GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HATPase_c - Histidine kinase- DNA gyrase B- and HSP90-like ATPase
Pfam: PF02518 (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: 111
Sequences: 73709
Seq/Len: 664.05
HH_delta: -0.089 (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
43_S103_T3.884072.955
37_H107_T3.650262.777
41_E103_T3.289952.503
93_T105_T3.235162.461
41_E105_T2.980692.268
82_K86_E2.931972.230
30_T41_E2.915062.218
39_S107_T2.851042.169
39_S105_T2.732812.079
26_K45_N2.717122.067
28_D43_S2.602191.980
50_P53_E2.480471.887
21_S45_N2.400811.826
34_D39_S2.349971.788
32_E39_S2.349581.787
44_D48_G2.311161.758
54_L96_S2.255071.716
97_S100_G2.157921.642
95_E105_T2.116981.610
81_V92_L2.075671.579
32_E41_E2.073741.578
30_T43_S2.067071.573
56_K62_F2.059641.567
51_P54_L2.038711.551
53_E56_K2.017161.535
15_D19_K1.92881.467
25_G45_N1.927841.467
95_E103_T1.924831.464
91_E107_T1.911071.454
9_I85_A1.882421.432
58_F92_L1.866071.420
49_I102_T1.851651.409
85_A90_G1.832141.394
5_R87_R1.82371.387
94_I104_V1.818321.383
53_E62_F1.808911.376
10_L40_I1.759431.338
56_K59_E1.750391.332
54_L94_I1.718531.307
9_I81_V1.711921.302
93_T107_T1.671191.271
13_L104_V1.620571.233
49_I57_L1.600691.218
53_E64_S1.600421.218
17_A27_I1.583031.204
13_L81_V1.57321.197
85_A106_F1.56391.190
50_P98_E1.52671.161
21_S25_G1.482211.128
9_I84_I1.453081.105
59_E62_F1.442521.097
80_I84_I1.427871.086
8_Q11_S1.419011.080
21_S27_I1.369931.042
7_R11_S1.365131.039
96_S102_T1.348741.026
86_E91_E1.318731.003
5_R8_Q1.308090.995
34_D107_T1.300280.989
49_I53_E1.280620.974
28_D45_N1.251750.952
12_E15_D1.236330.941
84_I88_H1.224460.932
3_P7_R1.222220.930
16_N77_G1.20710.918
5_R88_H1.198480.912
6_L88_H1.192940.908
37_H91_E1.192920.908
12_E81_V1.182760.900
4_D7_R1.156230.880
79_Y83_Q1.149730.875
11_S15_D1.149440.874
34_D37_H1.139580.867
83_Q87_R1.131770.861
5_R84_I1.127820.858
85_A92_L1.124260.855
40_I106_F1.103270.839
48_G102_T1.091720.831
9_I106_F1.084330.825
22_P47_V1.083250.824
58_F94_I1.079080.821
76_L80_I1.074190.817
44_D102_T1.072560.816
83_Q86_E1.024380.779
10_L42_I1.024350.779
17_A42_I1.019090.775
60_P83_Q1.000610.761
94_I102_T0.996260.758
44_D101_G0.991530.754
22_P25_G0.989720.753
90_G108_L0.985510.750
10_L14_L0.982490.747
96_S100_G0.978690.745
8_Q84_I0.945440.719
90_G106_F0.929940.707
63_T71_I0.908180.691
31_I38_L0.896160.682
19_K65_D0.891340.678
43_S97_S0.886330.674
58_F82_K0.882770.672
20_H47_V0.882210.671
8_Q80_I0.877110.667
29_I42_I0.875780.666
14_L29_I0.864640.658
49_I54_L0.842130.641
13_L78_L0.834770.635
16_N20_H0.826420.629
65_D71_I0.814640.620
37_H109_P0.81390.619
13_L42_I0.804930.612
31_I40_I0.80290.611
46_G49_I0.800980.609
96_S99_G0.792410.603
63_T73_G0.789390.601
16_N75_G0.787480.599
20_H63_T0.776430.591
36_D109_P0.771540.587
54_L58_F0.771040.587
33_E37_H0.770060.586
57_L94_I0.770040.586
33_E38_L0.76550.582
13_L92_L0.757530.576
47_V71_I0.757450.576
28_D31_I0.739720.563
14_L27_I0.738160.562
17_A21_S0.722620.550
66_K70_S0.716050.545
49_I96_S0.702540.534
14_L42_I0.694080.528
51_P96_S0.693170.527
60_P76_L0.686230.522
58_F104_V0.682490.519
85_A108_L0.675450.514
13_L106_F0.665150.506
9_I88_H0.664970.506
90_G109_P0.663560.505
39_S93_T0.662240.504
43_S101_G0.661330.503
27_I31_I0.658520.501
6_L10_L0.657340.500
81_V85_A0.648620.493
49_I55_E0.646850.492
43_S99_G0.639190.486
46_G102_T0.637970.485
85_A88_H0.635090.483
57_L79_Y0.631840.481
63_T66_K0.623250.474
57_L62_F0.622740.474
82_K91_E0.621670.473
11_S84_I0.620390.472
6_L40_I0.617420.470
51_P97_S0.614540.468
44_D47_V0.613740.467
50_P54_L0.610790.465
4_D11_S0.604770.460
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
1y8oA199.7-0.089
2q8gA199.7-0.084
2btzA199.7-0.077
2e0aA199.7-0.076
4i5sA199.7-0.075
1gkzA199.7-0.067
4e01A199.7-0.059
2c2aA199.7-0.057
4gczA0.95599.7-0.033
1b3qA199.7-0.026

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