GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AARP2CN - AARP2CN (NUC121) domain
Pfam: PF08142 (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: 85
Sequences: 414
Seq/Len: 4.87
HH_delta: 0.856 (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
63_Q75_I0.262042.116
64_L74_Q0.253742.049
61_V64_L0.203831.646
19_W37_P0.195921.582
66_H69_G0.188121.519
66_H72_D0.184311.489
1_E4_N0.181851.469
77_K80_S0.180211.455
36_D39_D0.17791.437
1_E25_Y0.174861.412
29_D60_S0.174091.406
4_N10_S0.173271.399
30_R51_Y0.17151.385
7_R11_V0.164011.325
24_P59_L0.161551.305
3_L67_I0.158911.283
2_I46_G0.157671.273
14_P59_L0.157281.270
3_L65_V0.154841.251
33_F46_G0.151041.220
4_N8_F0.150921.219
1_E6_L0.144311.166
5_L34_V0.143841.162
64_L75_I0.143091.156
34_V49_K0.142781.153
63_Q74_Q0.142461.151
24_P54_V0.137871.114
1_E30_R0.136471.102
5_L30_R0.135891.098
34_V67_I0.135211.092
17_I56_G0.134881.089
48_L72_D0.134751.088
30_R35_P0.134091.083
8_F11_V0.133721.080
73_F76_S0.132831.073
28_A55_R0.131411.061
11_V15_R0.130741.056
25_Y78_I0.130581.055
62_N74_Q0.130291.052
13_K84_P0.128311.036
69_G72_D0.127461.029
70_V78_I0.127291.028
49_K58_P0.126431.021
27_L70_V0.124591.006
9_I14_P0.123911.001
61_V73_F0.121010.977
5_L9_I0.120360.972
15_R59_L0.120120.970
48_L60_S0.118680.959
51_Y67_I0.117980.953
18_S47_T0.117840.952
61_V75_I0.117810.951
54_V58_P0.11670.943
31_V62_N0.116620.942
29_D37_P0.116360.940
26_M74_Q0.116280.939
60_S63_Q0.115940.936
28_A53_Y0.115570.933
6_L12_Q0.115470.933
53_Y84_P0.11450.925
32_E79_E0.114260.923
24_P57_S0.114210.922
69_G84_P0.114080.921
37_P82_P0.113990.921
64_L73_F0.113150.914
47_T76_S0.112980.912
28_A31_V0.112330.907
73_F77_K0.111950.904
24_P60_S0.110840.895
70_V81_L0.110570.893
2_I48_L0.110.888
24_P72_D0.109820.887
53_Y83_D0.10930.883
17_I83_D0.109290.883
3_L58_P0.109060.881
72_D78_I0.109030.881
28_A67_I0.107850.871
15_R33_F0.107550.869
31_V76_S0.107190.866
35_P50_V0.106710.862
64_L78_I0.105480.852
5_L84_P0.105280.850
50_V76_S0.104450.844
47_T73_F0.104020.840
38_E74_Q0.103550.836
27_L50_V0.102550.828
4_N56_G0.102530.828
27_L57_S0.10210.825
32_E84_P0.101660.821
12_Q66_H0.101020.816
23_R69_G0.100790.814
21_D64_L0.100710.813
55_R80_S0.100080.808
14_P19_W0.099490.804
18_S22_Q0.099320.802
50_V56_G0.098990.799
6_L62_N0.09730.786
53_Y57_S0.096960.783
29_D55_R0.096170.777
2_I9_I0.095590.772
48_L66_H0.095410.771
33_F48_L0.095120.768
14_P17_I0.094910.767
60_S79_E0.09480.766
14_P79_E0.094570.764
34_V81_L0.094150.760
26_M73_F0.092320.746
6_L77_K0.091950.743
47_T55_R0.091690.741
76_S80_S0.091670.740
12_Q77_K0.091560.739
54_V68_P0.091390.738
14_P25_Y0.091250.737
45_D81_L0.090560.731
6_L31_V0.090190.728
39_D50_V0.089810.725
5_L35_P0.089740.725
26_M62_N0.089680.724
26_M70_V0.088890.718
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
1d2eA0.894188.60.856
3sjyA0.988286.10.861
3avxA0.894180.80.869
2c78A0.894165.80.883
1s0uA0.9882620.886
3mcaA0.870643.70.897
1kk1A0.9882430.897
4gwmA0.717617.50.915
2axcA0.376516.10.916
1wb1A0.894114.60.918
If you are interested in a protein containing this domain,
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