GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_pol3_a_NI - DNA polymerase III polC-type N-terminus I
Pfam: PF14480 (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: 76
Sequences: 354
Seq/Len: 4.66
HH_delta: 0.747 (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
21_F24_A0.24322.259
21_F56_F0.212181.971
32_H35_S0.208431.936
3_F26_I0.200071.859
31_V38_W0.160131.488
24_A44_S0.158241.470
40_F64_F0.155091.441
55_K58_E0.150261.396
26_I40_F0.142531.324
6_L56_F0.139551.296
57_E72_L0.139151.293
14_D71_E0.133241.238
6_L38_W0.132441.230
38_W67_I0.128511.194
16_L20_L0.125621.167
6_L40_F0.124951.161
10_L48_L0.124021.152
42_L70_V0.122921.142
9_Q38_W0.121681.130
16_L71_E0.120781.122
48_L72_L0.120181.117
3_F6_L0.120011.115
23_D45_P0.119261.108
21_F49_P0.118751.103
11_Q59_K0.117431.091
4_F10_L0.116661.084
56_F72_L0.113021.050
28_K36_R0.111141.033
42_L72_L0.110851.030
28_K41_H0.110351.025
56_F60_L0.110311.025
3_F63_Q0.109621.018
27_E43_S0.109431.017
54_Q57_E0.10931.015
27_E58_E0.109111.014
6_L64_F0.108591.009
29_V59_K0.105740.982
7_L50_F0.105210.977
31_V60_L0.103880.965
51_E57_E0.103610.963
56_F68_A0.103190.959
4_F36_R0.102950.956
11_Q63_Q0.101560.944
3_F32_H0.101050.939
12_I47_I0.100870.937
10_L60_L0.100750.936
63_Q67_I0.099570.925
23_D34_K0.098760.918
7_L26_I0.098720.917
38_W68_A0.098560.916
11_Q14_D0.097980.910
3_F9_Q0.096710.898
29_V40_F0.096670.898
37_K73_I0.096660.898
22_E71_E0.096280.894
64_F67_I0.096050.892
41_H69_K0.095830.890
20_L52_V0.095240.885
22_E34_K0.094820.881
6_L35_S0.094520.878
14_D58_E0.093890.872
47_I50_F0.093890.872
39_R73_I0.093850.872
28_K45_P0.093710.871
32_H37_K0.093650.870
29_V33_K0.09280.862
24_A62_K0.092750.862
34_K71_E0.092540.860
24_A53_Y0.091940.854
67_I70_V0.09150.850
16_L58_E0.091440.850
24_A66_H0.091440.850
61_K72_L0.091420.849
52_V59_K0.091340.849
31_V48_L0.090690.843
9_Q67_I0.089960.836
27_E33_K0.089720.834
29_V44_S0.089620.833
7_L47_I0.089340.830
21_F59_K0.08930.830
6_L9_Q0.089120.828
24_A42_L0.089120.828
24_A48_L0.08910.828
54_Q71_E0.088790.825
29_V62_K0.088230.820
16_L35_S0.088060.818
49_P52_V0.087760.815
37_K71_E0.087220.810
58_E62_K0.086920.808
15_E21_F0.086570.804
33_K43_S0.086210.801
8_K63_Q0.086170.801
22_E73_I0.085540.795
43_S54_Q0.085540.795
14_D33_K0.085210.792
40_F67_I0.085010.790
20_L58_E0.0850.790
5_E55_K0.084730.787
56_F66_H0.084690.787
20_L36_R0.084550.786
34_K45_P0.084310.783
60_L69_K0.084240.783
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
2ayaA0.894744.90.747
2wssS0.947423.90.778
2lnaA0.960511.80.806
3lnoA0.986810.20.812
3cvzA0.89479.70.813
1abvA0.81589.60.814
1deqA0.85539.30.815
2z51A0.86847.50.822
2p3pA0.81586.10.829
4h7wA0.85535.80.83
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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