GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sigma54_DBD - Sigma-54 DNA binding domain
Pfam: PF04552 (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: CL0123
Length: 160
Sequences: 889
Seq/Len: 5.56
HH_delta: 0.527 (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
108_R134_E0.519943.912
109_I127_I0.385472.900
51_T54_D0.375052.822
31_A55_I0.373182.808
27_R59_L0.326822.459
113_I150_L0.317282.387
31_A58_E0.298482.246
61_L66_V0.29422.214
39_F82_F0.293122.206
82_F86_D0.261891.971
29_A75_I0.255551.923
125_Q129_E0.250781.887
37_K41_L0.24831.868
132_K137_K0.244251.838
31_A34_E0.239651.803
109_I131_L0.238681.796
35_R50_L0.235831.774
35_R55_I0.232781.752
59_L66_V0.229541.727
112_L130_L0.227361.711
111_E115_E0.225761.699
82_F87_F0.224691.691
126_E129_E0.21971.653
130_L133_E0.21961.652
45_G111_E0.2141.610
30_Q34_E0.208011.565
52_M85_K0.204931.542
13_W20_Q0.201411.515
39_F86_D0.193321.455
8_L12_K0.189331.425
52_M70_V0.189031.422
112_L127_I0.188551.419
27_R61_L0.186511.403
35_R58_E0.186331.402
110_K114_E0.186211.401
40_F77_T0.184721.390
39_F87_F0.184491.388
34_E58_E0.183261.379
77_T80_G0.179931.354
42_G46_A0.177381.335
111_E134_E0.177291.334
83_P86_D0.17691.331
40_F78_P0.176871.331
117_D121_P0.176691.329
126_E130_L0.17531.319
89_S101_S0.173541.306
11_A15_I0.172531.298
116_E121_P0.168791.270
8_L11_A0.168111.265
75_I84_L0.167951.264
24_T69_A0.165341.244
90_R102_S0.162351.222
40_F79_R0.158071.189
32_I50_L0.149691.126
139_S142_T0.146871.105
63_E144_A0.146621.103
25_L89_S0.145131.092
113_I116_E0.143341.079
7_K18_L0.140711.059
39_F83_P0.140491.057
35_R54_D0.140311.056
106_K149_E0.136751.029
9_K136_I0.136711.029
25_L69_A0.135541.020
27_R30_Q0.134611.013
50_L157_Q0.133351.003
142_T145_K0.133281.003
74_Y83_P0.133211.002
114_E118_K0.132710.999
104_A136_I0.132610.998
43_G46_A0.131180.987
48_K110_K0.128950.970
11_A139_S0.128640.968
19_E22_N0.127840.962
139_S154_S0.127140.957
119_K132_K0.126560.952
129_E133_E0.126440.951
25_L83_P0.126050.948
11_A43_G0.125360.943
138_I143_V0.125350.943
16_R62_H0.124470.937
156_S159_K0.124290.935
55_I88_F0.123860.932
44_P79_R0.123620.930
86_D103_E0.123240.927
112_L122_L0.122570.922
77_T85_K0.121940.918
122_L130_L0.121880.917
116_E158_R0.121290.913
32_I87_F0.121150.912
123_S126_E0.120730.908
20_Q25_L0.120570.907
93_S113_I0.12030.905
16_R63_E0.120140.904
122_L127_I0.120110.904
6_E105_I0.119920.902
75_I78_P0.119720.901
23_E27_R0.119180.897
153_P157_Q0.11870.893
27_R42_G0.118310.890
127_I130_L0.117890.887
33_V75_I0.117330.883
73_K146_Y0.117110.881
83_P87_F0.116820.879
57_D60_G0.116580.877
140_R147_R0.115970.873
53_K63_E0.115810.871
31_A35_R0.115580.870
127_I137_K0.114610.862
29_A84_L0.114480.861
131_L143_V0.114470.861
54_D57_D0.114090.858
17_A28_V0.113630.855
7_K22_N0.112730.848
105_I138_I0.112620.847
106_K153_P0.112510.847
139_S145_K0.112070.843
92_V105_I0.111530.839
76_Q84_L0.110630.832
4_L41_L0.110240.829
29_A40_F0.109950.827
