GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PapD_C - Pili assembly chaperone PapD C-terminal domain
Pfam: PF02753 (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: 68
Sequences: 1508
Seq/Len: 22.18
HH_delta: 0.062 (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
12_T32_M1.050853.791
10_Y34_A0.949513.425
4_K38_S0.855843.087
34_A37_S0.635112.291
3_V41_F0.623422.249
11_V56_Y0.619282.234
58_N64_I0.560612.022
2_T40_S0.512761.850
58_N62_G0.498211.797
15_S55_S0.476921.721
2_T38_S0.472751.705
12_T56_Y0.449611.622
33_I39_K0.40441.459
56_Y64_I0.382641.380
52_V56_Y0.373671.348
1_L52_V0.358161.292
26_K30_S0.342391.235
4_K36_F0.338081.220
59_D62_G0.319311.152
55_S65_E0.301941.089
27_I30_S0.301121.086
18_L52_V0.277921.003
17_K55_S0.257110.928
35_P60_Y0.25510.920
14_S57_I0.25260.911
8_P41_F0.252090.909
58_N61_G0.251750.908
16_L19_N0.24750.893
10_Y32_M0.246490.889
3_V54_F0.24430.881
17_K53_S0.24140.871
9_Y61_G0.239460.864
8_P36_F0.23840.860
24_K27_I0.234630.846
3_V13_L0.230920.833
55_S63_V0.230880.833
57_I63_V0.229430.828
19_N25_K0.22810.823
33_I37_S0.227370.820
4_K17_K0.226920.819
13_L56_Y0.225580.814
46_N49_S0.2250.812
16_L32_M0.22470.811
44_P47_S0.224040.808
13_L54_F0.223390.806
43_L47_S0.222920.804
19_N24_K0.21760.785
42_P45_A0.21160.763
47_S55_S0.210870.761
39_K42_P0.2090.754
19_N54_F0.207680.749
49_S53_S0.206970.747
28_D49_S0.205840.743
12_T33_I0.205720.742
40_S51_K0.20240.730
55_S64_I0.202340.730
54_F57_I0.199850.721
38_S42_P0.198450.716
44_P64_I0.193550.698
36_F60_Y0.189560.684
5_N8_P0.187370.676
1_L28_D0.187050.675
12_T39_K0.18550.669
10_Y37_S0.18510.668
6_P9_Y0.184930.667
39_K51_K0.184710.666
44_P51_K0.182560.659
17_K46_N0.182290.658
42_P49_S0.177460.640
25_K48_S0.175990.635
24_K30_S0.175110.632
2_T18_L0.174890.631
13_L64_I0.174070.628
25_K28_D0.173470.626
54_F64_I0.17230.622
16_L41_F0.170990.617
9_Y34_A0.170330.614
26_K49_S0.169750.612
4_K51_K0.169310.611
9_Y58_N0.168170.607
19_N43_L0.165450.597
45_A48_S0.16540.597
26_K40_S0.165150.596
13_L33_I0.165140.596
32_M35_P0.164470.593
9_Y62_G0.162150.585
36_F39_K0.162040.585
30_S47_S0.161910.584
18_L27_I0.161480.583
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
3q48A0.985399.40.062
4djmA0.926599.30.092
4ay0A0.926599.30.11
1klfA0.911899.30.116
2co7B0.926599.30.118
2xg5A0.955999.30.118
1l4iA0.926599.30.124
3gfuC0.897199.10.182
2huhA0.852926.90.819
1yycA0.985323.60.824

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