GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_mis_repair - DNA mismatch repair protein C-terminal domain
Pfam: PF01119 (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: CL0329
Length: 119
Sequences: 1908
Seq/Len: 16.03
HH_delta: 0.039 (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_S81_E0.725053.677
26_E81_E0.532572.701
60_I76_F0.521552.645
102_D105_E0.430682.184
17_D24_S0.429722.179
1_I28_Y0.41332.096
42_Q76_F0.412752.093
5_F43_F0.402972.044
17_D26_E0.368921.871
58_K107_L0.364461.848
19_E24_S0.34491.749
87_V98_V0.335051.699
53_N103_E0.320491.625
62_E111_E0.311271.579
30_S75_I0.305781.551
30_S35_S0.30211.532
16_I27_G0.291751.480
50_P96_R0.289841.470
46_V98_V0.286531.453
18_S113_A0.284611.443
39_R61_N0.284531.443
35_S72_R0.277561.408
92_H97_E0.271061.375
16_I29_I0.268551.362
45_F79_F0.267581.357
46_V100_F0.265591.347
30_S34_V0.263091.334
83_P86_E0.262771.333
52_E96_R0.261821.328
58_K62_E0.258251.310
19_E22_D0.255771.297
86_E102_D0.250561.271
44_I60_I0.241751.226
36_R40_D0.240621.220
91_V99_R0.240571.220
1_I77_V0.235691.195
60_I114_I0.235121.192
2_A10_A0.233841.186
14_I117_A0.231721.175
54_K58_K0.23061.170
82_I87_V0.227211.152
86_E101_R0.221621.124
69_P72_R0.220421.118
88_D93_P0.218211.107
90_N93_P0.216411.098
9_F75_I0.215041.091
102_D108_N0.214291.087
64_Y74_P0.21421.086
25_I109_L0.210581.068
63_A111_E0.210471.067
26_E79_F0.209511.063
9_F13_L0.209211.061
55_A103_E0.208331.057
18_S116_E0.205551.043
25_I80_I0.205091.040
111_E115_R0.204891.039
100_F107_L0.203731.033
13_L28_Y0.200471.017
90_N95_K0.199531.012
58_K61_N0.198011.004
38_S74_P0.196150.995
66_E69_P0.195370.991
62_E65_R0.192430.976
63_A114_I0.192370.976
5_F41_R0.19210.974
107_L111_E0.192050.974
88_D92_H0.191480.971
59_A63_A0.190330.965
16_I78_L0.190260.965
15_E28_Y0.189980.964
36_R41_R0.189510.961
88_D91_V0.18770.952
88_D95_K0.185810.942
92_H99_R0.185750.942
43_F50_P0.185290.940
5_F75_I0.184840.937
113_A116_E0.18480.937
44_I56_L0.184080.934
18_S109_L0.181550.921
27_G78_L0.181310.920
14_I29_I0.179750.912
7_K11_S0.178960.908
103_E107_L0.177780.902
12_N33_D0.175210.889
1_I13_L0.175090.888
42_Q61_N0.173280.879
23_F80_I0.172320.874
37_S72_R0.171840.872
4_I28_Y0.170650.865
64_Y118_L0.170620.865
53_N100_F0.169410.859
60_I110_I0.168870.856
82_I106_I0.16730.849
48_G81_E0.166270.843
108_N112_E0.165950.842
41_R75_I0.164620.835
12_N15_E0.163530.829
23_F106_I0.163490.829
65_R98_V0.162750.825
7_K10_A0.16230.823
23_F52_E0.1620.822
59_A107_L0.161920.821
112_E116_E0.159970.811
16_I25_I0.15980.810
36_R42_Q0.159760.810
80_I109_L0.15850.804
62_E107_L0.157910.801
80_I110_I0.157580.799
6_G28_Y0.157140.797
6_G10_A0.157040.796
27_G30_S0.156960.796
53_N56_L0.156680.795
12_N31_K0.156580.794
114_I118_L0.154960.786
13_L34_V0.154340.783
56_L60_I0.153460.778
114_I117_A0.151610.769
54_K87_V0.151020.766
25_I78_L0.149810.760
3_Q82_I0.149130.756
48_G52_E0.149060.756
23_F82_I0.148420.753
47_N87_V0.148270.752
48_G79_F0.148040.751
46_V51_V0.146940.745
27_G47_N0.145640.739
111_E116_E0.144710.734
20_D109_L0.144090.731
8_E11_S0.143320.727
13_L77_V0.14310.726
38_S62_E0.142520.723
104_D108_N0.141960.720
12_N116_E0.141890.720
49_R90_N0.141460.717
57_S76_F0.141350.717
1_I50_P0.141090.716
57_S100_F0.138930.705
105_E109_L0.13780.699
8_E117_A0.136650.693
90_N97_E0.136570.693
3_Q44_I0.136550.693
55_A100_F0.136340.691
30_S64_Y0.136240.691
36_R73_Y0.135810.689
39_R73_Y0.13580.689
49_R95_K0.135470.687
12_N52_E0.133560.677
73_Y79_F0.133440.677
34_V51_V0.133360.676
31_K41_R0.132740.673
1_I4_I0.132660.673
59_A114_I0.131510.667
36_R39_R0.130620.662
50_P94_A0.130620.662
63_A99_R0.130280.661
13_L75_I0.130070.660
64_Y117_A0.129410.656
2_A11_S0.12890.654
15_E27_G0.12860.652
4_I118_L0.128290.651
72_R91_V0.128240.650
10_A14_I0.128030.649
108_N111_E0.125750.638
60_I78_L0.125540.637
39_R53_N0.125510.637
2_A7_K0.125060.634
24_S116_E0.124880.633
21_E105_E0.12470.632
66_E70_K0.124620.632
36_R72_R0.124610.632
92_H118_L0.124350.631
23_F109_L0.124030.629
62_E98_V0.123940.629
9_F16_I0.123790.628
8_E14_I0.123720.627
97_E100_F0.123460.626
41_R50_P0.123370.626
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
3na3A0.99161000.039
3h4lA0.99161000.045
1h7sA0.99161000.067
1b63A11000.086
2ioqA0.840398.30.695
1y4sA0.840398.30.7
2o1uA0.840398.20.705
3cwvA0.924497.70.746
1ei1A0.924496.60.796
1s16A0.95896.60.796

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