GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2249 - Uncharacterized conserved protein (DUF2249)
Pfam: PF10006 (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: CL0397
Length: 69
Sequences: 2330
Seq/Len: 33.77
HH_delta: 0.005 (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
52_S68_T1.147553.127
24_P27_E1.074772.929
30_E64_R1.044282.846
5_R62_E0.8432.297
6_G34_D0.761282.075
5_R32_V0.744062.028
7_L15_R0.691671.885
30_E66_R0.670571.827
28_T68_T0.644591.757
23_L29_L0.593291.617
19_A22_E0.576351.571
32_V64_R0.563871.537
7_L11_E0.560191.527
17_L21_D0.552961.507
40_L43_Q0.546431.489
20_L44_L0.519161.415
4_V12_P0.498641.359
28_T66_R0.489271.333
4_V33_N0.485331.323
11_E15_R0.450761.228
15_R18_E0.428411.168
53_W65_V0.418461.140
36_D39_P0.416141.134
32_V62_E0.408021.112
54_E68_T0.40121.093
10_P14_E0.393321.072
14_E17_L0.386971.055
7_L12_P0.385751.051
5_R34_D0.376171.025
28_T54_E0.374821.021
45_E53_W0.372471.015
20_L50_F0.36741.001
23_L27_E0.364560.994
41_Y44_L0.355760.970
16_I31_L0.346270.944
58_Q64_R0.342990.935
11_E14_E0.336970.918
4_V7_L0.333480.909
33_N65_V0.330750.901
23_L26_G0.329830.899
19_A23_L0.32910.897
2_L29_L0.327710.893
9_P14_E0.320790.874
4_V15_R0.317290.865
33_N36_D0.313690.855
43_Q47_R0.308870.842
42_P46_E0.305590.833
7_L13_H0.302820.825
59_G62_E0.301560.822
21_D47_R0.301140.821
8_P11_E0.297040.810
2_L19_A0.297030.809
41_Y45_E0.296450.808
26_G50_F0.292670.798
39_P42_P0.289790.790
40_L45_E0.289040.788
13_H17_L0.288680.787
16_I29_L0.283080.771
57_E64_R0.282650.770
6_G10_P0.281840.768
56_E64_R0.279290.761
2_L31_L0.277690.757
6_G9_P0.275640.751
59_G64_R0.275240.750
34_D38_R0.269640.735
20_L23_L0.26850.732
11_E34_D0.267190.728
13_H44_L0.266250.726
40_L63_W0.260460.710
20_L69_R0.253660.691
11_E16_I0.252290.688
14_E33_N0.251880.686
55_Y66_R0.250140.682
22_E56_E0.248070.676
9_P12_P0.240640.656
17_L44_L0.240360.655
14_E18_E0.239220.652
45_E67_I0.238550.650
36_D63_W0.238510.650
58_Q61_G0.232150.633
58_Q62_E0.228120.622
14_E44_L0.22420.611
41_Y53_W0.222060.605
13_H43_Q0.221980.605
19_A29_L0.221220.603
22_E60_P0.218340.595
18_E22_E0.218230.595
54_E66_R0.218010.594
17_L47_R0.217920.594
56_E63_W0.21550.587
55_Y59_G0.215270.587
9_P17_L0.213080.581
25_P68_T0.212190.578
40_L44_L0.210010.572
43_Q46_E0.208540.568
42_P65_V0.206170.562
12_P34_D0.205690.561
38_R41_Y0.203250.554
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
1je3A0.985599.40.005
1jdqA0.985599.40.01
1pavA0.985599.40.021
3hz7A0.985599.40.024
3lvjC0.985599.40.028
1okgA0.739196.70.588
2vkcA0.94257.30.777
3fryA0.826149.70.786
2lxrA0.985547.40.79
3iwlA0.811646.40.79

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