GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RTP - Replication terminator protein
Pfam: PF02334 (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: CL0123
Length: 122
Sequences: 2916
Seq/Len: 23.9
HH_delta: 0.229 (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
31_R73_V0.81282.828
71_K89_H0.715912.491
27_V70_L0.609162.120
20_K63_E0.606112.109
107_L111_K0.58352.030
68_G93_E0.552441.922
65_V72_Q0.544051.893
31_R89_H0.523551.822
73_V89_H0.495261.723
23_I60_A0.489951.705
28_E95_K0.482741.680
34_G61_L0.454171.580
27_V32_G0.450311.567
26_M32_G0.436781.520
53_N56_E0.409721.426
23_I57_V0.407661.418
34_G58_Y0.400211.392
28_E96_A0.386851.346
74_K86_V0.377491.313
17_A20_K0.377341.313
91_T94_E0.374311.302
61_L88_Y0.366711.276
32_G37_L0.360471.254
33_Y85_I0.357751.245
104_K108_D0.356261.240
21_L99_Y0.353671.231
55_S59_R0.351181.222
100_K114_L0.346561.206
72_Q86_V0.340861.186
65_V70_L0.340631.185
108_D112_G0.3351.166
20_K60_A0.329381.146
101_K105_V0.328181.142
26_M40_E0.326911.137
30_E40_E0.326841.137
92_D95_K0.32471.130
33_Y87_L0.32261.122
32_G36_Q0.319451.111
75_R83_Q0.318971.110
20_K67_D0.318051.107
38_L57_V0.312141.086
64_L69_I0.311251.083
31_R75_R0.309631.077
71_K91_T0.301841.050
21_L114_L0.295681.029
90_F95_K0.290871.012
66_D112_G0.290061.009
19_L52_P0.289041.006
24_I90_F0.288911.005
22_Y110_C0.283770.987
101_K104_K0.283680.987
33_Y58_Y0.274510.955
31_R87_L0.266360.927
97_K100_K0.264820.921
53_N59_R0.263350.916
97_K105_V0.256180.891
110_C114_L0.250530.872
90_F94_E0.249170.867
28_E90_F0.248840.866
55_S58_Y0.247550.861
59_R86_V0.245660.855
60_A64_L0.24390.849
52_P57_V0.243660.848
19_L60_A0.243220.846
105_V108_D0.242970.845
36_Q109_R0.242910.845
34_G54_H0.242020.842
62_H65_V0.239990.835
30_E36_Q0.239190.832
98_L101_K0.237940.828
97_K101_K0.237330.826
35_L85_I0.237230.825
22_Y41_L0.236290.822
100_K104_K0.234540.816
32_G40_E0.234090.814
19_L56_E0.234090.814
97_K112_G0.233330.812
33_Y36_Q0.232650.809
58_Y88_Y0.231830.807
25_T28_E0.227970.793
26_M41_L0.227430.791
26_M37_L0.226260.787
22_Y103_V0.22240.774
39_D106_E0.221820.772
109_R112_G0.217780.758
23_I37_L0.217680.757
69_I93_E0.216530.753
54_H88_Y0.216410.753
101_K108_D0.216260.752
92_D98_L0.215910.751
75_R85_I0.21580.751
33_Y113_L0.214180.745
33_Y82_F0.213710.744
25_T100_K0.213520.743
59_R63_E0.21210.738
96_A100_K0.212010.738
24_I94_E0.211170.735
17_A56_E0.208680.726
22_Y60_A0.208220.724
22_Y113_L0.208030.724
26_M30_E0.206080.717
108_D114_L0.203790.709
95_K108_D0.202550.705
99_Y102_Q0.201210.700
34_G86_V0.197890.689
75_R81_K0.197630.688
62_H70_L0.196430.683
20_K54_H0.196320.683
36_Q40_E0.194110.675
63_E67_D0.193960.675
105_V112_G0.193150.672
111_K115_R0.192780.671
68_G71_K0.191430.666
104_K112_G0.191430.666
26_M29_Q0.18830.655
98_L108_D0.186330.648
35_L88_Y0.186140.648
109_R113_L0.185980.647
17_A41_L0.184550.642
51_R112_G0.1840.640
93_E97_K0.183440.638
112_G115_R0.182990.637
95_K115_R0.18240.635
33_Y55_S0.181320.631
108_D115_R0.18130.631
51_R100_K0.18060.628
26_M63_E0.180360.628
75_R82_F0.180030.626
25_T29_Q0.179660.625
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
1bm9A199.60.229
3f8bA0.926299.20.416
3ri2A0.934499.10.426
1xmaA0.926299.10.43
3f6oA0.868999.10.442
4esbA0.8852990.446
3l7wA0.8607990.447
4esfA0.9016990.448
3nqoA0.8852990.457
2p4wA0.8852990.457

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