GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PG_binding_2 - Putative peptidoglycan binding domain
Pfam: PF08823 (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: CL0244
Length: 74
Sequences: 3819
Seq/Len: 51.61
HH_delta: 0.087 (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_E48_R1.70923.017
63_D67_D1.536042.711
21_V66_I1.467652.591
30_Y53_T1.34632.376
22_Q37_G1.206632.130
51_A64_G1.036991.830
51_A70_V1.028981.816
39_W47_L0.976381.723
36_D40_D0.954491.685
22_Q43_T0.953211.683
67_D70_V0.94711.672
66_I71_L0.944591.667
22_Q40_D0.944331.667
39_W44_E0.839211.481
48_R62_G0.817111.442
50_W54_E0.799591.411
50_W73_Y0.771551.362
68_P72_A0.745361.316
14_D38_V0.738591.304
52_G62_G0.703881.242
47_L66_I0.699791.235
22_Q36_D0.699051.234
15_G18_A0.69381.225
41_E45_D0.689381.217
26_K35_A0.653531.154
51_A63_D0.651261.150
20_E24_A0.647021.142
18_A39_W0.632841.117
24_A28_L0.601761.062
16_D19_R0.588281.038
21_V47_L0.57981.023
26_K32_K0.573051.012
69_V72_A0.54760.967
17_V20_E0.534060.943
19_R23_E0.526890.930
49_A53_T0.518710.916
33_G42_A0.514580.908
48_R52_G0.513250.906
24_A27_R0.513170.906
45_D49_A0.499770.882
19_R35_A0.499290.881
26_K31_Y0.496710.877
17_V71_L0.494050.872
54_E73_Y0.487680.861
40_D43_T0.47530.839
19_R37_G0.474030.837
50_W70_V0.467630.825
56_F70_V0.465780.822
31_Y42_A0.444270.784
42_A45_D0.432980.764
30_Y49_A0.416160.735
28_L74_L0.415970.734
21_V74_L0.414950.732
28_L54_E0.406680.718
24_A74_L0.403630.712
20_E23_E0.394430.696
13_L17_V0.39430.696
26_K34_E0.393280.694
47_L70_V0.383140.676
23_E27_R0.379420.670
15_G39_W0.374060.660
69_V73_Y0.372460.657
31_Y36_D0.362790.640
23_E35_A0.355370.627
12_P38_V0.352120.622
13_L18_A0.347740.614
20_E27_R0.342060.604
61_R67_D0.341050.602
25_L43_T0.340290.601
31_Y35_A0.334580.591
18_A43_T0.333520.589
48_R64_G0.331890.586
31_Y49_A0.328230.579
15_G19_R0.324210.572
39_W66_I0.323230.571
45_D48_R0.31860.562
51_A62_G0.307110.542
12_P18_A0.306870.542
31_Y46_A0.305830.540
56_F63_D0.304450.537
49_A52_G0.302170.533
23_E26_K0.30190.533
28_L53_T0.298740.527
29_G46_A0.296780.524
50_W56_F0.291680.515
24_A71_L0.290070.512
34_E42_A0.284070.501
71_L74_L0.282340.498
47_L50_W0.281030.496
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
4fetB0.918999.40.087
3bkhA0.945999.30.101
1lbuA0.945999.30.135
4g54A0.945999.20.166
3d2yA0.918998.90.279
1l6jA0.918997.70.519
1ck7A0.878497.60.532
1su3A0.864997.60.533
1slmA0.864997.50.535
1eakA0.864997.50.538

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