GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PolyA_pol_RNAbd - Probable RNA and SrmB- binding site of polymerase A
Pfam: PF12627 (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: 64
Sequences: 3323
Seq/Len: 51.92
HH_delta: 0.053 (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
34_I43_A1.218893.098
9_E50_L0.976922.483
28_R32_E0.89672.279
29_E33_K0.839682.134
20_S55_Y0.742321.887
48_D61_D0.74231.887
54_E61_D0.696651.771
18_L21_K0.684081.739
26_R30_E0.661371.681
4_I8_T0.642271.632
15_N18_L0.634151.612
29_E32_E0.627861.596
9_E49_E0.621621.580
51_G54_E0.52431.332
46_L49_E0.503521.280
1_G42_R0.493071.253
16_A52_L0.492581.252
12_I15_N0.477231.213
5_E8_T0.475121.208
22_I40_P0.471511.198
1_G39_N0.471321.198
46_L50_L0.470721.196
10_E14_E0.467391.188
4_I9_E0.441341.122
45_K49_E0.433941.103
48_D53_L0.427231.086
12_I52_L0.42551.081
47_L53_L0.425271.081
9_E13_K0.420371.068
32_E36_S0.413441.051
31_L43_A0.41181.047
39_N42_R0.411481.046
41_S45_K0.396851.009
31_L56_I0.396541.008
3_K9_E0.396391.007
4_I46_L0.374770.952
6_P10_E0.373880.950
23_S27_I0.372730.947
31_L44_F0.372030.946
24_K28_R0.36960.939
47_L52_L0.369410.939
30_E33_K0.363970.925
26_R29_E0.348840.887
9_E46_L0.348730.886
33_K37_S0.346140.880
13_K50_L0.335310.852
19_L52_L0.334650.851
16_A51_G0.333650.848
8_T12_I0.332620.845
3_K6_P0.324510.825
12_I53_L0.320320.814
19_L22_I0.319960.813
10_E13_K0.315760.802
23_S30_E0.309890.788
23_S33_K0.309260.786
23_S26_R0.308790.785
3_K42_R0.30540.776
57_F60_L0.303160.770
45_K48_D0.298280.758
48_D54_E0.291680.741
16_A55_Y0.291150.740
31_L57_F0.28320.720
24_K56_I0.282480.718
45_K54_E0.27840.708
12_I22_I0.274160.697
13_K51_G0.272730.693
53_L57_F0.267260.679
4_I53_L0.266030.676
13_K16_A0.263880.671
19_L23_S0.262280.667
43_A47_L0.261060.663
19_L55_Y0.260030.661
6_P14_E0.253270.644
42_R45_K0.249930.635
27_I30_E0.249790.635
17_E55_Y0.247060.628
38_P41_S0.242210.616
42_R46_L0.239970.610
27_I56_I0.239620.609
3_K46_L0.235780.599
6_P9_E0.234670.596
12_I50_L0.234310.595
26_R33_K0.233580.594
22_I27_I0.232870.592
1_G9_E0.232780.592
31_L34_I0.230920.587
7_E42_R0.230630.586
25_E30_E0.230480.586
36_S39_N0.229530.583
1_G53_L0.227760.579
3_K45_K0.224160.570
23_S56_I0.22230.565
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
3aqlA199.10.053
1ou5A199.10.083
1vfgA1990.09
3h38A1990.109
1miwA0.9844990.111
2f3oA0.921932.60.782
1r9dA0.937528.50.788
4hkqA0.812526.80.791
3g9kL125.70.792
4etsA124.50.794

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