GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Tat - Transactivating regulatory protein (Tat)
Pfam: PF00539 (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: 68
Sequences: 1036
Seq/Len: 15.24
HH_delta: 0.02 (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
40_Q44_L1.382285.507
37_Y44_L0.68222.718
41_L45_Q0.582862.322
29_K45_Q0.562612.241
60_R63_Q0.559212.228
13_L18_H0.512362.041
64_S67_A0.500771.995
14_E17_K0.45571.816
37_Y41_L0.418421.667
63_Q67_A0.416941.661
36_C44_L0.416681.660
12_R17_K0.399411.591
8_P14_E0.380911.518
41_L44_L0.358581.429
37_Y40_Q0.337961.346
24_L28_N0.331681.321
45_Q52_Y0.33151.321
29_K37_Y0.320581.277
60_R66_K0.304561.213
16_W21_S0.299331.193
34_K37_Y0.292681.166
64_S68_H0.283841.131
29_K41_L0.280241.117
63_Q66_K0.276991.104
34_K45_Q0.273651.090
51_S55_K0.272141.084
13_L17_K0.267881.067
60_R67_A0.262181.045
28_N67_A0.25941.033
37_Y45_Q0.257051.024
34_K66_K0.255531.018
34_K40_Q0.247970.988
52_Y60_R0.234920.936
24_L40_Q0.224490.894
65_S68_H0.220220.877
19_P25_T0.214050.853
39_C42_C0.209270.834
34_K41_L0.204470.815
28_N44_L0.203230.810
8_P24_L0.201660.803
14_E40_Q0.20160.803
24_L29_K0.197680.788
41_L52_Y0.196470.783
28_N34_K0.194510.775
60_R64_S0.194220.774
13_L62_P0.192860.768
47_G63_Q0.192860.768
62_P68_H0.187750.748
32_C35_C0.185870.741
35_C42_C0.185750.740
36_C40_Q0.183880.733
37_Y60_R0.183780.732
44_L63_Q0.180040.717
40_Q66_K0.176870.705
14_E24_L0.176750.704
15_P23_P0.176210.702
42_C48_L0.173260.690
15_P20_G0.171490.683
24_L41_L0.171450.683
7_E10_D0.169580.676
9_V16_W0.167070.666
15_P19_P0.166790.665
36_C41_L0.166750.664
11_P18_H0.166610.664
35_C39_C0.16580.661
28_N47_G0.163870.653
41_L67_A0.16320.650
20_G23_P0.162440.647
11_P57_R0.161710.644
41_L64_S0.161680.644
61_T67_A0.161410.643
42_C49_G0.161080.642
31_Y61_T0.16010.638
54_R57_R0.159440.635
24_L67_A0.157990.629
20_G56_R0.157810.629
8_P12_R0.157480.627
39_C48_L0.157080.626
25_T53_G0.156510.624
15_P21_S0.155980.621
21_S56_R0.155540.620
35_C46_K0.155130.618
11_P54_R0.153270.611
27_C31_Y0.149860.597
18_H53_G0.149030.594
13_L51_S0.14810.590
9_V18_H0.146960.586
35_C48_L0.145220.579
13_L60_R0.144610.576
51_S54_R0.143970.574
22_Q56_R0.143970.574
35_C43_F0.143940.573
24_L63_Q0.143170.570
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
3mi9C0.92651000.02
1tacA0.92651000.025
2pk2A0.852999.30.586
1tvsA0.9559990.632
3l4aA0.33827.90.932
3ukxC0.23537.30.933
4b1qP0.33827.10.933
3ur8A0.33823.20.943
3dzyD13.10.943
2a5hA0.852930.944

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