GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DnaA_N - DnaA N-terminal domain
Pfam: PF11638 (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: CL0494
Length: 65
Sequences: 1533
Seq/Len: 23.58
HH_delta: -0.016 (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
29_P38_L0.610862.308
14_E58_L0.563852.130
30_L41_S0.556382.102
48_K52_E0.554412.094
50_W54_R0.536892.028
17_E21_N0.519921.964
21_N25_K0.436411.649
19_S55_Y0.425971.609
38_L63_L0.421271.591
44_N47_I0.418131.580
29_P32_L0.406681.536
27_L40_L0.399651.510
12_K20_F0.380211.436
9_E12_K0.334371.263
27_L42_V0.32921.244
23_W50_W0.327841.239
28_K41_S0.327761.238
3_I63_L0.32081.212
32_L38_L0.318931.205
31_S39_T0.317151.198
45_E49_D0.310851.174
7_V63_L0.308081.164
42_V51_I0.306851.159
10_R62_A0.297711.125
32_L35_N0.296981.122
11_L24_F0.294411.112
6_K10_R0.293721.110
58_L62_A0.290241.096
18_Q22_T0.288561.090
61_E64_Q0.282931.069
14_E61_E0.28271.068
43_P47_I0.281021.062
5_E9_E0.280371.059
27_L51_I0.279341.055
11_L58_L0.273391.033
44_N50_W0.272411.029
38_L64_Q0.268481.014
16_S19_S0.25620.968
8_L12_K0.251230.949
12_K25_K0.249750.944
10_R13_K0.248060.937
24_F51_I0.244060.922
42_V47_I0.242750.917
46_F55_Y0.241740.913
5_E31_S0.240280.908
2_E31_S0.236020.892
49_D63_L0.23490.887
20_F24_F0.226930.857
55_Y58_L0.223920.846
52_E62_A0.217940.823
58_L61_E0.217890.823
8_L24_F0.217880.823
10_R14_E0.212820.804
23_W26_P0.212170.802
13_K60_E0.209330.791
53_S56_L0.208670.788
16_S44_N0.205940.778
32_L39_T0.205890.778
12_K17_E0.204390.772
19_S22_T0.203810.770
8_L28_K0.202680.766
16_S55_Y0.199440.753
8_L40_L0.194160.734
46_F51_I0.193710.732
49_D52_E0.193670.732
11_L62_A0.192940.729
14_E62_A0.192650.728
8_L25_K0.191620.724
50_W53_S0.188420.712
57_D61_E0.186060.703
23_W55_Y0.186060.703
50_W55_Y0.185370.700
24_F27_L0.181640.686
5_E57_D0.18050.682
9_E25_K0.180360.681
23_W43_P0.179190.677
34_E37_N0.178840.676
31_S35_N0.178750.675
52_E60_E0.178210.673
30_L39_T0.177810.672
4_W8_L0.177560.671
14_E21_N0.177410.670
22_T55_Y0.176760.668
7_V26_P0.175840.664
3_I7_V0.175410.663
60_E64_Q0.175280.662
45_E48_K0.174460.659
18_Q52_E0.171160.647
2_E61_E0.170170.643
4_W7_V0.170110.643
42_V48_K0.169130.639
5_E17_E0.167830.634
12_K16_S0.166890.630
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
2e0gA0.969299.2-0.016
2wp0C0.984699.20.002
2z4sA0.953899.10.012
4iqjM0.892362.80.731
2jmpA0.969217.90.799
3u1hA0.892314.70.806
1u7lA0.969214.60.807
3uduA0.892313.50.809
1cnzA0.892313.40.81
1vlcA0.892312.90.811

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