GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF485 - Protein of unknown function DUF485
Pfam: PF04341 (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: 91
Sequences: 656
Seq/Len: 7.21
HH_delta: 0.865 (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
6_E87_A0.444562.848
28_L65_F0.406382.604
9_E13_R0.348922.235
28_L62_Q0.32612.089
19_W23_A0.293151.878
83_P87_A0.272851.748
13_R80_E0.259771.664
86_R90_E0.258581.657
68_V72_L0.25431.629
15_R19_W0.248391.591
12_R16_R0.239831.537
3_R8_Q0.238871.530
76_R81_F0.237731.523
39_A42_L0.234661.503
79_R83_P0.233931.499
86_R89_R0.2311.480
87_A90_E0.222261.424
59_G67_W0.220441.412
5_P8_Q0.204381.309
9_E84_L0.202221.296
34_L38_F0.188131.205
17_L76_R0.184681.183
66_A69_L0.18441.181
65_F69_L0.18161.163
47_V54_L0.181561.163
70_T74_V0.181461.163
15_R34_L0.176911.133
35_L42_L0.174711.119
76_R80_E0.173551.112
43_M53_T0.173051.109
21_L78_N0.169411.085
17_L63_I0.167471.073
55_G70_T0.16741.072
55_G78_N0.164971.057
57_V61_G0.164521.054
27_V45_T0.163441.047
32_F63_I0.161851.037
84_L87_A0.160361.027
75_R80_E0.158341.014
63_I66_A0.157811.011
14_R18_A0.157771.011
40_P55_G0.157491.009
2_L47_V0.156871.005
47_V57_V0.154870.992
33_V70_T0.154120.987
64_V68_V0.153480.983
76_R88_I0.153120.981
70_T77_A0.152450.977
63_I71_W0.151630.971
27_V31_G0.151020.968
35_L58_L0.150910.967
42_L52_L0.150860.967
65_F68_V0.150220.962
22_S25_F0.150190.962
44_A67_W0.149360.957
29_Y43_M0.147490.945
10_L37_A0.147130.943
59_G63_I0.146820.941
22_S26_L0.141790.908
42_L60_L0.141160.904
54_L58_L0.138090.885
43_M60_L0.137060.878
78_N84_L0.136910.877
46_P52_L0.13680.876
4_S87_A0.136560.875
24_I86_R0.136420.874
36_S62_Q0.135650.869
37_A88_I0.135410.868
26_L53_T0.13450.862
32_F70_T0.133090.853
39_A58_L0.131220.841
29_Y59_G0.13120.841
14_R21_L0.13060.837
23_A27_V0.129990.833
75_R79_R0.129850.832
68_V71_W0.12970.831
11_V21_L0.129440.829
42_L46_P0.12910.827
43_M66_A0.127920.820
32_F59_G0.127570.817
21_L69_L0.127550.817
79_R90_E0.125790.806
21_L84_L0.125240.802
35_L50_G0.125230.802
14_R30_F0.124680.799
8_Q23_A0.124270.796
32_F69_L0.123990.794
24_I44_A0.123670.792
35_L45_T0.123370.790
55_G74_V0.122980.788
40_P70_T0.122730.786
36_S58_L0.122660.786
38_F88_I0.122310.784
56_I59_G0.121640.779
77_A83_P0.121140.776
35_L40_P0.120940.775
29_Y66_A0.120810.774
14_R81_F0.120510.772
11_V15_R0.12050.772
41_E45_T0.120330.771
10_L83_P0.119940.768
14_R64_V0.118850.761
72_L76_R0.118240.758
7_F11_V0.117920.755
3_R12_R0.117630.754
5_P9_E0.117340.752
23_A80_E0.117280.751
13_R16_R0.116830.748
28_L32_F0.116020.743
28_L69_L0.115970.743
48_F72_L0.115970.743
19_W28_L0.115760.742
29_Y63_I0.115460.740
68_V86_R0.115030.737
74_V78_N0.115010.737
25_F28_L0.114370.733
56_I60_L0.113650.728
37_A40_P0.113290.726
71_W82_D0.112910.723
12_R68_V0.11270.722
56_I67_W0.112660.722
26_L69_L0.112290.719
80_E84_L0.11190.717
47_V60_L0.111830.716
42_L54_L0.111670.715
22_S50_G0.111010.711
38_F42_L0.110730.709
23_A26_L0.110610.709
6_E9_E0.110560.708
14_R76_R0.110070.705
6_E84_L0.110.705
28_L35_L0.109940.704
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
4he8M0.95651.20.865
4djkA0.97838.60.875
2iubA0.846222.70.887
4ev6A0.846221.70.888
4i0uA0.846219.80.891
3rkoN0.95619.10.891
3rlfF0.901114.90.896
4he8N0.95614.30.897
4he8L0.97812.80.899
3l1lA0.835210.40.903
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