GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
His_kinase - Histidine kinase
Pfam: PF06580 (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: 82
Sequences: 3342
Seq/Len: 40.76
HH_delta: 0.825 (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
25_A32_A1.984894.579
38_S68_E1.163982.685
26_R33_S1.011032.332
22_S33_S0.981832.265
67_L80_Y0.966962.231
41_D65_N0.965252.227
22_S37_L0.946112.183
38_S65_N0.943962.178
29_P32_A0.768471.773
14_L43_L0.764091.763
45_Y62_F0.758151.749
45_Y54_V0.752561.736
35_M72_I0.750811.732
55_T58_E0.736151.698
25_A29_P0.702911.622
21_I35_M0.685411.581
28_D31_K0.657821.518
12_H16_N0.643671.485
57_E61_E0.634171.463
61_E64_E0.631161.456
64_E68_E0.613661.416
21_I32_A0.602321.389
28_D32_A0.574111.324
24_L31_K0.574071.324
25_A36_I0.566091.306
61_E65_N0.56411.301
14_L39_L0.559041.290
19_N22_S0.530121.223
19_N23_W0.508891.174
48_S58_E0.485951.121
24_L35_M0.483681.116
34_E68_E0.482741.114
15_F19_N0.472221.089
18_L36_I0.465131.073
19_N40_S0.459561.060
71_K79_E0.455471.051
17_T69_I0.452441.044
39_L43_L0.447821.033
58_E61_E0.44781.033
68_E72_I0.442741.021
68_E71_K0.437631.010
71_K76_D0.433120.999
67_L78_L0.430280.993
23_W26_R0.426540.984
42_L62_F0.417010.962
54_V58_E0.407470.940
3_K6_Q0.405680.936
31_K34_E0.405130.935
66_Y70_Q0.397520.917
34_E38_S0.395620.913
5_L8_Q0.391940.904
75_G78_L0.380170.877
71_K78_L0.368560.850
31_K72_I0.368190.849
15_F44_R0.367330.847
51_E58_E0.361920.835
74_F77_R0.361080.833
22_S36_I0.357750.825
71_K80_Y0.35690.823
57_E81_E0.35630.822
20_S72_I0.352120.812
22_S26_R0.349390.806
70_Q73_R0.343920.793
41_D61_E0.342850.791
64_E71_K0.341710.788
65_N68_E0.340810.786
60_L64_E0.340120.785
10_N42_L0.335220.773
20_S24_L0.333110.768
40_S44_R0.331410.765
15_F47_L0.33090.763
46_S62_F0.323360.746
21_I36_I0.321710.742
32_A36_I0.321670.742
23_W27_I0.319330.737
25_A33_S0.319040.736
13_F42_L0.317860.733
21_I39_L0.311880.719
20_S70_Q0.308630.712
42_L70_Q0.299510.691
48_S51_E0.299340.691
37_L41_D0.295230.681
70_Q74_F0.294870.680
24_L29_P0.293630.677
24_L28_D0.28950.668
27_I75_G0.287140.662
9_I24_L0.28410.655
23_W40_S0.281860.650
4_A7_A0.281420.649
43_L46_S0.276550.638
70_Q78_L0.276350.638
9_I59_E0.274630.634
24_L72_I0.271730.627
50_K53_F0.270870.625
7_A10_N0.264750.611
33_S37_L0.263050.607
17_T35_M0.262950.607
29_P33_S0.260680.601
15_F36_I0.259640.599
9_I43_L0.258350.596
42_L46_S0.256840.593
56_L60_L0.251230.580
18_L43_L0.2510.579
14_L17_T0.250820.579
41_D45_Y0.248860.574
24_L32_A0.247330.571
66_Y69_I0.243320.561
26_R30_E0.24320.561
20_S39_L0.242690.560
13_F16_N0.242360.559
45_Y65_N0.240110.554
3_K47_L0.239910.553
74_F78_L0.239530.553
53_F57_E0.237880.549
6_Q9_I0.236190.545
8_Q56_L0.235220.543
4_A42_L0.233790.539
57_E64_E0.231630.534
52_E55_T0.230740.532
17_T73_R0.229880.530
21_I40_S0.228850.528
52_E63_I0.228610.527
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
4i5sA188.10.825
2p9xA0.902426.90.887
1wvfA0.341519.30.894
3mdoA0.792718.80.895
3a0rA0.9878160.898
3tshA0.341515.50.899
3kizA0.817114.10.9
4gczA0.987813.70.901
1i58A0.40248.20.909
3ghgA0.96345.80.915
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