GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_5 - AAA domain (dynein-related subfamily)
Pfam: PF07728 (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: CL0023
Length: 139
Sequences: 33789
Seq/Len: 243.09
HH_delta: 0.185 (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
70_V120_T2.175173.095
45_Y54_F2.010882.861
74_I119_A1.528462.175
58_P95_Q1.506342.143
75_N121_M1.425122.028
93_R102_E1.420822.022
95_Q102_E1.361131.937
16_A118_I1.22421.742
18_E22_L1.223031.740
93_R104_K1.205161.715
27_V70_V1.154181.642
58_P61_R1.110331.580
99_G103_I1.081051.538
94_I105_E1.064561.515
56_D60_V1.041351.482
76_R123_P1.023031.456
98_E101_E1.021151.453
18_E21_A1.006931.433
73_E122_N1.003591.428
75_N122_N0.969361.379
98_E106_P0.940381.338
14_T18_E0.911371.297
33_S37_T0.904561.287
16_A70_V0.902811.285
57_G60_V0.896911.276
50_G54_F0.892971.271
13_T87_S0.887211.262
55_K58_P0.887211.262
77_A81_V0.84251.199
33_S36_T0.836651.191
7_P10_T0.830161.181
85_L89_L0.82181.169
98_E103_I0.805141.146
98_E105_E0.803681.144
68_I116_R0.800671.139
26_P67_G0.79581.132
87_S91_E0.792581.128
98_E102_E0.784171.116
14_T17_R0.783051.114
17_R29_R0.779891.110
45_Y99_G0.776961.106
83_E86_L0.775041.103
50_G53_E0.774311.102
100_G103_I0.772761.100
32_C71_L0.772661.099
103_I106_P0.767141.092
56_D61_R0.764241.087
68_I118_I0.763371.086
59_L62_A0.749261.066
100_G106_P0.747541.064
51_Q55_K0.7411.054
59_L88_L0.736121.047
20_A27_V0.735011.046
46_D53_E0.731851.041
80_E84_S0.729031.037
69_L117_I0.727521.035
35_D39_E0.718671.023
51_Q54_F0.718331.022
13_T72_D0.716991.020
40_D44_S0.716371.019
53_E57_G0.710381.011
99_G106_P0.709961.010
101_E104_K0.703311.001
17_R91_E0.69170.984
28_I67_G0.688750.980
44_S47_P0.683170.972
99_G102_E0.680390.968
87_S90_E0.679750.967
94_I104_K0.674730.960
3_L121_M0.673270.958
101_E105_E0.671050.955
17_R21_A0.664720.946
4_L16_A0.656990.935
58_P62_A0.653930.931
25_R66_G0.651350.927
86_L89_L0.646440.920
82_L86_L0.643830.916
6_G12_K0.635480.904
98_E104_K0.631590.899
37_T40_D0.617850.879
39_E43_G0.617320.878
88_L94_I0.616970.878
23_L68_I0.616640.877
81_V84_S0.612250.871
86_L90_E0.608530.866
55_K61_R0.606350.863
41_L47_P0.60310.858
75_N123_P0.601310.856
36_T39_E0.600460.854
6_G9_G0.600450.854
28_I32_C0.597530.850
101_E106_P0.59460.846
99_G105_E0.592050.842
5_V124_R0.582980.830
42_I46_D0.580490.826
41_L45_Y0.577850.822
60_V103_I0.577850.822
31_N34_S0.577340.822
3_L119_A0.575530.819
30_I33_S0.575410.819
57_G61_R0.575160.818
34_S37_T0.574320.817
56_D59_L0.569860.811
43_G47_P0.567990.808
92_R95_Q0.565790.805
51_Q57_G0.564990.804
54_F60_V0.56470.804
43_G46_D0.564610.803
102_E106_P0.5640.803
52_F58_P0.560870.798
89_L92_R0.556440.792
55_K59_L0.555480.790
41_L46_D0.55150.785
33_S38_E0.549140.781
99_G104_K0.544750.775
102_E105_E0.544070.774
20_A68_I0.543610.774
5_V121_M0.543420.773
39_E42_I0.540970.770
40_D46_D0.539520.768
2_V5_V0.535550.762
50_G55_K0.532160.757
81_V86_L0.525590.748
46_D54_F0.524080.746
65_K105_E0.521540.742
6_G11_G0.520920.741
66_G116_R0.520880.741
2_V118_I0.519480.739
65_K115_F0.516550.735
78_P81_V0.515660.734
50_G60_V0.512910.730
52_F55_K0.510990.727
67_G115_F0.510320.726
46_D52_F0.507760.723
89_L93_R0.505080.719
84_S87_S0.503240.716
4_L15_L0.500680.712
90_E93_R0.497540.708
51_Q56_D0.495080.704
87_S93_R0.494560.704
33_S39_E0.493860.703
5_V75_N0.493450.702
55_K60_V0.491970.700
6_G10_T0.489710.697
29_R32_C0.48620.692
55_K100_G0.483920.689
35_D38_E0.482180.686
115_F119_A0.481640.685
87_S95_Q0.481410.685
39_E44_S0.479480.682
67_G70_V0.477040.679
116_R119_A0.47560.677
71_L117_I0.475370.676
54_F57_G0.47410.675
38_E42_I0.47360.674
82_L90_E0.472820.673
38_E84_S0.469280.668
8_P122_N0.468890.667
41_L44_S0.468070.666
54_F61_R0.463690.660
52_F56_D0.462020.657
4_L13_T0.458950.653
57_G62_A0.457040.650
84_S88_L0.455650.648
33_S83_E0.455540.648
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
3f9vA0.920999.60.185
4akgA0.899399.60.206
4akgA0.949699.60.214
3vkgA0.942499.50.242
2r44A0.906599.50.252
1r6bX0.928199.50.256
3cf2A0.870599.50.26
3vkgA0.899399.40.272
3pxiA0.863399.40.272
4b4tH0.812999.40.279

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