GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FBA_3 - F-box associated domain
Pfam: PF08268 (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: CL0162
Length: 129
Sequences: 1408
Seq/Len: 10.91
HH_delta: 0.828 (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_Y79_Y0.4413.629
62_Y65_Q0.233571.922
24_S33_R0.214961.769
25_F30_E0.213391.756
72_D86_K0.203521.675
25_F32_F0.20131.657
53_Y58_A0.190521.568
4_I22_I0.188041.548
51_I58_A0.18551.527
10_W32_F0.180981.489
24_S30_E0.18041.485
102_C118_A0.174441.436
56_K77_E0.172221.417
7_V76_L0.171451.411
10_W83_E0.163521.346
115_I118_A0.155471.280
50_L92_P0.154691.273
56_K79_Y0.152681.257
31_K73_I0.149351.229
73_I86_K0.149181.228
86_K89_I0.148831.225
37_L48_S0.148161.219
8_L55_G0.148031.218
106_F116_V0.146151.203
6_G113_G0.145461.197
35_I70_S0.145181.195
62_Y71_I0.14461.190
10_W23_V0.143281.179
20_N42_Y0.142971.177
114_E118_A0.141961.168
10_W53_Y0.141811.167
52_E56_K0.14161.165
11_L23_V0.136941.127
57_L90_V0.135031.111
3_C22_I0.134751.109
77_E83_E0.134261.105
106_F115_I0.133031.095
28_R51_I0.132761.093
14_S18_D0.132191.088
78_D83_E0.132151.088
59_L110_T0.131941.086
94_S97_H0.131761.084
7_V73_I0.131411.082
9_Y24_S0.130221.072
14_S34_F0.13021.072
13_W20_N0.128561.058
24_S35_I0.128181.055
3_C8_L0.127131.046
47_S63_N0.126841.044
48_S59_L0.126511.041
21_V35_I0.126391.040
110_T115_I0.12611.038
26_D95_W0.125741.035
79_Y82_Q0.123251.014
23_V61_S0.122921.012
21_V37_L0.121611.001
42_Y45_D0.121270.998
105_S109_V0.121010.996
75_V86_K0.120210.989
80_E104_F0.119860.986
43_S65_Q0.119780.986
73_I88_H0.11930.982
50_L85_S0.119130.980
109_V114_E0.118590.976
62_Y103_D0.117990.971
24_S27_V0.117980.971
70_S89_I0.117850.970
46_C65_Q0.114680.944
23_V74_W0.114240.940
50_L97_H0.114020.938
27_V35_I0.113420.933
24_S76_L0.113210.932
25_F77_E0.113140.931
23_V34_F0.112240.924
31_K51_I0.112210.924
109_V117_F0.111750.920
88_H91_L0.111610.919
14_S23_V0.111520.918
90_V111_D0.109950.905
57_L104_F0.109670.903
10_W25_F0.109010.897
30_E81_K0.108140.890
2_I52_E0.108090.890
5_N76_L0.10780.887
9_Y82_Q0.107750.887
7_V21_V0.107330.883
2_I112_T0.107290.883
32_F108_G0.107010.881
34_F79_Y0.106630.878
51_I106_F0.106110.873
49_T52_E0.105870.871
4_I105_S0.105330.867
21_V34_F0.105090.865
22_I87_K0.1050.864
51_I61_S0.104690.862
50_L82_Q0.10430.858
60_V92_P0.104070.857
4_I10_W0.103970.856
72_D88_H0.103580.852
14_S70_S0.103440.851
5_N111_D0.103270.850
26_D33_R0.102450.843
33_R82_Q0.102390.843
26_D86_K0.101370.834
29_S83_E0.101030.831
51_I60_V0.100870.830
4_I7_V0.100660.828
26_D48_S0.099840.822
63_N73_I0.099710.821
109_V116_V0.099440.818
22_I112_T0.099170.816
92_P113_G0.098960.814
108_G117_F0.098960.814
110_T114_E0.098650.812
46_C63_N0.098640.812
12_A77_E0.098470.810
108_G114_E0.097630.804
4_I65_Q0.097280.801
3_C32_F0.097190.800
22_I74_W0.096810.797
31_K64_D0.096280.792
75_V87_K0.095860.789
2_I33_R0.095780.788
26_D81_K0.095630.787
25_F113_G0.095620.787
5_N64_D0.095340.785
25_F108_G0.09520.784
31_K49_T0.095110.783
41_P94_S0.095110.783
6_G29_S0.09480.780
12_A114_E0.094760.780
3_C12_A0.094340.776
4_I52_E0.09420.775
49_T102_C0.094180.775
3_C58_A0.09410.774
80_E117_F0.093710.771
97_H104_F0.093670.771
13_W116_V0.093490.769
80_E95_W0.093380.769
4_I75_V0.092730.763
19_N36_K0.092230.759
48_S64_D0.091620.754
37_L59_L0.091610.754
6_G64_D0.091320.752
37_L81_K0.091060.749
77_E85_S0.090930.748
108_G111_D0.09070.746
11_L37_L0.090590.746
58_A108_G0.090510.745
97_H102_C0.090170.742
60_V111_D0.090140.742
43_S105_S0.09010.742
18_D47_S0.090.741
25_F29_S0.089710.738
71_I117_F0.089660.738
26_D85_S0.089110.733
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
2zwaA0.922591.70.828
4ascA0.883791.60.828
3ii7A0.883790.70.832
2uvkA0.922589.50.836
1zgkA0.751987.70.841
2zwaA0.914786.50.844
1k3iA0.8837860.845
2uvkA0.713285.90.845
2vpjA0.767485.80.846
3ii7A0.891585.40.846
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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