GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3343 - Protein of unknown function (DUF3343)
Pfam: PF11823 (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: 73
Sequences: 397
Seq/Len: 5.44
HH_delta: 0.808 (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
28_V45_L0.34572.367
3_Y46_R0.274871.882
10_S13_D0.25881.772
33_T44_A0.23021.576
56_K69_I0.229941.574
5_L31_I0.21511.473
6_I26_I0.205291.405
7_T33_T0.19981.368
17_A59_L0.196371.344
35_R38_S0.196361.344
48_E51_D0.19611.343
4_Y49_P0.195861.341
21_L45_L0.195261.337
11_T43_L0.189371.296
51_D54_K0.189041.294
24_N58_I0.188961.294
5_L43_L0.188211.289
35_R40_G0.186461.277
57_E60_E0.184661.264
56_K60_E0.181921.245
15_M30_L0.181751.244
8_F14_A0.17651.208
47_F55_I0.174761.196
57_E61_E0.173711.189
54_K57_E0.173581.188
15_M32_P0.170561.168
12_H15_M0.170121.165
8_F37_I0.169811.163
21_L55_I0.169311.159
11_T14_A0.167341.146
25_G53_E0.163131.117
52_L56_K0.161051.103
64_I68_G0.158021.082
13_D65_E0.157251.077
17_A21_L0.152481.044
21_L28_V0.152221.042
59_L66_Y0.15091.033
33_T42_G0.15011.028
20_L24_N0.147721.011
4_Y59_L0.147371.009
48_E58_I0.146711.004
24_N69_I0.145950.999
19_K23_K0.141160.966
6_I55_I0.140160.960
32_P43_L0.139490.955
14_A44_A0.139110.952
3_Y10_S0.138980.951
4_Y47_F0.136840.937
51_D56_K0.134840.923
12_H46_R0.134020.918
38_S42_G0.13240.906
13_D64_I0.131560.901
26_I58_I0.131450.900
9_P13_D0.130370.893
6_I33_T0.128420.879
5_L14_A0.128310.878
11_T18_E0.127150.870
16_K20_L0.125840.862
47_F69_I0.124860.855
36_E45_L0.123880.848
17_A45_L0.122660.840
8_F38_S0.12220.837
63_G68_G0.122030.835
8_F42_G0.121830.834
29_R39_A0.121730.833
28_V47_F0.120140.822
42_G67_E0.120.822
61_E65_E0.119810.820
22_K58_I0.11960.819
20_L27_P0.117820.807
47_F52_L0.117820.807
4_Y48_E0.117340.803
32_P35_R0.117110.802
17_A35_R0.116840.800
23_K67_E0.116650.799
8_F17_A0.116220.796
30_L44_A0.115280.789
5_L10_S0.115110.788
19_K52_L0.114490.784
21_L47_F0.114080.781
6_I14_A0.113810.779
3_Y63_G0.112210.768
11_T40_G0.112130.768
9_P35_R0.111990.767
23_K54_K0.111670.765
54_K58_I0.111640.764
25_G48_E0.111220.761
21_L33_T0.1110.760
5_L18_E0.11080.759
7_T28_V0.109910.752
54_K60_E0.109760.751
6_I47_F0.109740.751
18_E64_I0.109520.750
27_P52_L0.10910.747
57_E63_G0.109010.746
14_A40_G0.108250.741
9_P12_H0.107810.738
18_E22_K0.107690.737
18_E31_I0.107460.736
22_K61_E0.107410.735
18_E28_V0.106340.728
19_K24_N0.105890.725
17_A31_I0.10580.724
52_L55_I0.104640.716
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
2lepA0.86385.20.808
1yj7A0.931575.70.826
2hfvA0.931566.60.836
4aibA0.972653.50.848
4hddA0.876748.10.853
2aleA1440.856
2gqcA0.904141.40.859
3mcqA139.80.86
2f06A0.931539.80.86
2l69A0.986339.30.86
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.234 seconds.