GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_pRha - Phage regulatory protein Rha (Phage_pRha)
Pfam: PF09669 (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: 93
Sequences: 974
Seq/Len: 10.47
HH_delta: 0.857 (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
17_N20_R0.913193.475
85_R88_E0.70922.698
23_R54_P0.619022.355
61_D87_N0.590362.246
49_Q53_Y0.568562.163
60_K90_E0.525832.001
17_N41_I0.523781.993
47_D53_Y0.519931.978
65_L76_V0.515431.961
61_D84_E0.454611.730
48_G51_R0.428681.631
37_L41_I0.417361.588
17_N37_L0.407031.549
17_N21_D0.400641.524
20_R41_I0.391151.488
12_G74_K0.39031.485
4_S22_I0.384211.462
4_S15_H0.37911.442
14_R17_N0.37791.438
3_T55_C0.365491.391
45_Y49_Q0.360031.370
19_L23_R0.357411.360
16_K20_R0.346631.319
21_D70_Y0.329291.253
5_R55_C0.329091.252
64_T78_F0.32311.229
36_Q42_E0.317841.209
48_G53_Y0.315151.199
65_L80_A0.312331.188
68_M79_K0.306531.166
85_R90_E0.304461.158
16_K42_E0.30341.154
27_E73_K0.295931.126
7_I58_L0.291971.111
49_Q52_S0.285751.087
46_K52_S0.274411.044
47_D50_G0.27121.032
43_S49_Q0.270081.028
3_T57_L0.264041.005
35_G43_S0.260410.991
19_L54_P0.259370.987
39_F42_E0.256650.977
43_S51_R0.255540.972
59_T62_G0.25310.963
20_R39_F0.252970.963
20_R42_E0.25270.961
62_G65_L0.252360.960
16_K36_Q0.251670.958
88_E91_E0.25110.955
45_Y55_C0.251060.955
13_K21_D0.248860.947
64_T82_Y0.248180.944
17_N35_G0.247180.940
38_N41_I0.246930.940
5_R57_L0.246320.937
77_E81_A0.245710.935
44_K52_S0.24350.926
15_H19_L0.243030.925
64_T87_N0.241130.917
25_L66_L0.240280.914
48_G52_S0.239450.911
81_A84_E0.234050.891
61_D64_T0.228650.870
65_L83_I0.225340.857
60_K64_T0.220260.838
46_K50_G0.218140.830
47_D51_R0.218090.830
43_S53_Y0.21750.828
46_K49_Q0.217310.827
6_E9_E0.213710.813
1_T57_L0.212650.809
45_Y52_S0.210370.800
2_T6_E0.208580.794
71_S89_M0.208150.792
66_L69_G0.207690.790
60_K78_F0.207390.789
86_F89_M0.206860.787
76_V80_A0.206850.787
63_F68_M0.206440.785
6_E10_M0.205340.781
78_F90_E0.203490.774
46_K53_Y0.201970.768
80_A84_E0.201950.768
24_K28_K0.200940.765
68_M82_Y0.199940.761
45_Y53_Y0.198790.756
13_K72_G0.198180.754
64_T68_M0.196220.747
7_I18_V0.193990.738
68_M83_I0.192820.734
11_F75_A0.191920.730
28_K76_V0.190070.723
43_S52_S0.190040.723
47_D52_S0.18960.721
34_F38_N0.187270.713
38_N53_Y0.184880.703
44_K49_Q0.184830.703
68_M78_F0.184150.701
70_Y78_F0.183630.699
35_G38_N0.182860.696
59_T63_F0.182130.693
10_M78_F0.181770.692
84_E88_E0.181750.692
62_G72_G0.181610.691
20_R23_R0.181320.690
3_T6_E0.180510.687
81_A87_N0.180390.686
79_K89_M0.179520.683
87_N90_E0.179390.683
16_K19_L0.178240.678
65_L84_E0.177090.674
6_E90_E0.176830.673
32_P35_G0.175660.668
64_T75_A0.174730.665
78_F83_I0.17310.659
3_T18_V0.172360.656
38_N59_T0.171670.653
27_E50_G0.171010.651
64_T79_K0.170670.649
61_D65_L0.170280.648
2_T5_R0.169980.647
19_L53_Y0.168940.643
38_N42_E0.167810.638
69_G76_V0.167780.638
45_Y48_G0.16770.638
69_G75_A0.167130.636
74_K88_E0.165950.631
45_Y50_G0.16470.627
35_G53_Y0.164610.626
82_Y89_M0.163310.621
17_N32_P0.162990.620
61_D83_I0.162640.619
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
2frhA0.806570.20.857
2qvoA0.709769.60.857
2fxaA0.860268.10.859
3l7wA0.752763.10.863
2fa5A0.860262.60.863
4ijaA0.903262.60.863
4hblA0.82861.90.864
4em2A0.860259.70.865
3k0lA0.860258.80.867
3deuA0.860258.70.867
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