GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PCNA_C - Proliferating cell nuclear antigen C-terminal domain
Pfam: PF02747 (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: CL0060
Length: 128
Sequences: 2148
Seq/Len: 16.78
HH_delta: 0.048 (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
24_D54_V0.691193.263
10_T100_T0.545752.576
19_K87_N0.525412.480
14_P17_E0.522.455
12_T98_E0.516222.437
10_T102_E0.506392.390
40_S55_E0.499122.356
37_D76_P0.485812.293
35_S78_S0.482952.280
12_T100_T0.480072.266
89_F123_F0.461842.180
11_V36_A0.459162.167
42_I53_E0.457872.161
8_D75_E0.451432.131
25_L52_A0.43692.062
102_E112_E0.435262.055
21_I43_F0.404981.912
33_T78_S0.38891.836
14_P98_E0.347921.642
100_T112_E0.343781.623
35_S42_I0.338211.596
9_A71_I0.327511.546
81_F109_L0.32331.526
42_I55_E0.321761.519
10_T72_E0.293851.387
107_M124_Y0.283411.338
12_T70_E0.273681.292
90_S99_V0.268751.269
14_P97_D0.268031.265
18_F34_I0.263821.245
19_K23_K0.257721.217
96_S113_F0.257161.214
34_I43_F0.256921.213
50_G108_P0.254411.201
34_I41_V0.251271.186
7_Y104_G0.250051.180
37_D42_I0.247241.167
26_S83_L0.245911.161
89_F92_A0.245611.159
23_K91_K0.243591.150
69_I123_F0.243481.149
101_L109_L0.240511.135
33_T80_S0.234851.109
8_D104_G0.233571.103
17_E20_K0.231751.094
11_V101_L0.226131.067
13_M18_F0.223841.057
77_V103_L0.219691.037
89_F125_L0.217811.028
37_D40_S0.211050.996
7_Y102_E0.209210.988
35_S44_S0.208590.985
110_K122_K0.208470.984
31_T80_S0.2040.963
89_F111_L0.202030.954
11_V71_I0.19880.938
86_L111_L0.188340.889
93_A96_S0.187770.886
19_K91_K0.185560.876
41_V69_I0.18210.860
23_K45_A0.18040.852
114_E120_S0.180390.851
8_D107_M0.179880.849
81_F124_Y0.179670.848
71_I76_P0.178730.844
11_V69_I0.178120.841
32_V83_L0.178040.840
29_G83_L0.177010.836
28_V108_P0.176990.835
91_K126_A0.176940.835
56_F69_I0.174710.825
18_F99_V0.17430.823
39_D100_T0.174260.823
47_G50_G0.173290.818
39_D57_K0.173080.817
98_E114_E0.171720.811
23_K126_A0.171390.809
112_E120_S0.171080.808
28_V31_T0.170680.806
12_T114_E0.170470.805
34_I86_L0.170130.803
78_S106_D0.16980.802
35_S76_P0.16710.789
36_A77_V0.167050.789
82_S85_Y0.1670.788
6_E102_E0.165530.781
50_G91_K0.163510.772
44_S50_G0.162170.765
101_L111_L0.161660.763
46_E49_I0.159430.753
16_S94_P0.158340.747
10_T70_E0.158260.747
100_T114_E0.157890.745
86_L125_L0.156810.740
57_K98_E0.156630.739
29_G94_P0.156210.737
33_T97_D0.155450.734
32_V45_A0.154880.731
89_F124_Y0.154380.729
96_S116_A0.153690.725
100_T116_A0.153460.724
48_D75_E0.152520.720
47_G120_S0.152140.718
18_F84_D0.151070.713
110_K126_A0.149140.704
49_I111_L0.148990.703
108_P127_P0.148270.700
23_K87_N0.148050.699
101_L112_E0.147660.697
71_I126_A0.147620.697
15_S97_D0.146570.692
50_G82_S0.146420.691
84_D105_E0.146050.689
39_D70_E0.145490.687
3_P110_K0.144630.683
16_S20_K0.143760.679
112_E122_K0.14370.678
92_A112_E0.14330.676
70_E98_E0.14320.676
16_S111_L0.143080.675
84_D87_N0.141730.669
29_G47_G0.141630.669
3_P127_P0.141210.667
7_Y10_T0.140770.664
72_E119_G0.140530.663
6_E72_E0.140420.663
21_I55_E0.140320.662
79_S103_L0.14020.662
15_S93_A0.140160.662
11_V103_L0.139670.659
31_T124_Y0.139660.659
85_Y125_L0.139550.659
50_G84_D0.138750.655
110_K113_F0.138660.655
12_T42_I0.138250.653
31_T83_L0.137660.650
18_F35_S0.137460.649
13_M41_V0.137250.648
70_E100_T0.137190.648
9_A75_E0.136820.646
36_A69_I0.135390.639
38_K107_M0.135390.639
4_D34_I0.135350.639
99_V124_Y0.135190.638
40_S117_D0.134740.636
16_S51_S0.134730.636
22_C32_V0.134260.634
33_T96_S0.133830.632
6_E10_T0.13380.632
17_E38_K0.133520.630
27_S31_T0.133340.629
35_S53_E0.133290.629
19_K28_V0.132820.627
78_S85_Y0.132660.626
38_K118_G0.132490.625
15_S99_V0.132410.625
102_E110_K0.13240.625
27_S82_S0.132250.624
4_D7_Y0.131750.622
50_G80_S0.131590.621
38_K75_E0.131440.620
15_S96_S0.131080.619
107_M123_F0.130710.617
56_F86_L0.130580.616
24_D80_S0.129580.612
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
3k4xA0.992299.90.048
3fdsD0.953199.90.07
3p91A0.976699.90.076
3lx2A0.960999.90.081
2zvvA199.90.097
3k4xA0.992299.90.097
3ifvA0.937599.90.104
1u7bA199.90.113
1plqA0.992299.90.113
3aizA0.953199.80.125

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