GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2345 - Uncharacterized protein conserved in bacteria (DUF2345)
Pfam: PF10106 (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: 155
Sequences: 864
Seq/Len: 5.57
HH_delta: 0.86 (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
37_A41_I0.480043.616
45_A49_L0.415523.130
125_Y136_G0.375092.825
57_L61_A0.301142.268
96_A100_I0.299452.255
116_E129_S0.272232.050
118_T127_R0.268322.021
125_Y134_E0.249051.876
127_R134_E0.241261.817
29_T33_I0.234281.765
30_P38_G0.233371.758
31_Q39_E0.228371.720
22_P30_P0.227391.713
132_G137_T0.218821.648
53_A57_L0.207071.560
19_L27_L0.203111.530
40_N47_Q0.195051.469
119_L126_I0.194691.466
47_Q55_K0.194461.465
25_I29_T0.190621.436
82_K90_D0.186671.406
30_P33_I0.183331.381
116_E127_R0.18271.376
108_K116_E0.182441.374
110_V118_T0.179231.350
99_D107_G0.174881.317
42_D50_Q0.173861.310
108_K118_T0.169931.280
59_A65_I0.169221.275
129_S137_T0.167691.263
21_A24_G0.159831.204
37_A42_D0.158461.194
37_A62_G0.156451.178
119_L128_L0.15591.174
34_H46_G0.155461.171
117_I121_A0.154651.165
99_D104_S0.154611.165
126_I141_I0.1531.152
121_A137_T0.152751.151
53_A61_A0.151921.144
22_P25_I0.149741.128
14_Q17_L0.149031.122
61_A69_A0.149031.122
32_S45_A0.148761.120
21_A30_P0.148581.119
34_H42_D0.145871.099
127_R136_G0.14541.095
33_I37_A0.144841.091
73_G90_D0.144311.087
116_E122_G0.142261.071
39_E47_Q0.140181.056
104_S128_L0.139491.051
82_K91_D0.139431.050
133_I139_G0.139271.049
106_E115_K0.139141.048
107_G121_A0.137241.034
34_H50_Q0.137011.032
65_I69_A0.135461.020
96_A109_I0.133631.006
29_T36_S0.131050.987
109_I120_N0.130870.986
32_S39_E0.130010.979
20_S27_L0.129110.972
23_A31_Q0.128680.969
55_K63_E0.128570.968
107_G115_K0.128080.965
24_G48_D0.127790.963
113_A116_E0.127390.959
75_K126_I0.12660.954
28_T36_S0.125310.944
79_A89_S0.125180.943
116_E121_A0.124760.940
77_I80_Q0.124730.939
75_K84_E0.124650.939
27_L33_I0.124390.937
100_I104_S0.123590.931
129_S132_G0.122770.925
63_E69_A0.122720.924
20_S56_S0.121580.916
21_A25_I0.121470.915
20_S25_I0.121290.914
21_A28_T0.121180.913
91_D101_T0.120880.910
104_S107_G0.120720.909
43_L51_I0.119110.897
28_T43_L0.118550.893
48_D61_A0.118520.893
51_I59_A0.118220.890
19_L25_I0.117960.888
78_A83_V0.117690.886
109_I117_I0.117290.883
85_I95_T0.117080.882
23_A48_D0.117070.882
131_G135_I0.11690.880
114_K122_G0.116670.879
32_S40_N0.116610.878
71_K80_Q0.115930.873
93_E101_T0.115930.873
75_K94_L0.115360.869
137_T141_I0.114980.866
29_T34_H0.114960.866
68_F133_I0.114530.863
53_A78_A0.114430.862
22_P29_T0.114220.860
123_G134_E0.11290.850
58_T105_T0.112390.847
14_Q23_A0.112350.846
73_G81_G0.111790.842
112_T132_G0.111450.839
108_K129_S0.110830.835
45_A74_I0.108610.818
38_G48_D0.108040.814
120_N123_G0.107820.812
65_I71_K0.107590.810
27_L57_L0.107310.808
73_G77_I0.106840.805
24_G30_P0.106790.804
16_V21_A0.106550.803
38_G64_G0.105950.798
120_N137_T0.105610.795
37_A83_V0.105410.794
75_K92_M0.105190.792
27_L35_L0.105020.791
125_Y141_I0.104870.790
115_K122_G0.104810.789
106_E129_S0.104640.788
17_L35_L0.104390.786
41_I52_A0.104310.786
58_T61_A0.104280.785
77_I84_E0.103970.783
94_L130_G0.103970.783
135_I138_P0.103610.780
103_T111_I0.102480.772
135_I141_I0.102170.770
21_A32_S0.101610.765
107_G122_G0.101550.765
112_T131_G0.101390.764
37_A68_F0.101350.763
66_S83_V0.100980.761
116_E135_I0.10070.758
118_T129_S0.100680.758
66_S89_S0.099980.753
67_L133_I0.099920.753
75_K86_Q0.099480.749
119_L123_G0.099310.748
123_G130_G0.098820.744
72_G80_Q0.09880.744
28_T42_D0.09850.742
77_I86_Q0.098370.741
122_G130_G0.098240.740
126_I135_I0.098210.740
28_T78_A0.097920.738
23_A104_S0.097650.735
90_D98_K0.096450.726
55_K71_K0.096410.726
51_I57_L0.09620.725
121_A130_G0.096080.724
33_I41_I0.096040.723
102_I105_T0.095530.720
40_N45_A0.095510.719
77_I139_G0.095390.718
16_V74_I0.095310.718
128_L135_I0.095250.717
64_G67_L0.095060.716
112_T121_A0.094770.714
31_Q49_L0.094720.713
80_Q89_S0.094640.713
72_G76_L0.094480.712
25_I33_I0.094090.709
73_G86_Q0.093560.705
29_T52_A0.09340.703
22_P32_S0.093260.702
17_L25_I0.093210.702
116_E119_L0.092870.699
84_E95_T0.092850.699
62_G66_S0.092320.695
28_T75_K0.092250.695
114_K131_G0.092060.693
118_T125_Y0.092060.693
103_T110_V0.091730.691
16_V53_A0.091680.691
72_G77_I0.091510.689
130_G135_I0.091080.686
120_N135_I0.090830.684
44_T58_T0.089840.677
101_T110_V0.089760.676
50_Q53_A0.089620.675
45_A113_A0.089610.675
126_I130_G0.089490.674
123_G135_I0.08910.671
34_H53_A0.088790.669
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
1wthA0.987192.70.86
1wthA0.961389.40.87
3vtoA0.503240.70.911
3qr7A0.554822.60.921
3aqjA0.683921.10.922
3qr8A0.832317.70.925
1v1hA0.541916.90.925
3izoF0.883913.90.928
1qiuA0.5677120.93
3a1mA0.72911.70.93
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