GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FadR_C - FadR C-terminal domain
Pfam: PF07840 (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: CL0388
Length: 164
Sequences: 8892
Seq/Len: 54.22
HH_delta: 0.341 (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
43_R138_P2.162423.433
133_D136_Q2.055523.263
36_N40_I1.67512.659
29_N88_P1.469742.333
58_A130_E1.36652.169
50_P53_V1.34592.136
35_T146_I1.344842.135
128_A136_Q1.291722.050
47_K134_Y1.17161.860
32_S44_Y1.138881.808
136_Q140_V1.09551.739
49_N53_V1.082221.718
66_D69_A1.07511.707
57_L130_E1.065421.691
54_L130_E1.063141.688
138_P142_R1.062261.686
33_A93_I1.043971.657
80_R83_F1.013591.609
78_F122_Y1.0111.605
83_F91_G0.986381.566
29_N89_I0.981491.558
56_I80_R0.979121.554
127_E131_K0.975651.549
39_P138_P0.962031.527
39_P142_R0.960241.524
42_I141_V0.957411.520
43_R135_D0.939641.492
139_D143_Q0.922121.464
121_F144_Y0.914741.452
53_V86_G0.904591.436
79_R95_N0.896011.422
43_R134_Y0.882991.402
41_Y82_A0.853251.354
40_I43_R0.852561.353
82_A94_L0.841111.335
121_F147_E0.840051.333
42_I137_V0.833691.323
125_L141_V0.828591.315
123_R127_E0.821561.304
134_Y138_P0.816441.296
35_T142_R0.809261.285
124_E140_V0.808691.284
29_N87_N0.799751.269
131_K136_Q0.792191.257
81_L129_C0.791651.257
42_I46_V0.777881.235
92_L96_G0.758141.203
53_V84_A0.75721.202
74_D78_F0.750051.191
32_S87_N0.742411.178
76_Q80_R0.737521.171
80_R84_A0.732851.163
126_L130_E0.73151.161
34_R38_S0.723221.148
142_R146_I0.720461.144
136_Q139_D0.71821.140
89_I100_L0.709711.127
35_T39_P0.706331.121
39_P43_R0.701521.114
49_N84_A0.697161.107
35_T149_G0.670741.065
77_L126_L0.670191.064
85_S91_G0.664551.055
93_I96_G0.66381.054
128_A133_D0.655881.041
72_E76_Q0.653141.037
79_R83_F0.65141.034
125_L140_V0.642241.019
64_E123_R0.637131.011
135_D139_D0.633881.006
49_N129_C0.630561.001
73_F76_Q0.630131.000
46_V134_Y0.628960.998
28_D149_G0.617180.980
124_E143_Q0.614550.976
100_L103_R0.613390.974
62_K76_Q0.610380.969
69_A73_F0.606670.963
120_N124_E0.597960.949
60_L63_L0.597670.949
122_Y144_Y0.591290.939
25_E29_N0.588850.935
54_L57_L0.588470.934
124_E136_Q0.587140.932
91_G95_N0.586480.931
49_N54_L0.582540.925
34_R145_G0.577610.917
32_S48_N0.574920.913
46_V132_G0.569950.905
89_I93_I0.569660.904
74_D122_Y0.567570.901
33_A89_I0.566630.899
78_F144_Y0.552640.877
26_L89_I0.549720.873
127_E130_E0.541590.860
125_L137_V0.541030.859
46_V129_C0.539250.856
44_Y87_N0.536460.852
31_L148_S0.532990.846
59_E62_K0.527550.837
42_I134_Y0.527270.837
45_A84_A0.521650.828
103_R106_R0.521040.827
89_I92_L0.515630.818
40_I90_Y0.514720.817
128_A140_V0.514160.816
54_L58_A0.510170.810
51_E132_G0.507920.806
32_S149_G0.50550.802
140_V143_Q0.500720.795
69_A72_E0.499050.792
125_L144_Y0.497540.790
49_N132_G0.497120.789
119_L123_R0.492970.783
105_G108_Y0.490310.778
61_D123_R0.482710.766
45_A81_L0.478940.760
124_E127_E0.472660.750
139_D142_R0.469630.745
59_E73_F0.46840.744
40_I138_P0.467210.742
51_E55_E0.465210.738
62_K73_F0.46360.736
124_E128_A0.462950.735
100_L104_V0.462760.735
102_S106_R0.462740.735
143_Q147_E0.45840.728
48_N86_G0.450160.715
79_R98_K0.44830.712
38_S78_F0.443950.705
41_Y85_S0.441210.700
79_R91_G0.438570.696
56_I59_E0.432550.687
40_I44_Y0.43160.685
70_F118_A0.430950.684
102_S105_G0.430550.683
46_V137_V0.430010.683
60_L126_L0.428230.680
116_E120_N0.428220.680
53_V57_L0.426630.677
125_L128_A0.42570.676
39_P134_Y0.422240.670
44_Y48_N0.420960.668
146_I150_E0.419370.666
24_P28_D0.418950.665
135_D138_P0.418290.664
33_A41_Y0.414320.658
75_Y98_K0.409330.650
36_N39_P0.406640.645
101_Y104_V0.401480.637
98_K102_S0.400840.636
38_S145_G0.398030.632
30_L89_I0.396490.629
75_Y79_R0.395250.627
104_V108_Y0.391960.622
33_A37_I0.389920.619
25_E86_G0.389170.618
115_R118_A0.389110.618
128_A137_V0.388810.617
30_L97_F0.385880.613
53_V56_I0.384080.610
55_E58_A0.383710.609
141_V144_Y0.381030.605
36_N90_Y0.379780.603
97_F100_L0.379350.602
45_A85_S0.379150.602
43_R47_K0.377960.600
147_E151_I0.37710.599
87_N90_Y0.37520.596
103_R107_Y0.375120.595
53_V83_F0.372930.592
114_A118_A0.36870.585
58_A61_D0.367310.583
44_Y47_K0.367250.583
35_T145_G0.366650.582
33_A87_N0.363620.577
37_I94_L0.363420.577
58_A62_K0.359180.570
82_A98_K0.355870.565
61_D64_E0.35260.560
33_A36_N0.351660.558
95_N98_K0.347670.552
41_Y90_Y0.347060.551
75_Y102_S0.347030.551
32_S36_N0.346360.550
92_L95_N0.345040.548
104_V107_Y0.344340.547
121_F124_E0.343320.545
42_I129_C0.343040.545
28_D32_S0.342050.543
33_A97_F0.340780.541
32_S35_T0.339830.539
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
3sxmA0.817199.80.341
1hw1A199.70.379
3sxyA0.957399.60.407
2hs5A0.981799.60.411
3c7jA199.60.421
3ihuA0.945199.60.431
2di3A0.963499.60.446
2ek5A0.463456.50.885
3by6A0.414625.80.905
3soaA0.975623.60.907

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