GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Proteasome - Proteasome subunit
Pfam: PF00227 (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: CL0052
Length: 190
Sequences: 3967
Seq/Len: 20.88
HH_delta: 0.045 (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
19_A167_A0.925594.358
159_S162_E0.806153.796
9_G121_L0.671553.162
9_G18_L0.647453.049
164_I189_V0.569882.683
13_K157_D0.541832.551
109_L137_A0.536172.525
164_I168_L0.527172.482
162_E165_E0.524612.470
12_G15_G0.507862.391
120_Q132_E0.504042.373
7_V49_G0.483712.278
18_L111_A0.437572.060
93_Q97_Y0.429962.025
41_K44_D0.413051.945
153_L169_K0.403141.898
176_D183_D0.397361.871
48_I61_I0.376831.774
15_G189_V0.375471.768
43_N72_R0.36141.702
147_Q151_E0.359691.694
16_V111_A0.355531.674
109_L121_L0.354781.671
19_A171_L0.343031.615
10_I163_A0.342681.614
16_V121_L0.342511.613
160_L164_I0.338151.592
72_R78_P0.336421.584
169_K172_K0.333951.572
11_K132_E0.333541.571
12_G163_A0.332681.566
154_Y158_L0.327771.543
155_K162_E0.325591.533
82_E120_Q0.318891.502
24_I36_V0.31131.466
13_K159_S0.305991.441
48_I110_I0.302871.426
123_S137_A0.302081.422
37_D186_E0.301051.418
11_K135_R0.300461.415
7_V20_A0.298781.407
46_I81_P0.296231.395
50_F57_F0.286571.349
168_L172_K0.282921.332
155_K158_L0.282761.331
161_E165_E0.281191.324
63_R91_L0.278471.311
121_L137_A0.276541.302
6_T142_G0.275271.296
54_T57_F0.270911.276
165_E169_K0.268891.266
81_P112_G0.266541.255
102_R105_G0.266541.255
158_L169_K0.263771.242
17_V189_V0.263411.240
93_Q96_T0.259131.220
158_L166_L0.258821.219
135_R156_P0.257931.215
45_N115_E0.252771.190
168_L185_I0.251451.184
109_L123_S0.251431.184
175_I185_I0.250021.177
42_I48_I0.246471.161
43_N69_Q0.245081.154
67_E91_L0.244421.151
8_V150_L0.244091.149
110_I124_V0.243911.148
164_I187_V0.24281.143
122_Y132_E0.241321.136
17_V164_I0.241131.135
15_G160_L0.238761.124
5_T21_D0.235671.110
20_A39_I0.234281.103
45_N78_P0.233051.097
19_A187_V0.232451.095
95_Y98_R0.231421.090
153_L166_L0.231331.089
17_V167_A0.230471.085
39_I186_E0.230171.084
11_K121_L0.226791.068
94_N98_R0.225821.063
40_F61_I0.224531.057
67_E70_E0.223971.055
172_K183_D0.223621.053
92_I96_T0.221621.044
51_S139_I0.217181.023
40_F50_F0.216791.021
91_L95_Y0.216711.020
172_K175_I0.214971.012
6_T146_A0.214171.008
138_A150_L0.213951.007
63_R67_E0.210770.992
109_L139_I0.209130.985
18_L47_I0.207880.979
15_G162_E0.204680.964
12_G160_L0.204250.962
94_N97_Y0.203230.957
42_I68_A0.202670.954
175_I183_D0.200640.945
178_D181_S0.200020.942
144_Q147_Q0.199070.937
125_D129_S0.196280.924
39_I188_A0.194790.917
22_K186_E0.193620.912
168_L187_V0.193310.910
66_E70_E0.192250.905
138_A146_A0.19170.903
107_S126_P0.190790.898
46_I88_I0.190080.895
63_R66_E0.189130.891
15_G163_A0.188860.889
17_V163_A0.18780.884
142_G146_A0.185880.875
95_Y104_Y0.18570.874
61_I65_R0.185640.874
165_E168_L0.184290.868
10_I167_A0.183850.866
10_I17_V0.183530.864
149_I153_L0.183520.864
138_A143_S0.183430.864
128_G140_G0.182370.859
150_L170_A0.181590.855
39_I49_G0.181430.854
82_E122_Y0.181350.854
77_R116_D0.179750.846
96_T100_G0.173770.818
38_K52_G0.173580.817
46_I110_I0.171670.808
88_I91_L0.171030.805
54_T129_S0.170520.803
145_F151_E0.169650.799
96_T102_R0.169410.798
149_I166_L0.169350.797
