
35_G113_A0.164410.664
5_V62_I0.163110.659
103_R106_T0.162760.657
29_V133_K0.162740.657
201_L215_L0.162730.657
26_D35_G0.162010.654
15_L58_V0.16160.653
87_A90_L0.160740.649
110_P113_A0.160310.647
19_L23_A0.160270.647
51_G183_N0.159870.646
108_S111_S0.159820.645
189_T206_G0.159690.645
211_D214_L0.159310.643
217_D222_P0.159310.643
17_P150_G0.1590.642
93_G134_G0.158620.641
40_F44_K0.15860.641
118_S125_Q0.158510.640
125_Q129_F0.158490.640
194_D200_N0.158040.638
127_L219_E0.1580.638
202_L228_A0.156620.633
40_F182_D0.156480.632
25_H48_P0.156310.631
9_F91_C0.155570.628
185_V206_G0.155490.628
120_T216_N0.155170.627
17_P190_P0.154590.624
140_M210_S0.154350.623
6_R89_E0.154070.622
122_S209_P0.154070.622
85_R98_V0.153920.622
171_G174_G0.153820.621
12_D17_P0.153750.621
57_D64_A0.153590.620
22_L52_L0.153040.618
5_V58_V0.152950.618
11_K68_A0.152750.617
212_Q215_L0.152490.616
34_D195_N0.152440.616
154_C189_T0.152380.615
66_L79_I0.15210.614
93_G230_D0.151870.613
141_V202_L0.151840.613
101_G104_D0.151810.613
117_P126_L0.15180.613
10_K218_P0.151680.613
28_F48_P0.150790.609
141_V214_L0.150740.609
14_T90_L0.150690.609
225_E230_D0.150480.608
195_N201_L0.149580.604
53_R153_H0.149550.604
200_N203_N0.148910.601
219_E223_I0.14890.601
123_V127_L0.148690.600
128_A131_A0.146970.594
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
3hdlA0.99131000.057
1schA0.98261000.077
1qgjA0.99131000.077
1pa2A0.99131000.079
1fhfA0.99131000.081
1gwuA0.99131000.083
1bgpA0.99131000.084
1iynA0.93911000.211
2ccaA0.97391000.22
1itkA0.98261000.226

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