GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2188 - Uncharacterized protein conserved in bacteria (DUF2188)
Pfam: PF09954 (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: 62
Sequences: 384
Seq/Len: 6.19
HH_delta: 0.78 (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
2_H50_H0.712073.487
28_K57_R0.624083.056
4_V12_A0.462112.263
25_F34_A0.424982.081
7_E12_A0.405521.986
51_G57_R0.393361.927
23_K34_A0.387371.897
27_T30_E0.366711.796
35_A47_L0.364511.785
38_L41_N0.337311.652
29_A33_E0.328261.608
46_E60_R0.326541.599
50_H56_I0.323611.585
12_A24_T0.311581.526
14_K21_A0.295391.447
15_K18_A0.285181.397
48_I59_E0.280181.372
51_G55_K0.277771.360
1_Y22_S0.264561.296
18_A22_S0.263041.288
3_V35_A0.237871.165
1_Y59_E0.227421.114
46_E59_E0.224881.101
15_K22_S0.21691.062
1_Y42_Q0.212041.038
36_R46_E0.209161.024
12_A21_A0.202940.994
3_V47_L0.197230.966
25_F31_A0.194830.954
40_K61_S0.193530.948
1_Y38_L0.192850.944
5_P10_G0.192620.943
7_E10_G0.191410.937
56_I61_S0.18220.892
14_K47_L0.180280.883
29_A32_I0.179130.877
48_I58_E0.17890.876
28_K51_G0.17670.865
13_V35_A0.175160.858
9_G37_E0.174550.855
46_E61_S0.168970.828
3_V13_V0.167670.821
13_V31_A0.165690.811
10_G35_A0.1640.803
32_I47_L0.158940.778
7_E24_T0.158870.778
14_K17_G0.158680.777
38_L42_Q0.158670.777
15_K39_A0.157630.772
36_R60_R0.153590.752
47_L60_R0.153190.750
1_Y45_G0.152930.749
57_R60_R0.152250.746
26_D37_E0.149830.734
13_V22_S0.147910.724
44_G61_S0.146870.719
36_R61_S0.146660.718
20_R27_T0.145930.715
39_A45_G0.145170.711
35_A39_A0.144310.707
10_G24_T0.143880.705
26_D40_K0.143440.703
2_H56_I0.143190.701
16_E39_A0.137320.673
2_H48_I0.134520.659
39_A60_R0.13430.658
10_G33_E0.134180.657
31_A39_A0.133980.656
9_G58_E0.133830.655
4_V11_W0.133290.653
14_K59_E0.132040.647
17_G55_K0.131590.644
30_E37_E0.131010.642
34_A38_L0.130620.640
13_V38_L0.129590.635
7_E21_A0.128910.631
22_S42_Q0.125220.613
11_W53_D0.121190.594
28_K32_I0.120420.590
3_V52_R0.119970.588
5_P54_G0.119750.586
2_H54_G0.119650.586
34_A37_E0.119050.583
8_D21_A0.118390.580
49_I58_E0.118270.579
16_E33_E0.117090.573
15_K45_G0.117050.573
33_E37_E0.114190.559
37_E40_K0.113890.558
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
2ljuA0.887174.10.78
2jyaA0.887169.80.786
2dsyA0.919451.10.809
3vsvA0.774232.50.829
4kmqA0.854810.90.861
4aayA0.83879.40.864
2k8eA18.50.868
2yf0A0.91948.10.868
2h5gA0.935580.868
2bsgA0.45167.70.869
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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