GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ABC1 - ABC1 family
Pfam: PF03109 (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: CL0016
Length: 119
Sequences: 3096
Seq/Len: 26.02
HH_delta: 0.727 (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
13_E31_R1.425724.578
25_A93_F1.189243.819
29_R37_E1.08823.494
100_L118_V0.919682.953
14_F40_V0.821062.637
31_R37_E0.79422.550
12_D33_K0.791712.542
59_R84_R0.790582.539
43_Q93_F0.778242.499
36_E117_K0.740882.379
14_F30_A0.681222.187
19_L39_A0.678672.179
52_E88_L0.650832.090
5_K10_I0.612181.966
36_E119_Y0.605671.945
32_L38_V0.598561.922
12_D31_R0.596341.915
15_D29_R0.582771.871
104_R117_K0.547741.759
5_K9_E0.522621.678
97_A118_V0.502241.613
75_D78_E0.485311.558
22_A90_E0.482661.550
66_E75_D0.47821.536
21_S44_R0.471361.514
89_E95_R0.467991.503
30_A38_V0.46741.501
27_V39_A0.451511.450
105_K108_A0.446731.435
6_P9_E0.431231.385
55_L84_R0.426361.369
66_E77_E0.422561.357
84_R88_L0.410261.317
59_R81_D0.408371.311
11_F14_F0.398981.281
101_E104_R0.383921.233
104_R114_Y0.372591.196
107_F115_V0.368941.185
29_R39_A0.368321.183
63_R77_E0.366581.177
48_E52_E0.364881.172
9_E12_D0.364291.170
32_L119_Y0.360841.159
62_A77_E0.343611.103
43_Q48_E0.336441.080
21_S24_I0.336071.079
102_R106_N0.332151.067
7_I14_F0.330291.061
30_A40_V0.325031.044
12_D34_D0.322011.034
97_A101_E0.319861.027
51_I87_L0.316541.016
20_A23_S0.31120.999
46_G50_Q0.308860.992
9_E33_K0.307990.989
87_L107_F0.305950.982
44_R57_I0.305450.981
104_R108_A0.304620.978
82_E85_D0.303020.973
86_S89_E0.302590.972
3_L11_F0.295140.948
107_F110_S0.288410.926
98_A101_E0.28470.914
3_L10_I0.280540.901
32_L36_E0.275010.883
62_A80_V0.274120.880
101_E117_K0.271660.872
8_D16_P0.271150.871
23_S90_E0.270870.870
59_R77_E0.270280.868
20_A25_A0.269020.864
22_A27_V0.268230.861
58_L80_V0.263560.846
56_R59_R0.260560.837
110_S113_V0.259890.835
102_R105_K0.258580.830
83_F106_N0.256650.824
52_E84_R0.255930.822
60_R64_L0.255840.822
19_L29_R0.253250.813
44_R53_A0.252220.810
57_I61_L0.247490.795
95_R99_N0.245420.788
52_E56_R0.239380.769
7_I10_I0.238740.767
94_R101_E0.238220.765
47_I83_F0.237450.762
94_R98_A0.236090.758
103_F107_F0.236040.758
22_A93_F0.234440.753
100_L115_V0.232610.747
20_A112_R0.23250.747
24_I93_F0.231890.745
6_P33_K0.230150.739
46_G49_E0.230090.739
58_L79_I0.229970.738
51_I91_L0.228060.732
39_A60_R0.228020.732
77_E81_D0.227320.730
75_D82_E0.226930.729
6_P10_I0.2260.726
19_L28_H0.222430.714
24_I43_Q0.221180.710
74_L78_E0.220920.709
2_E43_Q0.220360.708
97_A119_Y0.220220.707
11_F40_V0.220060.707
57_I83_F0.218440.701
98_A102_R0.21720.697
100_L103_F0.21680.696
24_I47_I0.214510.689
104_R115_V0.21340.685
74_L83_F0.212540.682
114_Y117_K0.212170.681
59_R63_R0.210580.676
81_D84_R0.209610.673
48_E56_R0.209140.672
101_E105_K0.205780.661
1_E117_K0.205050.658
47_I76_L0.20330.653
91_L99_N0.201580.647
10_I32_L0.200030.642
51_I57_I0.198510.637
5_K33_K0.198040.636
62_A74_L0.196550.631
8_D12_D0.193260.621
12_D32_L0.19070.612
15_D19_L0.189720.609
44_R83_F0.188960.607
87_L91_L0.188920.607
15_D37_E0.188680.606
58_L62_A0.18750.602
53_A57_I0.186730.600
57_I67_R0.186350.598
107_F113_V0.184940.594
47_I50_Q0.184060.591
15_D39_A0.183990.591
83_F87_L0.183070.588
82_E113_V0.18290.587
103_F115_V0.182720.587
57_I113_V0.181130.582
41_K96_E0.180880.581
83_F91_L0.180850.581
43_Q54_D0.179170.575
79_I82_E0.178970.575
90_E96_E0.178850.574
4_G7_I0.175030.562
61_L65_L0.174640.561
62_A83_F0.17410.559
11_F30_A0.172980.555
99_N102_R0.172890.555
51_I88_L0.172570.554
28_H43_Q0.172410.554
10_I40_V0.172250.553
115_V118_V0.172090.553
45_P54_D0.170490.547
85_D103_F0.170240.547
89_E93_F0.168910.542
1_E111_P0.168840.542
53_A56_R0.166990.536
22_A71_F0.166940.536
32_L35_G0.166780.536
47_I87_L0.166250.534
22_A100_L0.165470.531
12_D101_E0.165380.531
32_L37_E0.164620.529
83_F107_F0.164530.528
79_I90_E0.163730.526
44_R90_E0.162170.521
92_D98_A0.162140.521
13_E37_E0.161630.519
91_L113_V0.161570.519
53_A66_E0.161190.518
12_D35_G0.160330.515
97_A100_L0.160020.514
47_I51_I0.159910.513
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
2y7jA0.949698.40.727
4gyiA0.806797.50.795
2c30A0.882497.30.805
1zthA0.823597.20.808
3byvA0.899296.90.816
3f7wA0.831996.70.823
3d1uA0.899296.20.833
3qd2B0.873996.10.835
3fpqA0.991696.10.835
2x4fA0.899296.10.836
If you are interested in a protein containing this domain,
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