GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2136 - Uncharacterized protein conserved in bacteria (DUF2136)
Pfam: PF09907 (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: 76
Sequences: 371
Seq/Len: 4.88
HH_delta: 0.851 (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
44_G47_K0.484713.157
43_I50_L0.386992.520
3_K7_E0.377432.458
39_V56_F0.317972.071
13_V61_V0.286591.866
55_D64_R0.251241.636
20_N23_E0.251111.635
17_D59_Q0.249471.625
1_D42_N0.240981.569
9_W41_F0.22421.460
32_D40_V0.220141.434
19_K59_Q0.219681.431
13_V18_W0.218151.421
25_K45_G0.216711.411
53_K64_R0.214721.398
67_G75_I0.211951.380
25_K32_D0.207011.348
1_D48_Y0.203341.324
32_D42_N0.201311.311
65_F75_I0.198551.293
19_K23_E0.198321.292
38_R65_F0.191211.245
6_L66_I0.187751.223
24_L30_S0.187161.219
4_Q7_E0.18641.214
31_A39_V0.178871.165
10_Y70_A0.177531.156
54_I61_V0.17711.153
55_D58_R0.174221.135
37_N56_F0.172251.122
12_E27_Q0.17221.121
38_R67_G0.167971.094
24_L52_A0.166971.087
2_A48_Y0.166361.083
49_R69_H0.165281.076
42_N46_N0.162631.059
12_E28_F0.160451.045
20_N71_E0.157441.025
52_A61_V0.154381.005
51_I68_T0.154111.004
40_V62_Y0.151430.986
8_A12_E0.150990.983
70_A74_K0.14830.966
3_K66_I0.147470.960
29_P63_I0.146340.953
14_K62_Y0.144620.942
26_Q70_A0.144390.940
29_P71_E0.14330.933
6_L43_I0.141510.922
25_K30_S0.140930.918
18_W24_L0.136510.889
3_K6_L0.136410.888
13_V24_L0.134550.876
2_A5_A0.132080.860
38_R75_I0.132030.860
69_H72_Y0.130970.853
7_E36_N0.130470.850
11_R26_Q0.129950.846
49_R72_Y0.128070.834
15_K51_I0.126660.825
31_A42_N0.126390.823
63_I66_I0.126120.821
39_V75_I0.125260.816
60_I64_R0.125070.814
53_K60_I0.124930.814
28_F32_D0.123760.806
21_P36_N0.123190.802
16_A27_Q0.122780.800
8_A13_V0.122390.797
53_K62_Y0.12150.791
1_D17_D0.121190.789
10_Y45_G0.12070.786
32_D46_N0.119850.780
33_I56_F0.119580.779
11_R15_K0.119090.776
17_D71_E0.118770.773
29_P54_I0.118390.771
31_A41_F0.117650.766
21_P65_F0.117110.763
40_V46_N0.116410.758
11_R22_A0.115840.754
51_I75_I0.115290.751
28_F31_A0.114310.744
66_I73_D0.113360.738
9_W31_A0.113340.738
68_T71_E0.112910.735
18_W31_A0.112450.732
32_D60_I0.111850.728
31_A48_Y0.111730.728
67_G76_D0.111470.726
25_K63_I0.111390.725
13_V41_F0.111340.725
55_D62_Y0.111340.725
22_A70_A0.111070.723
19_K26_Q0.110050.717
8_A19_K0.109960.716
46_N49_R0.109550.713
3_K71_E0.108440.706
10_Y57_E0.108030.704
30_S74_K0.106790.695
14_K74_K0.106350.693
22_A26_Q0.10410.678
36_N58_R0.10310.671
22_A74_K0.102430.667
33_I37_N0.102380.667
4_Q62_Y0.10220.666
25_K65_F0.101580.662
46_N50_L0.101190.659
4_Q8_A0.101080.658
12_E44_G0.100990.658
26_Q74_K0.100880.657
33_I39_V0.100330.653
27_Q51_I0.100280.653
39_V54_I0.099990.651
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
3g5oB0.934287.30.851
1z8mA0.921164.10.878
2otrA0.973757.90.882
2kheA0.934257.40.883
2a6sA0.868451.10.887
1wmiA0.921146.20.89
3bpqB0.947437.10.896
3oeiC0.868426.20.903
4fxiA0.868420.90.907
4ar9A0.684217.60.91
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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