GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ABC_tran_2 - ABC transporter
Pfam: PF12848 (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: 85
Sequences: 4524
Seq/Len: 53.22
HH_delta: 0.588 (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
9_T25_R1.437572.734
17_D21_Q1.221992.324
33_Y37_Q1.211982.305
44_E48_R1.165772.217
39_E42_R1.123652.137
17_D20_E1.057752.012
61_K64_E0.968221.842
1_I10_E0.96461.835
2_E22_K0.94891.805
28_R32_Q0.948171.803
47_I64_E0.90741.726
24_E28_R0.880721.675
1_I8_L0.866271.648
13_G17_D0.861391.638
47_I67_L0.851611.620
45_E48_R0.838431.595
21_Q24_E0.822571.564
20_E24_E0.811561.544
24_E27_E0.797241.516
2_E18_Y0.794921.512
30_E34_E0.779161.482
37_Q40_I0.773671.471
14_N17_D0.751921.430
11_Y25_R0.742751.413
53_K56_K0.741371.410
27_E31_R0.738491.405
64_E68_E0.726981.383
38_K41_K0.689271.311
51_R64_E0.68921.311
40_I67_L0.674061.282
4_E9_T0.631511.201
33_Y36_Q0.629281.197
21_Q25_R0.611611.163
26_R30_E0.605641.152
53_K57_A0.593741.129
39_E43_L0.58951.121
40_I44_E0.579631.102
31_R34_E0.571111.086
43_L66_R0.567431.079
3_L8_L0.56571.076
62_S65_K0.563611.072
23_E27_E0.550541.047
11_Y21_Q0.543131.033
13_G21_Q0.535051.018
40_I72_R0.525621.000
46_F59_Q0.522240.993
50_F53_K0.518430.986
50_F56_K0.512640.975
46_F63_R0.509840.970
65_K68_E0.509440.969
32_Q36_Q0.505840.962
34_E38_K0.505260.961
19_L23_E0.495390.942
63_R66_R0.492390.937
31_R35_K0.489780.932
61_K65_K0.474740.903
52_A55_K0.464010.883
52_A57_A0.462230.879
36_Q70_L0.454750.865
36_Q40_I0.443170.843
28_R31_R0.442080.841
36_Q73_I0.438270.834
39_E66_R0.426510.811
11_Y18_Y0.422930.804
39_E70_L0.42030.799
29_Q32_Q0.413830.787
62_S66_R0.411140.782
51_R57_A0.401030.763
35_K39_E0.400790.762
43_L46_F0.400530.762
44_E72_R0.38580.734
41_K45_E0.37790.719
40_I43_L0.377780.719
35_K38_K0.365120.694
23_E26_R0.363490.691
11_Y17_D0.356640.678
59_Q63_R0.356260.678
47_I68_E0.354030.673
19_L22_K0.34780.662
65_K69_K0.339960.647
27_E30_E0.328910.626
37_Q41_K0.328030.624
32_Q73_I0.326850.622
55_K59_Q0.32680.622
46_F50_F0.319270.607
43_L63_R0.317810.604
40_I71_E0.315290.600
41_K44_E0.312490.594
48_R51_R0.310250.590
11_Y15_Y0.306370.583
12_P38_K0.305730.581
16_S82_K0.3050.580
60_A64_E0.303660.578
40_I70_L0.303240.577
58_K63_R0.302890.576
73_I76_P0.297510.566
29_Q75_K0.29550.562
25_R29_Q0.295260.562
16_S20_E0.295240.562
15_Y19_L0.294990.561
51_R58_K0.290470.552
45_E49_R0.287910.548
33_Y75_K0.287280.546
55_K58_K0.285840.544
66_R69_K0.285210.542
57_A61_K0.282340.537
72_R75_K0.280090.533
29_Q73_I0.279180.531
19_L34_E0.277370.528
55_K62_S0.272620.519
58_K61_K0.271180.516
36_Q39_E0.269720.513
69_K74_E0.269070.512
57_A60_A0.268670.511
2_E9_T0.268640.511
12_P17_D0.268370.510
67_L71_E0.267240.508
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
4finA0.976596.60.588
2ve7A0.894112.10.838
3ktaB0.411810.60.841
3i2vA0.34125.60.859
2xzeA0.50594.80.863
3utnX0.37654.60.864
2wujA0.55294.60.864
3aayA0.35294.20.867
2xlkA0.341240.868
3fybA0.49413.80.869
If you are interested in a protein containing this domain,
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