GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1294 - Protein of unknown function (DUF1294)
Pfam: PF06961 (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: 55
Sequences: 606
Seq/Len: 11.02
HH_delta: 0.874 (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
9_G46_F0.78913.096
31_A55_F0.61342.407
7_L30_L0.575682.259
5_F45_L0.557432.187
8_Y39_A0.535252.100
4_T39_A0.500191.962
10_I14_A0.477621.874
4_T30_L0.387591.521
4_T8_Y0.383481.504
31_A39_A0.372061.460
28_L31_A0.360141.413
36_W43_M0.358461.406
10_I22_I0.352071.381
8_Y28_L0.344441.351
42_G46_F0.337951.326
4_T34_G0.330771.298
9_G13_R0.328351.288
29_L33_L0.316041.240
40_L44_Y0.315241.237
38_G42_G0.306061.201
1_N36_W0.30481.196
47_R50_T0.298991.173
8_Y36_W0.292421.147
16_R19_G0.28311.111
6_V10_I0.281171.103
1_N28_L0.276871.086
7_L22_I0.270921.063
1_N37_P0.269541.057
43_M52_K0.255251.001
5_F9_G0.247380.971
31_A36_W0.245180.962
13_R17_R0.244660.960
5_F46_F0.244060.958
43_M54_S0.237430.931
41_L53_Q0.233780.917
4_T36_W0.232610.913
23_P26_T0.22560.885
28_L54_S0.223990.879
44_Y51_R0.221530.869
24_E49_K0.220060.863
44_Y47_R0.219520.861
23_P34_G0.203890.800
16_R22_I0.203860.800
9_G42_G0.203310.798
9_G41_L0.202810.796
28_L36_W0.201650.791
21_R24_E0.194540.763
46_F52_K0.193610.760
49_K52_K0.193120.758
8_Y52_K0.19050.747
2_L45_L0.1890.741
20_W24_E0.188250.739
48_H52_K0.18820.738
41_L51_R0.181120.711
18_G26_T0.179560.704
13_R19_G0.177630.697
12_K21_R0.176490.692
13_R16_R0.174120.683
27_L40_L0.173940.682
14_A26_T0.172210.676
25_K30_L0.171250.672
5_F42_G0.168570.661
21_R49_K0.168090.659
20_W47_R0.167840.658
20_W25_K0.167190.656
23_P40_L0.166750.654
29_L44_Y0.166270.652
10_I45_L0.165520.649
2_L40_L0.165120.648
14_A22_I0.16410.644
14_A53_Q0.163570.642
10_I13_R0.163140.640
27_L52_K0.161440.633
28_L32_L0.159250.625
38_G46_F0.158140.620
1_N55_F0.157660.619
3_I30_L0.156650.615
3_I25_K0.15260.599
40_L45_L0.151660.595
14_A43_M0.151270.593
2_L18_G0.151090.593
12_K15_A0.150540.591
14_A20_W0.150290.590
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
3cx5D0.963624.90.874
1pp9D0.963619.10.88
1jsdB0.527312.40.889
2rftB0.527311.60.891
1k7kA110.60.892
4bnqA110.20.893
3m5gB0.52739.80.894
3tquA19.10.895
1zrtD0.927390.896
4i78C0.52738.10.897
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