GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RAP - RAP domain
Pfam: PF08373 (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: CL0236
Length: 58
Sequences: 453
Seq/Len: 7.81
HH_delta: 0.705 (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
4_D9_Y0.346552.274
2_E23_K0.343922.256
2_E8_H0.307172.015
22_L26_H0.270521.775
10_Y18_G0.260871.711
10_Y17_T0.2541.666
42_W51_K0.234671.540
37_I42_W0.216311.419
8_H20_T0.210021.378
10_Y15_N0.209141.372
27_L34_V0.206911.357
5_G8_H0.206681.356
16_L20_T0.185911.220
2_E20_T0.185151.215
38_P41_E0.18211.195
18_G25_R0.180261.183
26_H29_A0.179351.177
48_R52_I0.175151.149
4_D8_H0.173521.138
17_T24_H0.172381.131
47_S51_K0.17171.126
46_K50_E0.167211.097
12_N27_L0.16461.080
37_I55_L0.164211.077
34_V48_R0.163821.075
3_V8_H0.161741.061
38_P54_Y0.159111.044
18_G26_H0.157571.034
26_H30_L0.15571.022
16_L36_S0.155231.018
25_R31_G0.1551.017
12_N54_Y0.151510.994
16_L48_R0.149890.983
16_L34_V0.148680.975
10_Y13_S0.148010.971
53_E56_K0.147650.969
21_K25_R0.144620.949
18_G21_K0.14210.932
23_K34_V0.141950.931
16_L21_K0.139680.916
27_L31_G0.13750.902
14_N33_K0.137010.899
46_K49_E0.13430.881
15_N21_K0.134080.880
4_D24_H0.129350.849
8_H23_K0.128960.846
28_K50_E0.128380.842
38_P53_E0.127360.836
23_K30_L0.126550.830
32_Y37_I0.126180.828
17_T41_E0.125040.820
21_K24_H0.123390.810
13_S19_S0.122990.807
14_N18_G0.122240.802
9_Y56_K0.12140.796
2_E37_I0.121110.795
24_H36_S0.120540.791
43_N53_E0.120180.788
51_K56_K0.120040.788
43_N46_K0.119880.786
43_N47_S0.119740.786
49_E56_K0.119410.783
35_I38_P0.118190.775
5_G20_T0.116030.761
17_T39_Y0.114480.751
24_H30_L0.114280.750
41_E45_L0.11420.749
7_S13_S0.112850.740
49_E52_I0.111150.729
3_V23_K0.110580.725
22_L41_E0.10980.720
38_P43_N0.107820.707
45_L50_E0.107480.705
22_L25_R0.107270.704
25_R29_A0.107020.702
7_S50_E0.106730.700
7_S26_H0.106280.697
22_L54_Y0.105580.693
44_K52_I0.105580.693
3_V51_K0.105540.692
2_E5_G0.105470.692
15_N33_K0.104540.686
15_N35_I0.103990.682
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
3hrlA0.913895.20.705
3r3pA0.948393.90.724
1cw0A186.90.767
1vsrA186.50.768
3thdA0.93126.70.847
2pk8A0.965521.30.853
1s9rA0.93114.20.864
1h70A0.896613.90.864
1mrzA0.965513.30.866
3d3aA0.93112.40.867
If you are interested in a protein containing this domain,
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