GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Big_4 - Bacterial Ig-like domain (group 4)
Pfam: PF07532 (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: 59
Sequences: 377
Seq/Len: 6.39
HH_delta: 0.79 (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
22_V32_V0.403072.728
14_P52_V0.32142.175
24_Y52_V0.311432.108
39_I50_Y0.294011.990
8_T14_P0.289891.962
8_T44_Y0.267441.810
14_P44_Y0.245221.660
19_T35_T0.22681.535
20_V34_V0.226511.533
41_P45_N0.214831.454
30_E47_P0.189831.285
21_T31_E0.179761.217
14_P50_Y0.177271.200
11_G16_L0.176871.197
35_T55_T0.170411.153
20_V32_V0.166131.124
33_P38_P0.165241.118
13_K46_K0.163941.110
24_Y30_E0.162861.102
31_E53_T0.162451.100
13_K44_Y0.161761.095
10_V44_Y0.158821.075
15_Q23_T0.156391.059
38_P55_T0.15591.055
22_V44_Y0.155881.055
42_Y52_V0.152291.031
14_P39_I0.151861.028
6_V50_Y0.142880.967
7_T29_T0.142850.967
11_G42_Y0.142620.965
18_E32_V0.142580.965
19_T31_E0.141910.961
22_V56_V0.141820.960
23_T29_T0.140580.952
10_V14_P0.138490.937
13_K41_P0.134140.908
19_T33_P0.133890.906
35_T57_E0.132530.897
39_I45_N0.132180.895
18_E22_V0.131920.893
5_N18_E0.131560.890
7_T46_K0.131550.890
25_S28_S0.131410.889
12_E37_D0.130810.885
15_Q21_T0.12940.876
26_D35_T0.12890.872
8_T23_T0.127220.861
25_S37_D0.125220.848
21_T29_T0.124870.845
6_V14_P0.124860.845
49_T53_T0.123770.838
15_Q18_E0.123120.833
15_Q33_P0.119530.809
18_E38_P0.117920.798
8_T12_E0.117030.792
19_T51_T0.112290.760
46_K53_T0.112270.760
18_E39_I0.10970.743
21_T35_T0.108720.736
6_V23_T0.108180.732
22_V27_G0.106480.721
39_I52_V0.106470.721
8_T46_K0.106460.721
42_Y45_N0.105870.717
10_V41_P0.105690.715
31_E56_V0.104840.710
24_Y32_V0.103580.701
5_N34_V0.103130.698
6_V13_K0.10190.690
41_P52_V0.100660.681
7_T50_Y0.09990.676
19_T46_K0.099370.673
31_E35_T0.098990.670
27_G49_T0.098380.666
39_I57_E0.097910.663
10_V57_E0.097880.663
5_N53_T0.097210.658
22_V50_Y0.096880.656
13_K55_T0.096830.655
26_D48_G0.096750.655
9_A57_E0.096580.654
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
2l7yA154.50.79
2kpnA0.9492430.803
4hmeA0.966131.90.816
3p4lA0.830530.30.818
3isyA0.915326.90.822
1wgoA0.983125.90.824
4f8lA0.983124.60.825
2ee2A0.762720.10.832
1uenA0.830517.30.837
1wj3A0.813616.90.837
If you are interested in a protein containing this domain,
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