GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HATPase_c_2 - Histidine kinase-like ATPase domain
Pfam: PF13581 (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: CL0025
Length: 125
Sequences: 27183
Seq/Len: 217.46
HH_delta: 0.143 (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
72_R120_T3.070382.983
70_S120_T2.612312.538
70_S122_T2.579892.507
112_D122_T2.555462.483
68_R124_R2.524362.453
66_R124_R2.51222.441
68_R122_T2.463612.394
59_R70_S2.374882.308
73_D77_G2.231282.168
105_R109_D2.064252.006
79_D82_Q2.039481.982
57_D72_R2.006421.950
61_E68_R1.928721.874
39_A104_I1.854151.802
47_G74_N1.807311.756
80_P83_L1.764371.714
55_P74_N1.705331.657
82_Q91_P1.703881.656
35_A104_I1.633721.587
41_T45_E1.59291.548
82_Q85_Q1.522681.480
63_D68_R1.517531.475
61_E70_S1.515531.473
85_Q91_P1.461711.420
108_M123_L1.4341.393
35_A108_M1.422671.382
59_R72_R1.417961.378
36_V69_I1.384691.345
85_Q88_P1.382071.343
54_G74_N1.375351.336
79_D115_E1.359381.321
54_G58_V1.345981.308
47_G54_G1.327991.290
35_A107_L1.309881.273
88_P91_P1.298391.262
78_F82_Q1.290811.254
113_Y121_V1.289361.253
35_A123_L1.256191.221
112_D124_R1.208221.174
83_L113_Y1.187011.153
69_I123_L1.174871.142
29_R33_E1.143431.111
42_N100_G1.138131.106
31_D107_L1.130611.099
39_A121_V1.102931.072
31_D110_E1.10081.070
33_E37_S1.095721.065
47_G56_V1.070581.040
114_R119_N1.07011.040
34_L107_L1.042931.013
77_G119_N1.035221.006
31_D34_L1.025360.996
103_L107_L1.01290.984
78_F119_N1.009790.981
107_L111_V1.008290.980
38_E41_T0.990350.962
87_D90_E0.989910.962
34_L37_S0.98780.960
63_D124_R0.980880.953
30_D33_E0.969240.942
43_A71_V0.967680.940
102_F106_S0.954410.927
38_E104_I0.946170.919
36_V71_V0.938870.912
63_D66_R0.934970.909
28_D31_D0.915370.889
92_D95_R0.91020.884
78_F86_P0.898370.873
89_W106_S0.897140.872
37_S41_T0.892360.867
40_L56_V0.882590.858
43_A56_V0.878260.853
114_R117_G0.874740.850
73_D119_N0.860450.836
36_V40_L0.848060.824
34_L103_L0.845170.821
50_G54_G0.843250.819
73_D118_G0.840710.817
99_R103_L0.824310.801
57_D74_N0.820660.797
46_H76_P0.813070.790
106_S109_D0.780170.758
86_P90_E0.747140.726
42_N46_H0.717810.697
60_L67_L0.692550.673
78_F83_L0.684880.665
80_P84_P0.676320.657
76_P94_L0.67360.655
48_Y76_P0.672760.654
106_S110_E0.672320.653
48_Y54_G0.659830.641
42_N98_G0.652740.634
78_F113_Y0.651670.633
83_L114_R0.648370.630
39_A71_V0.641150.623
43_A46_H0.638130.620
83_L87_D0.637080.619
42_N73_D0.636010.618
32_L69_I0.631970.614
113_Y119_N0.630350.613
60_L69_I0.626540.609
87_D91_P0.624960.607
54_G60_L0.624830.607
83_L86_P0.624350.607
75_G119_N0.622480.605
87_D121_V0.613590.596
104_I111_V0.608310.591
72_R118_G0.591180.574
89_W102_F0.589210.573
40_L71_V0.583860.567
96_E99_R0.582980.566
31_D111_V0.581650.565
87_D105_R0.578090.562
62_V66_R0.577430.561
39_A123_L0.573050.557
89_W97_G0.566070.550
45_E95_R0.560880.545
103_L106_S0.550560.535
40_L58_V0.550320.535
79_D83_L0.549380.534
39_A43_A0.540580.525
34_L38_E0.540560.525
56_V71_V0.539150.524
32_L36_V0.534820.520
62_V67_L0.531790.517
48_Y74_N0.527820.513
73_D76_P0.51750.503
35_A111_V0.510680.496
68_R112_D0.509950.496
46_H94_L0.506420.492
84_P88_P0.49690.483
44_V47_G0.496860.483
58_V71_V0.493090.479
102_F105_R0.487040.473
55_P72_R0.485680.472
45_E97_G0.484940.471
86_P89_W0.478410.465
43_A47_G0.477410.464
57_D60_L0.476090.463
59_R120_T0.475090.462
62_V65_D0.472970.460
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
3ke6A0.9299.70.143
1th8A0.98499.60.204
1y8oA199.30.328
4i5sA0.97699.30.332
2q8gA199.30.334
1gkzA199.30.335
2c2aA199.30.337
2e0aA199.30.341
2btzA199.30.342
4e01A199.30.344

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