GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TfoX_N - TfoX N-terminal domain
Pfam: PF04993 (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. )
Length: 97
Sequences: 1631
Seq/Len: 16.81
HH_delta: 0.132 (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
8_L89_R0.702413.295
2_R13_E0.614112.881
14_K23_Y0.559512.625
38_Y59_Y0.517482.427
11_V29_F0.484612.273
12_T26_G0.477162.238
21_G28_M0.448842.106
73_V84_L0.344711.617
45_N90_L0.342821.608
90_L93_A0.34271.608
41_V46_R0.339641.593
16_M23_Y0.316291.484
30_A39_L0.31091.458
30_A37_L0.300621.410
56_P72_L0.297871.397
45_N48_E0.292211.371
54_A87_W0.291711.368
53_G77_I0.291231.366
2_R22_I0.279571.311
4_Q89_R0.279031.309
17_F21_G0.27651.297
81_D85_R0.27461.288
83_E86_Q0.274551.288
10_E25_D0.268511.260
17_F31_L0.264441.240
42_D46_R0.261241.225
56_P59_Y0.258171.211
23_Y28_M0.252181.183
41_V71_Y0.248081.164
89_R93_A0.239551.124
13_E20_Y0.235671.106
18_G28_M0.232861.092
15_K20_Y0.231261.085
29_F91_A0.231191.085
40_R67_M0.228541.072
85_R89_R0.22831.071
42_D94_A0.228181.070
69_G94_A0.227821.069
27_K95_A0.222811.045
8_L92_L0.222321.043
36_R72_L0.221761.040
34_D55_R0.214921.008
77_I80_D0.212330.996
24_V95_A0.207550.974
18_G33_C0.204130.958
78_L84_L0.202160.948
42_D45_N0.202110.948
4_Q85_R0.19980.937
80_D83_E0.199240.935
91_A94_A0.197780.928
30_A75_E0.197310.926
56_P67_M0.197130.925
43_P47_E0.195780.918
28_M31_L0.195310.916
55_R58_D0.192370.902
36_R55_R0.191820.900
90_L94_A0.191330.898
23_Y40_R0.189340.888
14_K18_G0.188990.887
4_Q7_P0.188240.883
43_P69_G0.18680.876
57_F68_K0.186660.876
35_D78_L0.186640.876
42_D50_E0.18640.874
80_D86_Q0.184540.866
4_Q8_L0.184280.864
48_E51_A0.184240.864
59_Y69_G0.182350.855
41_V49_F0.181650.852
7_P85_R0.181090.849
46_R71_Y0.175920.825
91_A95_A0.17170.805
29_F92_L0.171470.804
9_G82_E0.169460.795
21_G31_L0.16910.793
5_L13_E0.1690.793
14_K21_G0.168420.790
27_K40_R0.16790.788
36_R74_P0.167520.786
82_E89_R0.167290.785
24_V92_L0.165470.776
57_F84_L0.165360.776
5_L22_I0.16490.774
45_N86_Q0.162850.764
24_V30_A0.16230.761
6_A13_E0.161210.756
16_M21_G0.160880.755
44_E90_L0.160170.751
9_G89_R0.159990.751
6_A11_V0.159290.747
33_C38_Y0.1580.741
67_M92_L0.157660.740
54_A73_V0.156720.735
83_E87_W0.156160.733
87_W90_L0.156150.732
32_V82_E0.155620.730
13_E22_I0.155190.728
85_R88_I0.154250.724
19_G35_D0.154120.723
2_R6_A0.153450.720
55_R67_M0.153210.719
80_D85_R0.153080.718
22_I29_F0.152760.717
56_P68_K0.152560.716
82_E85_R0.151590.711
22_I30_A0.149290.700
38_Y57_F0.149080.699
67_M91_A0.148030.694
42_D90_L0.147620.692
7_P81_D0.147260.691
7_P11_V0.14670.688
35_D75_E0.146450.687
28_M59_Y0.145710.684
3_E26_G0.144390.677
67_M72_L0.14430.677
25_D82_E0.143640.674
17_F38_Y0.142230.667
8_L24_V0.141970.666
74_P77_I0.141670.665
82_E86_Q0.140390.659
3_E45_N0.14030.658
55_R59_Y0.139870.656
49_F92_L0.139650.655
58_D67_M0.139630.655
54_A83_E0.139450.654
22_I32_V0.139330.654
37_L75_E0.139320.654
51_A83_E0.139020.652
86_Q90_L0.138790.651
75_E80_D0.138460.650
48_E90_L0.138370.649
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
2od0A199.70.132
2fkiA0.938199.50.284
2a1vA0.938199.40.315
2kfpA0.938199.40.332
2i8dA0.917595.50.745
2oc6A0.927895.10.753
2kl4A0.917593.70.77
3u7vA0.907254.90.847
1tg7A0.8351270.871
3d3aA0.855724.40.873

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