GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PCMT - Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
Pfam: PF01135 (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: CL0063
Length: 209
Sequences: 2612
Seq/Len: 12.5
HH_delta: 0.305 (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
143_D163_K0.576982.746
104_E110_A0.571022.717
74_D144_R0.50882.421
156_E160_E0.505922.408
81_T102_S0.497412.367
110_A127_V0.487682.321
92_H122_I0.483932.303
159_L191_F0.477682.273
102_S127_V0.461482.196
135_G161_Q0.459252.186
112_R116_N0.441212.100
110_A129_V0.432662.059
185_K191_F0.431162.052
167_R182_R0.42792.036
26_A92_H0.41691.984
167_R184_T0.413491.968
147_V170_A0.412451.963
136_W142_F0.40861.945
9_L13_G0.407031.937
16_T66_E0.386241.838
107_P129_V0.357211.700
128_V136_W0.352281.676
78_E102_S0.351651.673
144_R167_R0.349211.662
117_L125_V0.347241.653
70_L144_R0.345761.645
18_P22_D0.34061.621
107_P111_E0.340261.619
182_R194_E0.338861.613
187_G190_E0.327321.558
164_P187_G0.325221.548
7_D11_R0.322371.534
67_A196_L0.32121.529
147_V158_L0.321181.528
68_L144_R0.319491.520
65_L86_Q0.318081.514
179_R195_E0.317321.510
5_L24_F0.31651.506
70_L90_L0.315311.501
65_L89_L0.310681.479
117_L127_V0.308691.469
186_K190_E0.307171.462
181_V195_E0.30171.436
5_L9_L0.300511.430
116_N120_L0.300061.428
24_F89_L0.29881.422
31_D119_R0.295351.406
164_P186_K0.294871.403
139_E142_F0.29411.400
171_P201_F0.292731.393
9_L15_V0.291751.388
141_P161_Q0.290881.384
186_K192_S0.289541.378
145_I162_L0.288291.372
135_G141_P0.287041.366
162_L168_L0.282081.342
78_E148_T0.281291.339
22_D26_A0.277591.321
181_V193_R0.274371.306
184_T194_E0.268691.279
185_K189_G0.263011.252
101_V128_V0.259181.233
91_A124_N0.258491.230
75_R139_E0.25781.227
76_V90_L0.257331.225
94_V124_N0.252191.200
140_A161_Q0.251531.197
182_R196_L0.250471.192
74_D143_D0.250331.191
111_E114_R0.250051.190
51_C108_E0.249661.188
51_C106_D0.247771.179
135_G140_A0.244461.163
63_R197_F0.241861.151
10_I13_G0.238681.136
70_L94_V0.237011.128
44_D59_S0.236821.127
60_M199_V0.236121.124
85_Y89_L0.23591.123
5_L8_N0.234631.117
77_L142_F0.233491.111
133_S151_V0.233071.109
64_M201_F0.233031.109
164_P189_G0.227471.083
87_A127_V0.227411.082
110_A114_R0.225021.071
154_I183_I0.224581.069
70_L73_G0.220831.051
147_V151_V0.220081.047
8_N12_P0.21931.044
164_P185_K0.218471.040
8_N11_R0.217521.035
19_R72_P0.215151.024
101_V139_E0.214981.023
153_E156_E0.213531.016
30_E42_Y0.21341.016
86_Q148_T0.213071.014
180_L197_F0.213051.014
71_K74_D0.212971.014
61_V86_Q0.212351.011
87_A102_S0.211051.004
23_A89_L0.210441.001
183_I191_F0.209990.999
73_G94_V0.209950.999
56_S171_P0.208670.993
168_L183_I0.208610.993
179_R183_I0.207250.986
31_D120_L0.206290.982
86_Q146_I0.20620.981
70_L74_D0.206040.981
151_V170_A0.205520.978
71_K144_R0.204870.975
64_M146_I0.204620.974
19_R22_D0.203860.970
17_D66_E0.202350.963
55_I61_V0.201870.961
21_L25_R0.200950.956
33_V47_L0.199210.948
68_L90_L0.198820.946
28_P31_D0.197660.941
104_E109_L0.197630.941
10_I18_P0.194620.926
87_A125_V0.194580.926
9_L12_P0.194410.925
102_S148_T0.19380.922
50_G106_D0.191540.912
114_R118_A0.189920.904
10_I21_L0.189170.900
5_L12_P0.188770.898
27_V92_H0.187980.895
83_S109_L0.187660.893
23_A93_L0.187150.891
81_T113_A0.187030.890
91_A122_I0.186950.890
74_D167_R0.186540.888
57_A60_M0.185270.882
196_L199_V0.184540.878
116_N119_R0.183350.873
184_T192_S0.182980.871
173_G178_Q0.180080.857
27_V85_Y0.179750.855
24_F62_A0.179110.852
