GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1456 - Protein of unknown function (DUF1456)
Pfam: PF07308 (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: 68
Sequences: 446
Seq/Len: 6.56
HH_delta: 0.88 (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
23_F54_L0.297671.865
5_L19_M0.258781.622
32_K36_S0.248321.556
7_K11_A0.237291.487
14_L22_I0.233041.460
19_M23_F0.231981.454
63_I68_G0.227281.424
12_L62_L0.22671.421
8_L11_A0.220951.385
19_M35_L0.217991.366
20_I35_L0.217691.364
9_R16_D0.212461.331
6_R16_D0.210881.321
30_V38_W0.210871.321
24_A29_E0.209871.315
21_E65_H0.209611.314
3_D68_G0.205961.291
60_N63_I0.205271.286
50_C54_L0.20461.282
52_D59_L0.203281.274
31_S34_E0.201981.266
38_W54_L0.201711.264
25_L65_H0.194451.219
4_I55_L0.192381.206
4_I27_G0.191281.199
25_L64_I0.189571.188
28_F57_N0.187191.173
7_K10_Y0.184811.158
46_G60_N0.182131.141
22_I58_F0.180421.131
8_L14_L0.17851.119
12_L64_I0.178061.116
19_M58_F0.176941.109
14_L19_M0.176851.108
5_L59_L0.173741.089
3_D63_I0.17361.088
35_L40_R0.173271.086
11_A56_R0.172871.083
6_R10_Y0.170561.069
47_Y59_L0.166111.041
21_E27_G0.163341.024
3_D60_N0.162321.017
3_D24_A0.162241.017
15_K39_L0.161221.010
20_I32_K0.159611.000
22_I65_H0.157520.987
1_N52_D0.1570.984
58_F62_L0.155310.973
50_C62_L0.154530.968
28_F53_Q0.149980.940
63_I67_R0.148360.930
26_A35_L0.148270.929
15_K18_D0.147420.924
3_D45_K0.14450.906
50_C58_F0.143580.900
7_K23_F0.141960.890
53_Q56_R0.141310.886
18_D40_R0.140950.883
3_D9_R0.140610.881
11_A15_K0.137730.863
6_R44_E0.136560.856
25_L45_K0.136230.854
19_M63_I0.136140.853
24_A27_G0.135250.848
30_V66_K0.134620.844
5_L14_L0.132240.829
64_I68_G0.131520.824
60_N68_G0.130980.821
41_K67_R0.129070.809
50_C59_L0.128690.806
60_N67_R0.127080.796
24_A28_F0.126940.795
51_S63_I0.125610.787
9_R61_G0.124580.781
20_I42_E0.12440.780
35_L39_L0.123030.771
10_Y44_E0.122850.770
33_A51_S0.122070.765
7_K57_N0.121940.764
34_E38_W0.121810.763
25_L29_E0.121140.759
5_L38_W0.120510.755
43_D62_L0.120260.754
16_D32_K0.120230.753
34_E48_K0.119620.750
10_Y20_I0.119150.747
20_I33_A0.119080.746
21_E28_F0.117550.737
28_F32_K0.117250.735
23_F57_N0.117110.734
36_S40_R0.116940.733
9_R44_E0.116580.731
27_G57_N0.115940.727
9_R51_S0.114570.718
37_A48_K0.113480.711
43_D50_C0.113060.708
5_L12_L0.113010.708
13_D43_D0.111620.699
36_S48_K0.111240.697
44_E54_L0.111140.696
6_R46_G0.110650.693
19_M32_K0.110640.693
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
2ahqA0.794140.60.88
2mysC0.897128.10.889
2becA126.90.89
4eadA0.955925.90.891
1wlzA0.941225.50.891
2l2eA0.955925.40.891
2zkmX0.926525.10.891
2pvbA0.897123.40.893
1tizA0.852923.20.893
1dtlA0.9265220.895
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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