GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4161 - C-terminal domain on CstA (DUF4161)
Pfam: PF13722 (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: 127
Sequences: 707
Seq/Len: 5.57
HH_delta: 0.919 (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
97_T113_T0.606464.821
30_A61_A0.33652.675
123_V126_T0.256892.042
34_I61_A0.244531.944
90_A121_T0.241411.919
110_A114_L0.237741.890
22_T84_A0.226441.800
50_W53_N0.218361.736
34_I57_A0.199641.587
18_F32_Y0.189091.503
101_I110_A0.188191.496
22_T29_L0.184181.464
30_A34_I0.182071.447
66_G70_L0.180041.431
90_A124_T0.175251.393
78_W120_M0.17471.389
58_T98_V0.174581.388
121_T125_I0.168941.343
47_D50_W0.166311.322
93_L100_L0.163891.303
100_L113_T0.15941.267
64_L97_T0.158291.258
106_N110_A0.157731.254
88_L92_A0.157691.253
23_L94_L0.154891.231
25_T29_L0.152381.211
15_V19_A0.151451.204
118_V125_I0.150421.196
33_I88_L0.149691.190
37_L87_L0.149571.189
17_A88_L0.148941.184
13_L21_T0.146761.167
46_G104_G0.144891.152
106_N118_V0.144811.151
23_L26_A0.144421.148
23_L27_T0.143511.141
77_L92_A0.143221.138
71_M105_K0.142721.134
94_L117_A0.142661.134
35_Q57_A0.140521.117
68_L71_M0.140291.115
22_T61_A0.138241.099
47_D51_L0.138121.098
23_L74_F0.136081.082
67_Y70_L0.134491.069
48_Q54_R0.131941.049
7_G11_A0.130561.038
48_Q60_I0.128721.023
13_L92_A0.128311.020
103_K106_N0.127921.017
114_L118_V0.126511.006
21_T24_D0.126491.005
115_I118_V0.123720.983
26_A65_A0.123450.981
98_V106_N0.122340.972
74_F80_L0.122120.971
52_P56_V0.12030.956
55_Y59_I0.120180.955
117_A120_M0.120040.954
7_G15_V0.11980.952
97_T118_V0.119250.948
38_F57_A0.119080.947
53_N56_V0.118640.943
82_G127_A0.117910.937
21_T25_T0.117690.935
36_E58_T0.11750.934
97_T114_L0.117280.932
91_L127_A0.117180.931
49_K53_N0.117020.930
94_L120_M0.116830.929
37_L78_W0.116720.928
32_Y89_A0.116380.925
30_A35_Q0.116050.922
95_T123_V0.115540.918
34_I93_L0.115220.916
63_A118_V0.114030.906
94_L123_V0.114030.906
76_I79_P0.113460.902
9_T65_A0.113390.901
100_L117_A0.112630.895
26_A99_W0.112590.895
94_L121_T0.112380.893
11_A65_A0.111790.889
34_I38_F0.111380.885
55_Y78_W0.111170.884
54_R57_A0.110960.882
84_A124_T0.110670.880
46_G125_I0.110340.877
60_I64_L0.110310.877
67_Y100_L0.110250.876
16_A127_A0.109090.867
11_A19_A0.108970.866
59_I118_V0.108970.866
56_V67_Y0.108560.863
11_A92_A0.108330.861
97_T110_A0.107550.855
82_G91_L0.10750.854
105_K119_F0.107140.852
51_L56_V0.10710.851
29_L99_W0.106710.848
61_A71_M0.106020.843
9_T15_V0.105970.842
112_I123_V0.105860.841
52_P115_I0.105820.841
47_D68_L0.105310.837
91_L122_V0.105180.836
30_A127_A0.104970.834
106_N111_W0.104820.833
17_A26_A0.104490.831
9_T69_A0.103140.820
63_A122_V0.102880.818
8_Y11_A0.102650.816
105_K123_V0.102440.814
47_D59_I0.102320.813
100_L105_K0.101720.809
84_A123_V0.101620.808
70_L76_I0.101530.807
14_F32_Y0.101490.807
78_W100_L0.100810.801
14_F77_L0.10020.796
21_T26_A0.099980.795
51_L63_A0.099480.791
23_L29_L0.099270.789
92_A96_I0.099120.788
18_F88_L0.098720.785
90_A120_M0.09790.778
36_E69_A0.097540.775
114_L122_V0.097510.775
9_T12_I0.097130.772
8_Y12_I0.097030.771
51_L54_R0.096880.770
100_L120_M0.096880.770
9_T16_A0.09670.769
18_F82_G0.096650.768
13_L87_L0.096640.768
98_V104_G0.096240.765
84_A90_A0.096210.765
38_F53_N0.096180.765
7_G26_A0.096060.764
101_I106_N0.095880.762
14_F18_F0.095780.761
20_L74_F0.095770.761
110_A127_A0.095750.761
14_F29_L0.095730.761
36_E127_A0.095710.761
39_G47_D0.095660.760
50_W56_V0.095530.759
99_W119_F0.095390.758
5_S21_T0.095210.757
23_L121_T0.095170.756
119_F123_V0.093910.746
100_L112_I0.093510.743
30_A91_L0.093350.742
97_T119_F0.093120.740
35_Q48_Q0.092980.739
5_S52_P0.092740.737
56_V96_I0.092420.735
33_I62_V0.092380.734
51_L114_L0.092330.734
7_G19_A0.091890.730
34_I87_L0.091630.728
64_L99_W0.091420.727
12_I19_A0.091110.724
48_Q59_I0.090870.722
13_L17_A0.090840.722
69_A72_G0.090840.722
19_A74_F0.090770.722
71_M96_I0.09070.721
48_Q78_W0.090630.720
56_V75_N0.090440.719
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
2wswA0.7323530.919
4ainA0.7323520.919
2xq2A0.944922.30.933
3giaA0.944910.80.942
3m73A0.85834.50.95
3rfuA0.88194.40.951
4gc0A0.39373.80.952
4aw6A0.78742.80.955
4hg6A0.62992.70.955
3j08A0.60632.30.957
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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