GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Big_3_2 - Bacterial Ig-like domain (group 3)
Pfam: PF12245 (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: CL0159
Length: 60
Sequences: 754
Seq/Len: 12.57
HH_delta: 0.265 (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
7_S11_V0.766783.873
33_D37_N0.567082.864
21_A25_Y0.33441.689
32_T38_T0.328061.657
22_D25_Y0.301261.522
26_T43_T0.269291.360
31_A34_K0.261711.322
20_D25_Y0.261381.320
24_E45_I0.257361.300
22_D51_T0.255051.288
33_D36_G0.248841.257
12_W48_V0.244111.233
6_A31_A0.24241.224
12_W46_V0.234441.184
16_I20_D0.229981.162
49_D52_A0.222171.122
7_S29_V0.212271.072
19_N22_D0.212261.072
30_T38_T0.2071.046
27_L44_Q0.203431.028
10_G23_G0.200951.015
26_T30_T0.200921.015
25_Y48_V0.199451.007
22_D44_Q0.196180.991
41_S44_Q0.192320.971
34_K40_S0.191180.966
16_I19_N0.188290.951
11_V24_E0.18730.946
12_W25_Y0.185350.936
15_V23_G0.184910.934
20_D23_G0.183660.928
30_T45_I0.173920.878
47_I50_N0.173770.878
14_T44_Q0.173660.877
16_I27_L0.172680.872
44_Q51_T0.166860.843
19_N41_S0.161880.818
49_D53_P0.161870.818
6_A39_S0.161670.817
24_E27_L0.159810.807
20_D41_S0.158510.801
38_T43_T0.158370.800
10_G53_P0.15650.791
28_T31_A0.1560.788
15_V38_T0.155730.787
24_E47_I0.155150.784
14_T29_V0.154610.781
15_V25_Y0.154460.780
25_Y44_Q0.153920.777
13_S30_T0.153490.775
28_T43_T0.153260.774
30_T39_S0.152870.772
18_E22_D0.151970.768
26_T38_T0.151810.767
30_T43_T0.150650.761
18_E46_V0.150340.759
23_G48_V0.150270.759
18_E54_A0.149030.753
14_T27_L0.148450.750
9_S38_T0.148350.749
18_E30_T0.14830.749
18_E43_T0.147350.744
31_A39_S0.146590.740
30_T40_S0.145330.734
10_G47_I0.145040.733
10_G41_S0.142880.722
51_T54_A0.14260.720
41_S48_V0.141810.716
27_L31_A0.139710.706
9_S24_E0.138430.699
26_T34_K0.138310.699
29_V52_A0.138270.698
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
2yn5A198.90.265
2yn5A0.998.90.288
3pddA0.983397.40.55
3pddA0.966796.30.628
3pe9A0.933393.60.687
1xf1A191.70.706
4ak1A0.966791.40.708
3arxA0.966786.50.734
4aqoA0.8167830.745
4hmeA0.966782.70.745

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