GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MarR - MarR family
Pfam: PF01047 (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: CL0123
Length: 59
Sequences: 47610
Seq/Len: 806.95
HH_delta: -0.078 (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
11_I26_K3.161072.500
19_T22_E2.575882.037
5_Q40_R2.453351.940
24_A31_R2.383081.884
5_Q37_I2.322281.836
42_E49_R2.270351.795
15_N18_I2.050751.622
5_Q44_K1.848121.461
18_I26_K1.819621.439
35_T39_K1.770541.400
20_Q35_T1.653051.307
32_S35_T1.609741.273
31_R35_T1.595071.261
40_R44_K1.593381.260
22_E26_K1.553231.228
18_I22_E1.541911.219
15_N26_K1.529511.209
11_I15_N1.518591.201
11_I27_L1.498091.185
30_S33_T1.480511.171
21_S31_R1.457411.152
8_I37_I1.443641.142
32_S36_R1.439791.138
21_S25_E1.431761.132
8_I34_V1.424661.127
7_R11_I1.389461.099
20_Q31_R1.387091.097
24_A34_V1.362191.077
8_I23_L1.350921.068
39_K43_K1.317061.041
6_F10_R1.277561.010
29_I33_T1.276651.009
33_T36_R1.253580.991
39_K42_E1.248930.988
11_I18_I1.21640.962
22_E25_E1.208090.955
9_L13_Y1.172220.927
11_I14_E1.170720.926
42_E47_I1.13640.899
20_Q38_I1.124790.889
7_R10_R1.109270.877
29_I34_V1.0870.860
30_S36_R1.039750.822
38_I47_I1.021920.808
36_R39_K1.014780.802
36_R40_R0.995620.787
39_K49_R0.978540.774
23_L38_I0.974860.771
12_L47_I0.968880.766
17_G50_E0.958180.758
12_L18_I0.948120.750
9_L46_L0.923320.730
23_L34_V0.906120.717
21_S35_T0.893210.706
20_Q24_A0.886160.701
40_R43_K0.883280.698
33_T37_I0.874160.691
27_L34_V0.813240.643
37_I40_R0.806630.638
7_R27_L0.778210.615
10_R14_E0.762080.603
34_V38_I0.704740.557
21_S24_A0.70230.555
38_I42_E0.663210.524
10_R13_Y0.659110.521
20_Q34_V0.64870.513
13_Y16_G0.634180.501
11_I23_L0.628760.497
15_N22_E0.627440.496
41_L47_I0.624520.494
24_A29_I0.612980.485
41_L46_L0.607250.480
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
1hsjA198.6-0.078
4em2A198.4-0.036
3hsrA198.4-0.035
4hblA198.4-0.031
3k0lA198.4-0.031
2fxaA198.4-0.029
3echA198.4-0.027
1p4xA198.4-0.025
3s2wA198.4-0.025
3e6mA198.4-0.023

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