GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2171 - Uncharacterized protein conserved in bacteria (DUF2171)
Pfam: PF09939 (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. )
Clan: CL0350
Length: 67
Sequences: 370
Seq/Len: 5.52
HH_delta: 0.512 (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
10_G65_A0.248011.995
49_D59_S0.226251.820
50_S57_H0.206431.661
48_V62_A0.202561.630
19_V56_V0.200941.617
21_H40_H0.196781.583
43_I47_W0.187971.512
44_P47_W0.180271.450
26_R42_Y0.178391.435
52_D57_H0.174361.403
8_V29_L0.174221.402
61_T64_E0.168221.353
16_V28_K0.162511.308
6_M51_V0.161461.299
8_V64_E0.160581.292
11_S59_S0.15861.276
5_H31_K0.150511.211
23_E36_H0.145481.171
25_D34_S0.145231.169
28_K40_H0.143551.155
47_W60_K0.140411.130
7_E15_H0.139661.124
46_S51_V0.137691.108
48_V58_L0.137611.107
7_E56_V0.135151.087
9_I23_E0.134211.080
5_H30_T0.133291.072
6_M27_I0.132821.069
20_D40_H0.132461.066
33_D36_H0.129821.045
58_L64_E0.129221.040
30_T58_L0.127111.023
27_I30_T0.124291.000
39_Q62_A0.123380.993
29_L46_S0.1230.990
19_V50_S0.122620.987
45_L48_V0.122130.983
5_H8_V0.122020.982
15_H18_T0.121010.974
19_V29_L0.120580.970
20_D30_T0.120440.969
35_G42_Y0.120020.966
46_S57_H0.116750.939
53_D64_E0.114520.921
6_M58_L0.113180.911
6_M29_L0.112740.907
11_S43_I0.11190.900
54_D57_H0.109850.884
52_D55_K0.109270.879
33_D58_L0.108020.869
22_V25_D0.107860.868
22_V27_I0.107740.867
49_D54_D0.107510.865
34_S38_G0.107360.864
11_S49_D0.10710.862
24_G27_I0.106890.860
15_H57_H0.104490.841
29_L45_L0.104310.839
10_G58_L0.104250.839
21_H47_W0.104230.839
18_T22_V0.101210.814
49_D57_H0.101160.814
42_Y51_V0.100370.808
11_S24_G0.100120.806
28_K38_G0.099940.804
36_H44_P0.099540.801
4_E15_H0.099440.800
10_G33_D0.098880.796
6_M30_T0.096470.776
8_V58_L0.096450.776
27_I45_L0.09530.767
20_D38_G0.095280.767
43_I60_K0.095190.766
16_V36_H0.094750.762
20_D41_H0.092760.746
4_E40_H0.092340.743
51_V56_V0.092080.741
48_V63_D0.091770.738
43_I59_S0.091210.734
22_V53_D0.091130.733
18_T34_S0.090740.730
48_V57_H0.090610.729
25_D62_A0.090610.729
7_E49_D0.090610.729
10_G43_I0.090080.725
19_V60_K0.089980.724
23_E28_K0.089810.723
24_G44_P0.089760.722
12_D58_L0.089760.722
4_E29_L0.089140.717
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
1eysH0.9552980.512
3htrA0.970197.70.547
2wjnH0.955297.50.577
1rzhH0.940397.40.581
1pm3A0.9104930.714
2dyiA0.895592.10.723
2f1lA0.9104890.741
3h9nA188.70.742
2qggA0.955286.40.752
2kk4A0.895565.70.793
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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