GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ImpA-rel_N - ImpA-related N-terminal
Pfam: PF06812 (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: 599
Seq/Len: 9.66
HH_delta: 0.851 (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
18_K53_Y0.49312.710
12_L21_R0.369952.033
12_L22_V0.344241.892
1_D4_K0.338751.862
6_E10_L0.326481.794
6_E29_A0.312291.716
4_K7_E0.307761.692
6_E30_L0.307241.689
25_W39_L0.292831.609
25_W28_E0.284131.562
49_L57_L0.277281.524
13_L18_K0.272121.496
3_D33_L0.271741.494
35_G38_G0.270741.488
12_L17_S0.269351.480
38_G42_G0.259291.425
21_R25_W0.25131.381
9_A22_V0.23541.294
24_V46_L0.228481.256
23_A49_L0.224931.236
27_T42_G0.223381.228
47_A51_E0.223291.227
26_L30_L0.214641.180
7_E11_E0.206711.136
30_L41_E0.20651.135
13_L53_Y0.205281.128
37_A41_E0.204961.127
50_L61_L0.203821.120
34_E41_E0.189141.040
20_L46_L0.181720.999
38_G45_L0.181590.998
54_W61_L0.180110.990
3_D15_E0.178030.979
2_W6_E0.174570.959
8_L22_V0.172890.950
21_R58_H0.172580.949
13_L17_S0.172240.947
5_V29_A0.171710.944
26_L56_S0.170570.938
3_D56_S0.170310.936
15_E39_L0.167450.920
50_L55_D0.166960.918
37_A40_A0.160260.881
40_A43_L0.156460.860
48_D52_N0.155250.853
1_D5_V0.155210.853
31_L39_L0.154710.850
19_D45_L0.14990.824
21_R24_V0.148150.814
43_L58_H0.146280.804
52_N60_Q0.144160.792
20_L57_L0.143170.787
10_L26_L0.142680.784
8_L35_G0.142560.784
11_E44_E0.141150.776
24_V28_E0.139430.766
15_E56_S0.13850.761
6_E33_L0.136840.752
11_E51_E0.136530.750
27_T46_L0.136070.748
57_L60_Q0.133850.736
22_V40_A0.131830.725
10_L14_S0.131340.722
11_E15_E0.131120.721
3_D44_E0.130470.717
23_A27_T0.129810.713
56_S60_Q0.129720.713
6_E20_L0.129370.711
3_D25_W0.129290.711
1_D30_L0.129150.710
41_E60_Q0.12910.710
11_E55_D0.128970.709
4_K8_L0.128750.708
31_L43_L0.128740.708
40_A47_A0.128640.707
34_E38_G0.127070.698
5_V39_L0.126170.693
18_K49_L0.125890.692
17_S20_L0.125210.688
8_L11_E0.124710.685
32_R55_D0.12350.679
54_W59_P0.123340.678
20_L58_H0.122920.676
19_D55_D0.122830.675
34_E44_E0.122310.672
2_W25_W0.122310.672
7_E50_L0.122010.671
44_E56_S0.121480.668
3_D48_D0.118990.654
11_E16_Q0.11890.654
50_L58_H0.118840.653
2_W21_R0.118760.653
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
4j5rA0.403224.20.851
1x5bA0.983921.40.854
2jycA0.403220.30.856
2eeeA0.403219.50.857
3zyqA0.983916.30.862
2fg1A0.403216.20.862
1itwA0.951615.80.862
2b0tA0.951615.70.862
1juqA0.983915.10.863
2jgdA114.80.864
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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