GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YbjN - Putative bacterial sensory transduction regulator
Pfam: PF10722 (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: CL0097
Length: 127
Sequences: 961
Seq/Len: 7.57
HH_delta: 0.505 (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
62_Q65_E0.236042.488
4_R104_D0.210392.218
6_E10_E0.20892.202
6_E18_V0.207042.183
10_E16_Y0.169621.788
81_K93_E0.169441.786
83_Y93_E0.150981.592
3_D7_A0.147031.550
20_E87_D0.13661.440
85_D89_D0.135341.427
77_Y82_F0.135311.426
70_V84_L0.133151.404
67_L71_N0.132021.392
103_S106_Q0.130411.375
109_S112_D0.128121.351
72_E76_E0.127731.346
118_A122_F0.127511.344
69_A72_E0.123761.305
61_E64_A0.123121.298
106_Q114_F0.12031.268
4_R7_A0.118011.244
20_E24_G0.117521.239
4_R107_L0.116611.229
97_P102_L0.114611.208
80_P92_L0.114351.205
50_V103_S0.113431.196
80_P95_D0.113251.194
12_A108_D0.112991.191
30_F37_V0.112781.189
77_Y88_G0.112121.182
11_E104_D0.111861.179
71_N74_N0.110391.164
66_L116_S0.10941.153
65_E72_E0.108651.145
12_A119_D0.107241.130
81_K121_F0.106621.124
55_P114_F0.106051.118
73_W121_F0.105711.114
25_D40_R0.105661.114
30_F33_G0.105271.110
70_V82_F0.104971.107
96_L102_L0.104131.098
23_D65_E0.10391.095
5_L36_R0.103161.087
80_P93_E0.10291.085
64_A86_E0.102791.084
88_G91_V0.102521.081
110_A119_D0.101331.068
73_W82_F0.100491.059
94_Y114_F0.100451.059
119_D123_D0.100371.058
45_D69_A0.10011.055
73_W92_L0.099641.050
92_L121_F0.099481.049
101_G105_E0.098961.043
113_R116_S0.098781.041
29_R33_G0.097691.030
10_E15_K0.096861.021
39_I44_D0.096261.015
30_F108_D0.095831.010
97_P109_S0.095651.008
42_D111_L0.095491.007
21_D25_D0.094931.001
83_Y87_D0.094831.000
39_I87_D0.094610.997
51_V91_V0.094430.995
13_G66_L0.093770.988
75_R83_Y0.093340.984
116_S120_Q0.09330.984
37_V124_A0.09190.969
41_F105_E0.091810.968
108_D111_L0.091660.966
15_K34_G0.091410.964
23_D107_L0.09120.961
18_V24_G0.0910.959
98_L107_L0.090810.957
65_E68_E0.090770.957
68_E72_E0.089090.939
3_D11_E0.088880.937
13_G125_L0.088620.934
5_L40_R0.088210.930
68_E71_N0.088020.928
15_K21_D0.087320.920
24_G125_L0.087230.920
117_T120_Q0.086840.915
12_A63_R0.086730.914
11_E63_R0.086680.914
56_M123_D0.086670.914
9_L111_L0.086450.911
77_Y81_K0.086430.911
97_P111_L0.086330.910
63_R72_E0.086070.907
57_D88_G0.086010.907
3_D15_K0.085950.906
51_V90_V0.085550.902
19_E22_E0.085410.900
100_A106_Q0.0850.896
7_A11_E0.084930.895
66_L90_V0.084910.895
18_V21_D0.084750.893
71_N77_Y0.084670.893
5_L8_F0.084640.892
63_R67_L0.084540.891
100_A111_L0.084360.889
31_E113_R0.084260.888
12_A107_L0.084160.887
18_V40_R0.083640.882
30_F110_A0.08360.881
119_D122_F0.08350.880
71_N106_Q0.083480.880
4_R66_L0.083160.877
20_E72_E0.083090.876
47_D97_P0.082790.873
75_R93_E0.082760.872
24_G42_D0.08240.869
64_A120_Q0.081870.863
78_R106_Q0.081520.859
3_D18_V0.081370.858
34_G60_E0.081270.857
3_D23_D0.081090.855
43_E63_R0.081060.855
96_L106_Q0.081020.854
113_R117_T0.080360.847
84_L87_D0.080310.847
73_W114_F0.080280.846
14_Y96_L0.079690.840
109_S116_S0.079520.838
3_D68_E0.07940.837
48_V106_Q0.078990.833
97_P113_R0.078980.833
63_R68_E0.078320.826
31_E63_R0.077910.821
44_D90_V0.077750.820
5_L103_S0.077640.818
101_G106_Q0.077550.818
9_L14_Y0.077520.817
14_Y91_V0.077450.816
54_F94_Y0.07730.815
16_Y25_D0.077280.815
39_I42_D0.07720.814
82_F125_L0.077080.813
25_D109_S0.076910.811
47_D111_L0.076660.808
21_D86_E0.076480.806
55_P125_L0.076440.806
37_V96_L0.075890.800
32_F39_I0.075860.800
14_Y90_V0.075610.797
35_I122_F0.075570.797
60_E95_D0.075550.796
51_V83_Y0.075470.796
52_L83_Y0.075260.793
9_L16_Y0.075120.792
28_L64_A0.07490.790
79_F85_D0.074760.788
80_P106_Q0.074580.786
5_L9_L0.074510.785
14_Y80_P0.07440.784
110_A117_T0.074390.784
42_D78_R0.074370.784
77_Y117_T0.074370.784
77_Y110_A0.07430.783
96_L101_G0.074290.783
92_L122_F0.074270.783
16_Y52_L0.074020.780
77_Y92_L0.073610.776
38_F42_D0.073590.776
13_G40_R0.073510.775
50_V80_P0.073490.775
73_W76_E0.073490.775
41_F48_V0.073390.774
67_L74_N0.073360.773
111_L123_D0.073230.772
56_M61_E0.073180.771
13_G104_D0.073050.770
103_S108_D0.072860.768
37_V119_D0.072730.767
45_D48_V0.072690.766
34_G123_D0.072670.766
52_L56_M0.072580.765
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
2plgA0.976498.70.505
4h5bA0.984397.40.667
1k3eA0.952893.10.769
1xkpC0.960691.30.781
3cxjA0.952883.40.807
1jyoA0.93772.70.825
1s28A0.960660.20.839
1ttwA0.952846.40.85
4g6tA0.929136.20.859
3gknA0.559132.10.863
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