102_S117_L0.177990.847
101_V126_E0.177130.843
81_T148_T0.177110.843
69_D167_R0.177090.843
180_L199_V0.176790.841
91_A125_V0.176720.841
96_P126_E0.17650.840
56_S201_F0.174850.832
183_I193_R0.174630.831
64_M169_V0.172260.820
68_L146_I0.172130.819
178_Q185_K0.171990.818
23_A27_V0.171390.816
78_E90_L0.170570.812
103_V130_G0.170520.811
78_E86_Q0.170360.811
5_L10_I0.169640.807
70_L76_V0.168360.801
73_G95_G0.16780.799
32_F120_L0.16770.798
61_V78_E0.166910.794
15_V66_E0.166420.792
67_A169_V0.16530.787
27_V122_I0.165160.786
22_D25_R0.165060.786
164_P191_F0.164850.785
53_Q105_R0.163830.780
87_A91_A0.162990.776
10_I25_R0.162960.776
7_D12_P0.162560.774
173_G199_V0.161490.769
136_W139_E0.161480.768
115_R119_R0.160370.763
6_V10_I0.160150.762
134_E157_A0.160040.762
56_S60_M0.158670.755
149_A171_P0.158630.755
159_L183_I0.15620.743
104_E130_G0.155970.742
133_S152_P0.155750.741
130_G134_E0.155250.739
24_F58_P0.154830.737
79_I158_L0.153940.733
6_V25_R0.15330.730
88_A117_L0.15260.726
164_P190_E0.151280.720
15_V62_A0.151280.720
149_A201_F0.149940.714
128_V138_E0.148570.707
19_R93_L0.148330.706
75_R163_K0.148160.705
17_D69_D0.147870.704
7_D25_R0.147860.704
56_S149_A0.147410.702
78_E81_T0.147360.701
55_I83_S0.146840.699
113_A116_N0.145130.691
179_R192_S0.14480.689
64_M86_Q0.144770.689
77_L161_Q0.144390.687
110_A113_A0.144270.687
65_L146_I0.143730.684
80_G84_G0.143360.682
15_V21_L0.1430.681
178_Q199_V0.142870.680
154_I170_A0.142840.680
135_G142_F0.14190.675
61_V148_T0.14130.672
111_E115_R0.141030.671
19_R23_A0.140750.670
179_R185_K0.140390.668
56_S148_T0.140020.666
6_V42_Y0.139550.664
137_P141_P0.139520.664
147_V150_A0.139270.663
6_V9_L0.139120.662
5_L13_G0.138460.659
29_R68_L0.138310.658
135_G138_E0.137960.657
6_V12_P0.137860.656
9_L66_E0.137810.656
94_V100_V0.137340.654
69_D190_E0.13730.653
136_W141_P0.137220.653
68_L169_V0.136830.651
23_A88_A0.136820.651
53_Q86_Q0.136070.648
101_V142_F0.13580.646
20_V66_E0.135070.643
91_A94_V0.134730.641
7_D193_R0.134720.641
126_E139_E0.134470.640
49_I53_Q0.134050.638
158_L168_L0.133930.637
65_L148_T0.133890.637
65_L93_L0.133650.636
12_P44_D0.133280.634
46_P54_T0.132940.633
169_V182_R0.132920.633
60_M180_L0.132830.632
73_G144_R0.132050.628
69_D182_R0.131710.627
56_S64_M0.131470.626
5_L11_R0.131180.624
90_L146_I0.131090.624
79_I132_G0.131040.624
65_L144_R0.130990.623
186_K194_E0.130170.619
61_V64_M0.130080.619
157_A160_E0.129610.617
7_D10_I0.129050.614
58_P62_A0.128950.614
53_Q148_T0.128780.613
174_Q186_K0.127870.609
32_F88_A0.127560.607
80_G132_G0.127430.606
50_G53_Q0.126880.604
159_L185_K0.126410.602
78_E146_I0.126310.601
69_D72_P0.125920.599
160_E185_K0.125680.598
46_P56_S0.125010.595
31_D38_R0.124840.594
53_Q64_M0.124810.594
53_Q149_A0.124590.593
37_F47_L0.124560.593
162_L166_G0.124490.592
186_K189_G0.124380.592
72_P94_V0.124260.591
77_L132_G0.123880.590
115_R118_A0.123580.588
116_N125_V0.122880.585
116_N123_D0.122770.584
101_V138_E0.122650.584
79_I149_A0.122620.584
192_S195_E0.122410.583
10_I15_V0.122340.582
172_I181_V0.122130.581
6_V11_R0.122120.581
175_G179_R0.121520.578
46_P171_P0.121260.577
27_V32_F0.12120.577
160_E189_G0.120940.576
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
1r18A0.95691000.305
2pbfA0.96651000.323
3lbfA0.97131000.332
1jg1A0.98561000.338
2yxeA0.98561000.36
1dl5A0.98561000.368
1i1nA0.98091000.374
1vbfA0.94741000.419
1u2zA0.952299.90.53
2b25A0.995299.80.566

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