GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sigma54_activat - Sigma-54 interaction domain
Pfam: PF00158 (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: 168
Sequences: 25313
Seq/Len: 150.67
HH_delta: 0.106 (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
74_E84_D2.218823.934
148_L153_R2.166193.841
98_F140_S1.780183.157
143_K148_L1.49612.653
121_K132_P1.47322.612
63_E108_E1.340262.376
15_A38_L1.185522.102
89_L116_V1.154972.048
67_E112_K1.089741.932
144_D147_E1.083871.922
41_A45_N1.053241.868
86_K90_E1.046211.855
139_A162_L1.009661.790
75_K82_R0.976541.732
59_A111_A0.952611.689
16_K45_N0.951191.687
103_E141_T0.949741.684
104_D143_K0.939231.665
10_R14_Q0.93111.651
40_R55_S0.924751.640
36_E115_R0.924311.639
75_K84_D0.909051.612
13_E16_K0.893241.584
8_M12_R0.886651.572
41_A44_N0.874951.551
73_H78_F0.848481.504
11_L38_L0.848181.504
12_R15_A0.844761.498
6_P10_R0.842791.494
8_M11_L0.827341.467
75_K83_S0.800291.419
28_T146_E0.795851.411
105_L109_L0.795111.410
6_P9_K0.791461.403
10_R13_E0.774311.373
93_N134_D0.771991.369
7_A10_R0.765311.357
12_R16_K0.75421.337
65_L68_S0.742041.316
9_K13_E0.732481.299
9_K12_R0.73181.298
94_G134_D0.72941.293
101_E142_S0.729011.293
36_E100_D0.723741.283
93_N133_V0.717871.273
156_E160_Y0.715121.268
103_E142_S0.714971.268
40_R44_N0.705781.251
66_L109_L0.662311.174
88_L91_Q0.65881.168
39_A140_S0.657831.166
12_R38_L0.639971.135
24_P120_G0.63951.134
145_L154_F0.628421.114
103_E145_L0.619761.099
157_D160_Y0.613441.088
37_L41_A0.612421.086
39_A98_F0.596531.058
30_E33_T0.596091.057
85_K91_Q0.593791.053
58_C99_L0.593321.052
97_L137_I0.591931.050
40_R119_E0.589841.046
27_I39_A0.587681.042
66_L70_L0.586631.040
86_K91_Q0.582891.034
63_E106_P0.579551.028
73_H76_G0.577721.024
29_G35_K0.577311.024
103_E143_K0.576021.021
53_F98_F0.574711.019
39_A138_I0.573461.017
145_L148_L0.57251.015
87_G90_E0.567021.005
51_G94_G0.563691.000
115_R119_E0.555870.986
20_S47_P0.554610.983
48_R134_D0.554360.983
78_F81_A0.551780.978
102_I139_A0.5510.977
157_D161_R0.54920.974
26_L141_T0.544610.966
11_L15_A0.539880.957
85_K88_L0.537870.954
22_D48_R0.529510.939
120_G132_P0.525820.932
96_T138_I0.521810.925
73_H77_A0.515450.914
24_P139_A0.514660.913
65_L69_E0.514290.912
53_F95_G0.508920.902
135_V139_A0.507370.900
154_F157_D0.504090.894
62_P66_L0.499050.885
62_P65_L0.498580.884
68_S73_H0.495730.879
7_A11_L0.495450.879
89_L97_L0.493180.874
72_G75_K0.492480.873
52_P95_G0.487880.865
158_L162_L0.483130.857
102_I105_L0.481090.853
73_H85_K0.479110.850
106_P109_L0.478020.848
43_H53_F0.477840.847
19_A22_D0.477510.847
57_N60_A0.477260.846
77_A80_G0.47550.843
48_R51_G0.472680.838
13_E17_R0.472560.838
96_T136_R0.472520.838
76_G79_T0.470050.833
143_K153_R0.467390.829
29_G32_G0.465030.825
18_A21_S0.464450.824
43_H96_T0.462290.820
15_A41_A0.460740.817
37_L40_R0.458150.812
104_D142_S0.457310.811
84_D90_E0.455920.808
87_G91_Q0.454090.805
111_A114_L0.4540.805
22_D47_P0.453960.805
59_A104_D0.452660.803
36_E55_S0.451390.800
69_E85_K0.445460.790
12_R41_A0.442150.784
92_A95_G0.437710.776
55_S115_R0.4350.771
72_G78_F0.433920.769
55_S58_C0.433760.769
24_P117_L0.431980.766
73_H81_A0.430230.763
26_L139_A0.425860.755
73_H82_R0.425530.755
14_Q17_R0.424020.752
77_A81_A0.42020.745
112_K116_V0.417030.739
102_I110_Q0.41680.739
47_P50_N0.4160.738
61_L65_L0.414790.735
103_E140_S0.413530.733
146_E159_Y0.412810.732
155_R158_L0.409710.726
99_L139_A0.409010.725
155_R160_Y0.408380.724
66_L112_K0.408180.724
155_R159_Y0.407120.722
20_S46_S0.406070.720
108_E111_A0.405340.719
64_E68_S0.40480.718
11_L14_Q0.402670.714
29_G33_T0.402260.713
8_M41_A0.399070.708
15_A42_I0.397050.704
46_S96_T0.395120.701
12_R45_N0.394710.700
90_E93_N0.392570.696
68_S72_G0.39190.695
153_R158_L0.39070.693
9_K16_K0.384520.682
27_I38_L0.379930.674
35_K100_D0.377960.670
20_S45_N0.377830.670
12_R17_R0.374530.664
153_R157_D0.372460.660
56_V88_L0.371810.659
8_M38_L0.371170.658
46_S49_K0.366530.650
18_A25_V0.366410.650
16_K20_S0.364570.646
158_L161_R0.363790.645
52_P91_Q0.363710.645
18_A23_L0.358960.636
62_P67_E0.357170.633
81_A84_D0.355180.630
69_E72_G0.354960.629
65_L78_F0.352120.624
93_N135_V0.350630.622
58_C61_L0.349930.620
156_E161_R0.34640.614
31_T104_D0.345040.612
76_G81_A0.344890.612
132_P135_V0.344480.611
117_L137_I0.344170.610
66_L69_E0.344080.610
115_R118_E0.342040.606
144_D148_L0.340020.603
34_G38_L0.339240.602
31_T142_S0.339170.601
87_G92_A0.338970.601
56_V61_L0.337710.599
36_E40_R0.335490.595
64_E108_E0.335410.595
146_E156_E0.334730.594
72_G76_G0.334090.592
7_A14_Q0.333630.592
79_T83_S0.333520.591
80_G83_S0.331820.588
61_L64_E0.328480.582
103_E154_F0.327040.580
57_N101_E0.326030.578
58_C105_L0.325390.577
101_E141_T0.324590.576
114_L118_E0.324520.575
111_A118_E0.323910.574
157_D162_L0.322080.571
17_R21_S0.321540.570
64_E67_E0.32110.569
139_A142_S0.318560.565
28_T141_T0.318260.564
154_F158_L0.317270.563
15_A20_S0.316760.562
120_G135_V0.316350.561
63_E67_E0.316050.560
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
1ojlA199.90.106
2bjvA199.90.141
1ny5A199.80.155
3dzdA0.99499.80.18
1qvrA199.80.227
1r6bX0.982199.80.24
3pxiA0.922699.80.243
3n70A0.821499.70.251
4fcwA199.70.269
3co5A0.791799.70.27

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