GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HATPase_c_4 - ATP-dependent DNA helicase recG C-terminal
Pfam: PF13749 (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: 89
Sequences: 1115
Seq/Len: 12.53
HH_delta: 0.057 (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
9_F12_R0.455982.489
46_E50_R0.371732.029
78_F87_V0.340561.859
66_D70_E0.337631.843
16_S86_K0.336521.837
26_T29_N0.322451.760
9_F14_E0.316091.725
79_E86_K0.313921.713
61_I78_F0.305681.669
67_A70_E0.30531.666
69_K75_P0.298991.632
79_E88_T0.297741.625
78_F85_F0.293681.603
8_I13_I0.27781.516
22_P38_R0.269861.473
12_R88_T0.269791.473
49_R56_R0.26771.461
17_N68_M0.264591.444
14_E86_K0.261971.430
19_G40_R0.259921.419
64_I87_V0.252231.377
55_E59_S0.251891.375
47_I50_R0.241661.319
80_E85_F0.240681.314
7_E16_S0.238781.303
7_E14_E0.238271.301
20_G80_E0.228241.246
24_G55_E0.223161.218
68_M73_L0.218361.192
68_M72_G0.218151.191
39_P56_R0.213521.165
4_I18_P0.21031.148
43_L46_E0.205471.122
21_L85_F0.204921.119
68_M76_P0.202451.105
46_E49_R0.199931.091
21_L25_V0.198141.082
20_G27_I0.195651.068
48_F59_S0.191751.047
4_I15_I0.188991.032
14_E88_T0.180070.983
42_P45_A0.17920.978
49_R54_V0.178950.977
47_I57_F0.178650.975
6_I15_I0.177380.968
35_G62_R0.17510.956
61_I85_F0.173470.947
37_S59_S0.173120.945
7_E57_F0.168990.922
68_M71_A0.168720.921
3_P51_L0.167730.916
65_F76_P0.166410.908
84_S87_V0.165690.904
59_S63_R0.164690.899
6_I34_G0.163960.895
25_V35_G0.159880.873
65_F68_M0.15850.865
21_L26_T0.157510.860
9_F47_I0.156320.853
48_F56_R0.155890.851
70_E77_E0.155340.848
41_N64_I0.153660.839
66_D69_K0.153490.838
7_E10_D0.152140.830
4_I84_S0.151710.828
73_L76_P0.151530.827
76_P87_V0.150960.824
55_E58_G0.150240.820
45_A49_R0.150190.820
39_P45_A0.149870.818
62_R65_F0.149130.814
19_G44_I0.148920.813
54_V57_F0.148710.812
70_E86_K0.14750.805
20_G24_G0.146690.801
61_I64_I0.146320.799
17_N59_S0.145150.792
56_R63_R0.144990.791
38_R49_R0.14460.789
80_E83_N0.143720.784
45_A56_R0.143450.783
32_L75_P0.142830.780
39_P62_R0.142420.777
33_L69_K0.142240.776
53_Y75_P0.14180.774
6_I37_S0.140890.769
35_G61_I0.140850.769
48_F55_E0.140750.768
69_K72_G0.140330.766
32_L35_G0.139920.764
72_G81_D0.139050.759
33_L53_Y0.138490.756
27_I70_E0.138280.755
18_P59_S0.13710.748
10_D69_K0.136960.748
8_I47_I0.136830.747
77_E86_K0.136580.746
10_D79_E0.135960.742
44_I48_F0.135730.741
69_K74_P0.135620.740
28_E33_L0.135480.739
48_F54_V0.135250.738
3_P13_I0.134670.735
64_I68_M0.134660.735
48_F51_L0.134630.735
25_V59_S0.134030.732
21_L78_F0.13380.730
81_D84_S0.133150.727
50_R56_R0.132880.725
52_G87_V0.132750.725
22_P39_P0.132340.722
65_F69_K0.132280.722
40_R63_R0.132010.721
17_N37_S0.131870.720
44_I52_G0.131450.718
49_R84_S0.130270.711
17_N23_G0.130120.710
48_F53_Y0.129470.707
65_F75_P0.129230.705
6_I23_G0.128730.703
29_N62_R0.128620.702
32_L77_E0.127550.696
15_I39_P0.127470.696
52_G67_A0.127130.694
49_R57_F0.12630.689
77_E88_T0.126150.689
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
3lmmA0.966399.90.057
3jz3A0.842766.40.849
3d36A0.831548.40.863
4ew8A0.820243.50.867
2q8gA0.831540.90.869
3a0yA0.820238.40.871
2e0aA0.831530.30.877
1y8oA0.831529.10.879
3ehhA0.685428.80.879
2btzA0.831528.60.879

Page generated in 0.0277 seconds.