GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FtsH_ext - FtsH Extracellular
Pfam: PF06480 (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: 110
Sequences: 1553
Seq/Len: 14.12
HH_delta: 0.589 (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
38_M43_N0.865354.117
68_G76_Y0.698043.321
35_F39_L0.666623.171
93_F96_E0.55942.661
39_L44_V0.45722.175
31_S34_E0.444282.114
98_L103_V0.370661.763
42_G101_K0.369091.756
40_E97_A0.364281.733
96_E100_E0.348911.660
3_L8_I0.346681.649
46_K104_K0.332521.582
35_F47_V0.327331.557
79_F109_P0.32581.550
11_I15_F0.316161.504
46_K69_K0.307281.462
99_V105_Y0.294311.400
76_Y81_T0.284481.353
48_V108_V0.276381.315
96_E99_V0.271691.292
32_Y36_L0.271441.291
31_S104_K0.264871.260
2_I10_V0.261491.244
70_T74_S0.260321.238
95_I105_Y0.259911.236
2_I5_I0.252881.203
13_L17_F0.249921.189
40_E99_V0.249791.188
36_L40_E0.242661.154
69_K75_K0.24211.152
47_V105_Y0.240041.142
34_E38_M0.231071.099
10_V14_L0.226161.076
95_I98_L0.22311.061
15_F18_F0.221171.052
30_I38_M0.219521.044
94_L102_G0.21891.041
37_Q41_K0.214771.022
6_L10_V0.212781.012
8_I15_F0.208630.992
8_I11_I0.207140.985
12_L96_E0.206560.983
4_Y7_I0.20450.973
36_L99_V0.204460.973
30_I34_E0.203840.970
47_V98_L0.199470.949
28_K34_E0.198390.944
36_L95_I0.196560.935
51_N54_I0.195250.929
76_Y82_P0.194550.926
76_Y80_Y0.193670.921
22_S25_S0.193270.919
79_F82_P0.190540.906
14_L17_F0.190070.904
40_E101_K0.186160.886
29_E34_E0.184570.878
68_G77_T0.183560.873
42_G47_V0.183280.872
46_K106_E0.182250.867
10_V15_F0.181020.861
24_N27_T0.177530.845
13_L22_S0.176280.839
14_L21_N0.175960.837
80_Y83_S0.175480.835
73_G76_Y0.17330.824
98_L105_Y0.17280.822
45_K74_S0.169210.805
9_L48_V0.166840.794
97_A100_E0.165550.788
105_Y109_P0.165540.788
7_I13_L0.164830.784
4_Y54_I0.163560.778
2_I17_F0.161640.769
92_E102_G0.159160.757
51_N55_T0.1590.756
39_L98_L0.157780.751
5_I9_L0.15550.740
74_S77_T0.154760.736
9_L80_Y0.153990.733
34_E37_Q0.153040.728
17_F23_N0.153020.728
14_L50_Q0.152750.727
95_I107_S0.152660.726
73_G78_T0.15260.726
6_L14_L0.151990.723
45_K100_E0.151820.722
11_I102_G0.151520.721
14_L53_K0.151460.721
47_V94_L0.15090.718
38_M103_V0.150410.716
4_Y17_F0.148080.704
30_I76_Y0.147530.702
94_L109_P0.14730.701
39_L47_V0.147190.700
30_I35_F0.14680.698
97_A101_K0.146610.697
72_D75_K0.146220.696
98_L107_S0.145840.694
68_G78_T0.145750.693
16_N53_K0.14450.687
16_N36_L0.144260.686
31_S52_D0.143940.685
24_N28_K0.143470.683
55_T75_K0.143090.681
98_L101_K0.14220.676
99_V106_E0.141280.672
37_Q100_E0.140560.669
50_Q108_V0.140550.669
69_K73_G0.140020.666
12_L53_K0.139060.662
32_Y35_F0.136810.651
22_S109_P0.136520.649
32_Y47_V0.136120.648
10_V97_A0.134250.639
3_L107_S0.134190.638
49_I95_I0.133970.637
9_L18_F0.133810.637
23_N72_D0.133680.636
49_I54_I0.133550.635
49_I83_S0.133390.635
35_F78_T0.133320.634
8_I16_N0.133220.634
39_L103_V0.132450.630
2_I15_F0.131990.628
77_T100_E0.131820.627
51_N81_T0.13180.627
23_N45_K0.131670.626
35_F52_D0.131280.625
38_M70_T0.130870.623
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
2lnaA0.809197.10.589
3si5X0.21825.60.872
2j5lA0.60915.10.874
3cx5D0.37274.70.875
3arcI0.34.70.876
2qjyB0.37274.60.876
3ixzA0.31823.60.883
3lb6C0.33643.30.884
2rddB0.32733.30.884
2w3zA0.96362.80.888
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