GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PWWP - PWWP domain
Pfam: PF00855 (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: CL0049
Length: 86
Sequences: 890
Seq/Len: 10.35
HH_delta: 0.047 (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_W80_I0.373062.436
7_V19_A0.35072.290
9_A19_A0.329242.150
8_W16_W0.295951.932
43_G82_E0.274271.791
76_F80_I0.27021.764
41_F48_A0.264531.727
38_L47_Y0.256761.676
53_S79_A0.240061.567
7_V18_P0.239021.560
10_K15_P0.236551.544
21_V37_V0.233191.522
58_F83_A0.228761.494
24_P38_L0.210551.375
10_K18_P0.205221.340
45_N82_E0.20161.316
10_K14_Y0.200131.307
10_K16_W0.199161.300
75_S78_K0.196271.281
58_F62_K0.193641.264
8_W66_K0.193461.263
9_A41_F0.192271.255
52_P74_K0.190261.242
38_L49_W0.179881.174
2_R5_D0.177421.158
12_K54_N0.175751.147
58_F80_I0.173691.134
41_F49_W0.172521.126
25_D38_L0.170511.113
19_A25_D0.170271.112
7_V10_K0.170051.110
63_E67_K0.169481.106
68_K71_K0.168831.102
11_L14_Y0.163871.070
41_F46_D0.163851.070
61_F64_K0.163851.070
58_F76_F0.16311.065
74_K77_R0.162241.059
9_A55_I0.162021.058
60_E84_E0.160581.048
58_F84_E0.15871.036
9_A13_G0.157341.027
10_K39_V0.155231.013
41_F80_I0.153141.000
8_W61_F0.150850.985
61_F68_K0.150020.979
43_G80_I0.147710.964
41_F47_Y0.147680.964
60_E67_K0.147110.960
11_L22_C0.14620.955
30_K53_S0.143970.940
26_E33_K0.142810.932
72_K77_R0.142760.932
74_K78_K0.14080.919
12_K17_W0.140090.915
67_K74_K0.135050.882
80_I84_E0.134990.881
16_W44_D0.134970.881
51_K75_S0.134880.881
37_V74_K0.134550.878
26_E34_D0.134080.875
6_L42_F0.134020.875
4_G20_R0.132260.863
9_A48_A0.131540.859
37_V52_P0.130950.855
11_L41_F0.130680.853
46_D54_N0.130230.850
55_I76_F0.128660.840
21_V36_H0.127910.835
67_K71_K0.127780.834
3_P24_P0.127710.834
5_D10_K0.126950.829
19_A22_C0.126150.824
15_P18_P0.125940.822
8_W58_F0.125050.816
73_R77_R0.124870.815
78_K82_E0.124120.810
71_K74_K0.123670.807
23_D38_L0.120970.790
26_E29_K0.120090.784
5_D44_D0.119880.783
40_R46_D0.119450.780
22_C27_K0.118980.777
20_R50_V0.118360.773
8_W59_S0.1180.770
44_D72_K0.117670.768
20_R26_E0.117620.768
36_H49_W0.117450.767
59_S63_E0.116770.762
30_K67_K0.115870.756
3_P11_L0.115820.756
62_K83_A0.11550.754
56_K65_L0.114510.748
14_Y41_F0.113670.742
11_L16_W0.112870.737
65_L81_E0.112650.735
48_A54_N0.112380.734
35_G52_P0.112020.731
6_L12_K0.111750.730
66_K75_S0.111710.729
37_V42_F0.111650.729
31_K84_E0.111350.727
25_D47_Y0.110620.722
55_I59_S0.110530.722
55_I62_K0.109840.717
34_D51_K0.109770.717
34_D64_K0.109750.717
10_K19_A0.109470.715
48_A72_K0.10920.713
13_G54_N0.10850.708
15_P46_D0.108280.707
51_K81_E0.10820.706
38_L41_F0.107370.701
32_R39_V0.107330.701
20_R23_D0.107120.699
39_V45_N0.106970.698
24_P45_N0.106870.698
8_W62_K0.106540.696
4_G18_P0.106470.695
51_K61_F0.106270.694
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
3llrA199.80.047
4fu6A0.965199.80.05
2daqA199.80.062
1khcA199.80.064
1ri0A0.965199.80.09
2l89A199.80.09
3qbyA0.965199.80.103
2gfuA199.80.114
1h3zA199.80.119
3pfsA199.70.163

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