125_Q156_S0.109930.827
14_L62_H0.10970.825
38_D48_K0.109630.825
53_K77_T0.109620.825
115_E122_L0.108990.820
2_K18_L0.108720.818
105_I131_L0.107630.810
93_S132_K0.107520.809
144_A148_E0.107170.806
120_K148_E0.106510.801
71_K85_K0.105340.793
113_I152_I0.105170.791
98_E113_I0.104770.788
84_L128_A0.104570.787
51_T139_S0.104430.786
39_F43_G0.104430.786
3_Y7_K0.104420.786
130_L134_E0.104420.786
14_L155_S0.103820.781
38_D42_G0.102840.774
17_A138_I0.102840.774
128_A132_K0.102830.774
25_L28_V0.102640.772
27_R127_I0.101970.767
117_D120_K0.101520.764
102_S106_K0.10120.761
26_L30_Q0.100830.759
51_T160_R0.099870.751
52_M64_S0.099860.751
65_T68_R0.099740.750
125_Q128_A0.099730.750
144_A152_I0.098720.743
18_L76_Q0.098320.740
17_A157_Q0.098290.740
50_L99_E0.098120.738
4_L8_L0.098020.738
129_E132_K0.097740.735
130_L138_I0.097540.734
13_W69_A0.097390.733
94_S97_G0.097170.731
119_K159_K0.0970.730
12_K46_A0.096980.730
8_L96_S0.096970.730
32_I131_L0.09670.728
22_N139_S0.096590.727
2_K151_G0.096470.726
44_P86_D0.09610.723
141_R145_K0.09590.722
47_L134_E0.095870.721
107_A126_E0.095650.720
70_V88_F0.095590.719
28_V52_M0.095460.718
102_S155_S0.095420.718
7_K47_L0.095250.717
42_G48_K0.094960.715
19_E25_L0.094880.714
29_A33_V0.094750.713
24_T88_F0.094660.712
154_S157_Q0.094280.709
85_K104_A0.094270.709
112_L123_S0.094260.709
38_D129_E0.094250.709
50_L89_S0.094240.709
24_T62_H0.094210.709
95_G132_K0.094150.708
18_L91_S0.094040.708
30_Q137_K0.093970.707
9_K160_R0.093890.706
25_L40_F0.093870.706
121_P159_K0.093810.706
33_V92_V0.093770.706
84_L102_S0.093730.705
6_E134_E0.093460.703
69_A139_S0.093440.703
28_V136_I0.093410.703
38_D115_E0.093320.702
23_E149_E0.093150.701
70_V84_L0.093050.700
26_L106_K0.092760.698
30_Q132_K0.092160.693
7_K20_Q0.092120.693
59_L84_L0.09210.693
7_K159_K0.092040.693
20_Q91_S0.091690.690
90_R126_E0.091180.686
139_S160_R0.091070.685
118_K160_R0.090840.684
141_R147_R0.090230.679
28_V85_K0.090090.678
57_D143_V0.090.677
18_L131_L0.089820.676
21_R68_R0.089630.674
17_A25_L0.08950.673
139_S149_E0.089460.673
94_S100_F0.089240.671
127_I143_V0.089120.671
4_L99_E0.089070.670
51_T90_R0.089040.670
67_S140_R0.088910.669
64_S102_S0.088720.668
31_A59_L0.08870.667
22_N76_Q0.088650.667
61_L92_V0.088560.666
85_K102_S0.088530.666
13_W70_V0.088520.666
131_L138_I0.088410.665
133_E153_P0.087670.660
10_E13_W0.087450.658
36_Q49_P0.087330.657
52_M69_A0.087280.657
20_Q144_A0.087150.656
53_K69_A0.087110.655
66_V75_I0.087030.655
42_G45_G0.086930.654
144_A154_S0.086860.654
45_G107_A0.086750.653
61_L64_S0.086570.651
39_F142_T0.086340.650
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
2ahqA0.47599.90.527
2lvsA0.656297.20.877
1jyeA0.6438970.883
3h5tA0.512596.90.885
2hsgA0.52596.90.885
3ctpA0.52596.80.886
1qpzA0.618896.70.888
2l8nA0.418896.70.889
1u78A0.706396.60.89
1jhgA0.57596.50.891
If you are interested in a protein containing this domain,
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