45_N114_D0.169010.796
159_S163_A0.168750.795
9_G109_L0.168320.793
136_F154_Y0.167980.791
28_S179_I0.16740.788
90_S97_Y0.16590.781
23_R141_S0.165780.781
12_G17_V0.165530.779
23_R182_G0.164610.775
149_I170_A0.163910.772
92_I95_Y0.163860.772
89_A122_Y0.163630.770
43_N81_P0.163460.770
91_L97_Y0.163150.768
10_I166_L0.16280.767
89_A130_Y0.162250.764
71_Y75_Y0.161820.762
18_L49_G0.161110.759
42_I61_I0.160310.755
71_Y80_S0.158450.746
170_A174_A0.158340.746
11_K16_V0.157940.744
41_K188_A0.157840.743
17_V187_V0.157590.742
42_I65_R0.157510.742
77_R115_E0.157210.740
60_L106_V0.156240.736
87_A90_S0.156220.736
47_I188_A0.155720.733
70_E74_S0.154640.728
151_E177_R0.153360.722
149_I152_K0.153320.722
173_E184_N0.153220.721
146_A170_A0.152440.718
122_Y130_Y0.152310.717
109_L136_F0.152210.717
60_L104_Y0.151810.715
92_I108_L0.151070.711
13_K161_E0.150910.711
100_G112_G0.150720.710
70_E73_F0.150710.710
11_K119_P0.150220.707
18_L188_A0.149540.704
93_Q99_S0.149330.703
43_N78_P0.149130.702
147_Q177_R0.148650.700
154_Y166_L0.148620.700
152_K173_E0.148270.698
19_A185_I0.147940.697
13_K156_P0.147790.696
142_G174_A0.147280.693
80_S89_A0.146490.690
50_F108_L0.146370.689
136_F147_Q0.146340.689
57_F106_V0.146330.689
67_E87_A0.145730.686
66_E69_Q0.145070.683
160_L189_V0.144350.680
123_S133_C0.143960.678
96_T105_G0.143710.677
161_E164_I0.14350.676
136_F150_L0.143490.676
166_L169_K0.143390.675
29_K144_Q0.143020.673
82_E132_E0.142940.673
71_Y79_I0.142870.673
40_F57_F0.142050.669
114_D120_Q0.141830.668
167_A170_A0.141130.665
178_D182_G0.13990.659
4_G112_G0.139770.658
21_D25_S0.139680.658
10_I154_Y0.139260.656
132_E135_R0.138890.654
43_N46_I0.138760.653
157_D161_E0.13870.653
14_D160_L0.138690.653
16_V119_P0.138570.652
37_D40_F0.138310.651
16_V19_A0.137970.650
174_A178_D0.137790.649
115_E119_P0.137620.648
65_R69_Q0.137050.645
25_S179_I0.136790.644
28_S180_L0.136120.641
48_I91_L0.136030.641
158_L163_A0.135830.640
105_G126_P0.135370.637
59_Y62_R0.135070.636
63_R95_Y0.13480.635
133_C137_A0.13420.632
9_G111_A0.133870.630
18_L63_R0.132240.623
81_P110_I0.131050.617
56_D102_R0.131010.617
169_K173_E0.130810.616
12_G16_V0.130710.615
58_Q64_L0.130610.615
136_F151_E0.130020.612
5_T53_L0.130.612
172_K176_D0.129690.611
87_A98_R0.129140.608
47_I111_A0.128780.606
12_G154_Y0.128510.605
160_L163_A0.128440.605
15_G185_I0.128340.604
17_V64_L0.128210.604
99_S103_P0.12790.602
164_I172_K0.127270.599
55_A176_D0.127120.599
14_D157_D0.126770.597
141_S146_A0.126640.596
20_A49_G0.12660.596
96_T106_V0.126550.596
4_G186_E0.126290.595
5_T38_K0.125980.593
12_G159_S0.124750.587
69_Q73_F0.124630.587
126_P139_I0.124510.586
7_V50_F0.124490.586
64_L92_I0.124280.585
121_L135_R0.123820.583
114_D119_P0.123580.582
93_Q102_R0.123480.581
6_T138_A0.123130.580
154_Y157_D0.122910.579
98_R101_R0.122880.579
5_T51_S0.122640.577
51_S129_S0.122210.575
5_T25_S0.122190.575
92_I124_V0.122080.575
95_Y101_R0.122020.575
97_Y100_G0.121980.574
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
1iruC0.98951000.045
1rypA0.97891000.051
1rypC0.98951000.052
3nzjF0.97891000.058
1iruA0.97891000.06
3h4pA0.96841000.06
1iruG0.98421000.062
1iruB0.97371000.064
1rypE0.97891000.065
1yarA0.97371000.068

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