GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Multi_Drug_Res - Small Multidrug Resistance protein
Pfam: PF00893 (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: CL0184
Length: 93
Sequences: 13495
Seq/Len: 145.11
HH_delta: 0.105 (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
48_L52_K1.675443.119
74_G80_E1.51542.821
48_L51_K1.275972.375
83_S86_K1.267122.359
73_V77_F1.137262.117
53_L58_A1.104852.057
84_L88_L1.055181.964
20_L47_S1.051081.957
4_L8_L0.980291.825
54_P57_V0.936281.743
87_W91_G0.919531.712
75_V82_L0.917821.709
65_L69_G0.82881.543
39_Y43_F0.82511.536
71_T90_I0.786831.465
49_A53_L0.761051.417
74_G78_F0.738651.375
68_V90_I0.714981.331
41_L45_F0.713851.329
32_T35_A0.711151.324
14_V18_I0.70361.310
84_L87_W0.674911.256
46_L50_L0.671861.251
76_F79_G0.654771.219
53_L57_V0.65181.213
69_G73_V0.63661.185
44_Y48_L0.625851.165
82_L87_W0.61891.152
7_L10_I0.610151.136
35_A40_G0.595421.108
34_L38_G0.594761.107
83_S87_W0.587731.094
19_A22_A0.573641.068
16_G47_S0.572471.066
16_G20_L0.57091.063
50_L58_A0.569331.060
15_V19_A0.564131.050
43_F47_S0.560811.044
86_K90_I0.553141.030
54_P58_A0.549941.024
22_A25_G0.547361.019
13_E66_G0.538921.003
45_F49_A0.531850.990
6_L10_I0.531250.989
72_L76_F0.522630.973
47_S51_K0.521840.971
20_L24_H0.517040.962
24_H27_T0.514790.958
49_A58_A0.514470.958
56_S59_Y0.509640.949
14_V69_G0.506530.943
21_K55_L0.503450.937
45_F48_L0.501510.934
40_G44_Y0.497220.926
89_G92_L0.488860.910
70_V74_G0.485990.905
5_F8_L0.477070.888
71_T82_L0.476990.888
23_S26_F0.47650.887
37_V41_L0.475730.886
49_A52_K0.474960.884
82_L86_K0.474030.882
17_T59_Y0.473720.882
73_V76_F0.469090.873
72_L75_V0.467910.871
61_V65_L0.465140.866
81_S86_K0.461420.859
10_I14_V0.461080.858
50_L54_P0.454140.845
29_L32_T0.449710.837
17_T55_L0.448910.836
39_Y67_I0.445650.830
85_S88_L0.444890.828
80_E86_K0.44260.824
74_G77_F0.44040.820
16_G49_A0.438760.817
21_K25_G0.438720.817
87_W90_I0.434970.810
18_I55_L0.433830.808
11_L15_V0.428330.797
81_S84_L0.427950.797
71_T74_G0.423620.789
16_G46_L0.422020.786
20_L23_S0.421980.786
50_L55_L0.419920.782
47_S64_G0.418370.779
30_I33_I0.417330.777
33_I37_V0.414060.771
71_T75_V0.411670.766
55_L59_Y0.407730.759
10_I13_E0.406250.756
33_I36_V0.401560.748
30_I34_L0.401370.747
17_T46_L0.399320.743
23_S27_T0.398980.743
13_E17_T0.397060.739
60_A64_G0.395530.736
56_S60_A0.39550.736
16_G63_T0.393790.733
73_V78_F0.384260.715
35_A39_Y0.377920.703
49_A69_G0.376730.701
17_T50_L0.37490.698
39_Y50_L0.373990.696
10_I70_V0.373250.695
75_V80_E0.372780.694
75_V81_S0.372640.694
39_Y42_S0.372120.693
7_L11_L0.371370.691
88_L92_L0.370540.690
81_S85_S0.369090.687
63_T67_I0.364740.679
49_A64_G0.364060.678
16_G19_A0.363920.677
46_L61_V0.363830.677
8_L12_F0.356250.663
71_T86_K0.355450.662
53_L60_A0.354040.659
12_F63_T0.353270.658
16_G39_Y0.352750.657
42_S63_T0.351880.655
28_Q31_P0.351740.655
6_L13_E0.351330.654
35_A55_L0.349810.651
13_E73_V0.349440.650
9_A13_E0.349250.650
6_L46_L0.347590.647
57_V60_A0.346740.645
86_K89_G0.346470.645
16_G38_G0.345070.642
83_S88_L0.343120.639
46_L66_G0.34130.635
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
2i68A199.10.105
3b5dA1990.136
2cfqA0.97851.90.881
3rkoM0.38711.60.886
3o7qA0.97851.40.889
4dx5A0.88171.30.891
2wswA0.88171.30.891
3ne5A0.88171.30.891
3pjzA11.20.892
3w9iA0.88171.10.895

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