GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BBS2_Mid - Ciliary BBSome complex subunit 2 middle region
Pfam: PF14783 (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: 111
Sequences: 54837
Seq/Len: 494.03
HH_delta: -0.034 (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
57_A67_V2.41942.537
19_L29_V2.284522.395
47_S59_A2.26672.377
20_V30_F2.206312.313
87_A104_S2.204272.311
49_C90_D2.165382.270
88_F102_G2.162842.268
4_A21_G2.080242.181
100_I110_V2.030832.129
19_L50_S2.025122.123
6_C49_C1.976642.073
46_T61_A1.966682.062
51_L91_I1.741031.825
58_Y68_Y1.727261.811
82_Q101_V1.689891.772
19_L56_F1.639341.719
75_W78_K1.586041.663
20_V28_R1.561441.637
72_Q75_W1.535051.610
8_F50_S1.515781.589
27_I58_Y1.513971.587
31_K34_E1.457481.528
57_A91_I1.451721.522
94_D97_P1.425951.495
65_V101_V1.420281.489
19_L48_L1.403631.472
85_S104_S1.327421.392
58_Y66_G1.259751.321
21_G48_L1.229281.289
21_G45_V1.223221.283
92_N98_E1.222711.282
23_D44_K1.216931.276
28_R38_E1.199341.258
57_A99_L1.157051.213
101_V109_E1.12931.184
47_S88_F1.090171.143
41_E58_Y1.089111.142
82_Q103_W1.087611.140
22_S26_E1.074071.126
51_L55_R1.062091.114
73_R76_R1.039781.090
101_V111_R1.032921.083
8_F16_N1.030761.081
59_A86_M1.017361.067
6_C48_L1.016971.066
16_N33_D1.005341.054
49_C89_Y0.995561.044
103_W107_K0.992591.041
51_L54_G0.990281.038
74_L78_K0.988041.036
32_G35_I0.982451.030
44_K61_A0.972921.020
61_A85_S0.948950.995
47_S89_Y0.945990.992
4_A47_S0.944080.990
74_L77_I0.941220.987
90_D100_I0.937860.983
92_N97_P0.935790.981
69_D72_Q0.932680.978
22_S28_R0.89860.942
17_E70_R0.895640.939
91_I99_L0.892160.935
72_Q76_R0.891570.935
73_R78_K0.868520.911
17_E29_V0.865840.908
60_L64_T0.853040.894
82_Q86_M0.846960.888
92_N95_G0.845550.887
5_L20_V0.838370.879
98_E110_V0.817380.857
26_E38_E0.808890.848
41_E45_V0.804730.844
24_D28_R0.804580.844
74_L79_S0.804210.843
50_S70_R0.792240.831
8_F15_E0.789580.828
55_R67_V0.788850.827
16_N31_K0.786970.825
50_S56_F0.784940.823
59_A89_Y0.778970.817
75_W79_S0.777290.815
4_A48_L0.768530.806
7_L18_L0.760670.798
26_E40_T0.75830.795
73_R77_I0.756040.793
49_C91_I0.752350.789
51_L57_A0.748990.785
21_G58_Y0.747850.784
102_G108_V0.737320.773
45_V60_L0.735160.771
57_A89_Y0.726830.762
27_I48_L0.723880.759
94_D98_E0.722010.757
8_F17_E0.71620.751
6_C50_S0.71610.751
23_D46_T0.702450.737
18_L32_G0.69780.732
60_L63_G0.695350.729
20_V24_D0.692790.726
86_M89_Y0.68780.721
92_N100_I0.687720.721
22_S25_F0.680430.713
46_T87_A0.680020.713
52_G95_G0.675570.708
6_C9_D0.668590.701
31_K36_V0.667190.700
23_D61_A0.660410.692
76_R80_K0.659580.692
45_V48_L0.655470.687
5_L18_L0.628830.659
84_T104_S0.626020.656
66_G77_I0.614890.645
17_E33_D0.613150.643
38_E41_E0.612510.642
37_A41_E0.61140.641
65_V89_Y0.6070.636
41_E68_Y0.606620.636
41_E60_L0.605930.635
46_T85_S0.602950.632
49_C57_A0.601010.630
28_R37_A0.596090.625
52_G91_I0.593780.623
29_V50_S0.590150.619
9_D50_S0.588170.617
89_Y101_V0.587970.616
61_A87_A0.587550.616
7_L32_G0.583350.612
60_L66_G0.578630.607
41_E66_G0.57480.603
46_T104_S0.572440.600
103_W109_E0.57130.599
50_S91_I0.571240.599
72_Q77_I0.562810.590
72_Q78_K0.559590.587
27_I56_F0.559040.586
45_V58_Y0.557510.585
84_T103_W0.557030.584
8_F19_L0.550690.577
17_E50_S0.542850.569
76_R79_S0.541510.568
54_G69_D0.541010.567
43_D61_A0.537250.563
95_G98_E0.535950.562
29_V70_R0.529070.555
82_Q111_R0.528790.554
58_Y62_N0.526090.552
16_N32_G0.513720.539
65_V99_L0.507340.532
105_N109_E0.502330.527
21_G24_D0.499850.524
102_G106_G0.499060.523
87_A90_D0.496990.521
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
4gqbB0.96499.5-0.034
2oajA0.96499.5-0.029
2oajA0.945999.5-0.026
3ow8A0.95599.5-0.015
2ymuA0.945999.5-0.012
1vyhC0.95599.5-0.012
4gqbB0.95599.5-0.006
2oitA0.95599.5-0.005
2ynnA0.95599.4-0.004
2ymuA0.945999.4-0.002

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