GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ABC_tran - ABC transporter
Pfam: PF00005 (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: CL0023
Length: 137
Sequences: 70052
Seq/Len: 511.33
HH_delta: -0.036 (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
97_L100_R3.50313.461
41_S48_D3.382513.342
90_K95_E3.314093.274
9_K12_E3.159913.122
60_R128_K2.993942.958
76_V109_L2.556182.525
89_L98_L2.472772.443
45_N128_K2.359272.331
84_R126_N2.337712.310
86_E98_L2.312362.285
77_R99_D2.298932.271
95_E98_L2.295192.268
66_Q111_G2.180842.155
77_R85_I2.081672.057
77_R86_E2.06972.045
77_R98_L2.024352.000
87_E91_K1.997361.973
8_I14_V1.870991.848
43_L48_D1.827091.805
28_L131_L1.811141.789
82_D86_E1.805611.784
77_R82_D1.794261.773
10_P128_K1.743481.723
86_E90_K1.662661.643
84_R87_E1.629111.610
30_A37_P1.628231.609
86_E95_E1.610141.591
79_N121_R1.568311.549
100_R108_S1.566031.547
53_D56_E1.558961.540
32_A63_Y1.456011.439
76_V117_L1.45421.437
84_R88_V1.410071.393
83_E87_E1.396661.380
75_T78_E1.362581.346
29_K35_L1.350671.334
88_V120_A1.33851.322
45_N60_R1.326031.310
97_L113_E1.306621.291
16_I27_L1.304661.289
30_A38_D1.287771.272
1_L30_A1.276411.261
64_V119_L1.272761.257
92_L120_A1.270691.255
33_G36_P1.254531.239
20_N116_R1.250961.236
89_L94_L1.246011.231
81_S84_R1.245061.230
32_A131_L1.200331.186
48_D51_D1.183031.169
64_V122_A1.177411.163
10_P45_N1.17661.162
4_V27_L1.172841.159
87_E90_K1.169411.155
68_P114_K1.117211.104
62_G125_K1.116511.103
62_G127_P1.112371.099
6_L27_L1.108671.095
30_A35_L1.105871.093
67_D114_K1.105791.092
74_L78_E1.080041.067
64_V132_L1.05921.046
88_V92_L1.058511.046
75_T79_N1.053021.040
56_E59_R1.05081.038
87_E126_N1.045171.033
47_K60_R1.042341.030
101_K108_S1.038271.026
80_E84_R1.027041.015
88_V123_L1.024151.012
73_G78_E1.016221.004
94_L97_L1.008990.997
109_L117_L1.004970.993
79_N102_I1.003990.992
1_L4_V0.998440.986
1_L27_L0.99520.983
30_A42_I0.979160.967
122_A130_L0.95830.947
83_E86_E0.954560.943
80_E83_E0.950660.939
71_F79_N0.949080.938
101_K107_S0.942040.931
37_P50_S0.940040.929
88_V124_L0.927170.916
53_D57_L0.925530.914
75_T101_K0.92390.913
20_N134_E0.899580.889
89_L95_E0.899120.888
81_S85_I0.899010.888
41_S50_S0.898910.888
82_D85_I0.89760.887
75_T99_D0.891330.881
94_L117_L0.878180.868
86_E89_L0.868720.858
56_E60_R0.858590.848
54_I57_L0.855710.845
115_Q137_N0.853950.844
43_L46_G0.842190.832
36_P50_S0.837590.828
115_Q118_A0.829570.820
88_V91_K0.826740.817
113_E116_R0.821850.812
71_F74_L0.81060.801
29_K63_Y0.801190.792
84_R124_L0.794430.785
79_N118_A0.793530.784
45_N129_L0.786970.778
109_L113_E0.785040.776
110_S113_E0.781920.773
70_L114_K0.778480.769
54_I58_R0.777530.768
7_E43_L0.762410.753
31_L131_L0.755080.746
55_E59_R0.750880.742
42_I49_I0.750510.741
3_N39_S0.743730.735
47_K56_E0.723640.715
71_F132_L0.721260.713
72_P114_K0.712760.704
85_I89_L0.706430.698
62_G122_A0.706090.698
74_L79_N0.702510.694
118_A121_R0.702430.694
6_L14_V0.676580.668
64_V118_A0.676430.668
8_I12_E0.66990.662
68_P118_A0.669220.661
85_I88_V0.668580.661
2_K5_S0.666260.658
96_D113_E0.66410.656
64_V115_Q0.657960.650
65_P68_P0.65420.646
89_L92_L0.644020.636
33_G49_I0.641070.633
91_K95_E0.637910.630
55_E58_R0.636540.629
124_L127_P0.625940.618
65_P118_A0.62170.614
83_E90_K0.621260.614
66_Q137_N0.612250.605
47_K51_D0.608580.601
114_K118_A0.606790.599
73_G136_T0.60590.599
44_I129_L0.600530.593
132_L137_N0.599560.592
68_P115_Q0.592870.586
61_I129_L0.590490.583
96_D100_R0.585320.578
70_L79_N0.581290.574
1_L22_S0.579670.573
97_L109_L0.572980.566
29_K32_A0.572870.566
65_P137_N0.570270.563
31_L42_I0.566280.559
57_L60_R0.564210.557
90_K96_D0.56350.557
43_L47_K0.562180.555
20_N132_L0.562020.555
9_K14_V0.561740.555
102_I117_L0.550710.544
45_N49_I0.55050.544
33_G42_I0.543750.537
85_I124_L0.543630.537
73_G107_S0.543030.536
70_L102_I0.539690.533
7_E10_P0.539430.533
92_L116_R0.532510.526
47_K53_D0.52660.520
44_I49_I0.526140.520
44_I47_K0.524670.518
72_P107_S0.522270.516
33_G37_P0.517970.512
57_L61_I0.517970.512
132_L135_P0.51340.507
93_G96_D0.511880.506
29_K34_L0.510.504
111_G115_Q0.509090.503
65_P111_G0.507170.501
26_T30_A0.507140.501
111_G137_N0.503060.497
92_L123_L0.501480.495
80_E126_N0.50080.495
25_S29_K0.498280.492
27_L31_L0.495090.489
25_S111_G0.488840.483
70_L121_R0.487530.482
58_R61_I0.482560.477
85_I98_L0.481590.476
120_A124_L0.479320.474
70_L117_L0.478090.472
37_P42_I0.47790.472
90_K98_L0.477860.472
41_S51_D0.472070.466
20_N121_R0.471780.466
34_L63_Y0.471590.466
81_S124_L0.465090.459
127_P130_L0.457090.452
65_P69_Q0.456520.451
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
3tuiC0.9708100-0.036
3fvqA0.9708100-0.03
3rlfA0.9562100-0.024
4f4cA0.9927100-0.021
1oxxK0.9708100-0.011
1z47A0.9562100-0.008
2yyzA0.9562100-0.008
3d31A0.9562100-0.008
1v43A0.9562100-0.005
2it1A0.9562100-0.005

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