GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PapD_N - Pili and flagellar-assembly chaperone PapD N-terminal domain
Pfam: PF00345 (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: 122
Sequences: 1791
Seq/Len: 14.68
HH_delta: 0.097 (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_N15_Q0.555572.946
76_L84_Y0.457242.425
89_R109_R0.434062.302
9_I18_A0.428182.271
4_I112_I0.424322.250
30_Y90_E0.399552.119
61_E64_E0.395762.099
9_I70_V0.377442.002
21_T65_S0.364581.933
27_D63_G0.352761.871
29_P61_E0.351191.862
87_S111_S0.344491.827
13_E78_I0.342021.814
37_Y111_S0.339521.801
83_L115_F0.338431.795
36_V114_V0.336811.786
77_P82_S0.334971.776
9_I86_L0.331911.760
14_S119_A0.322131.708
29_P59_R0.305491.620
26_S30_Y0.303111.607
43_D46_E0.29531.566
4_I88_F0.288021.527
3_Q6_P0.283561.504
37_Y87_S0.282571.499
35_W87_S0.278931.479
39_Q43_D0.272291.444
34_V88_F0.269871.431
9_I112_I0.260171.380
51_F70_V0.259631.377
4_I20_I0.255931.357
53_V70_V0.241541.281
81_E117_R0.240311.274
1_G90_E0.234831.245
34_V68_V0.232831.235
77_P80_R0.228031.209
12_N18_A0.227341.206
78_I120_G0.221081.172
53_V68_V0.219911.166
11_F18_A0.215351.142
5_S21_T0.214971.140
35_W89_R0.214851.139
102_N111_S0.214041.135
60_L66_Q0.212831.129
70_V114_V0.211331.121
38_D45_D0.208671.107
20_I86_L0.202371.073
88_F112_I0.200011.061
60_L64_E0.19851.053
85_R111_S0.1971.045
23_T65_S0.196461.042
58_F66_Q0.195761.038
87_S109_R0.193871.028
85_R89_R0.193751.028
36_V49_D0.192611.021
2_I22_V0.190671.011
90_E109_R0.189811.007
68_V88_F0.188841.001
37_Y85_R0.188551.000
80_R118_P0.185770.985
78_I119_A0.182820.970
32_V58_F0.182260.967
33_Q89_R0.180460.957
12_N53_V0.179990.955
58_F68_V0.177950.944
11_F51_F0.176290.935
68_V86_L0.175140.929
31_L59_R0.17360.921
79_D117_R0.173190.918
79_D118_P0.17220.913
32_V90_E0.171970.912
82_S116_Y0.171480.909
53_V56_P0.170110.902
50_P84_Y0.167030.886
13_E120_G0.166890.885
29_P106_I0.164620.873
3_Q110_Y0.164280.871
71_Y74_S0.163010.864
36_V53_V0.161190.855
69_R92_P0.15910.844
31_L57_I0.158880.843
17_S69_R0.158750.842
71_Y116_Y0.157850.837
6_P9_I0.156370.829
30_Y34_V0.156360.829
66_Q90_E0.156330.829
96_A101_K0.155390.824
69_R81_E0.154940.822
34_V66_Q0.153990.817
53_V86_L0.153090.812
51_F116_Y0.152050.806
96_A99_E0.151310.802
14_S104_V0.150870.800
1_G25_N0.14950.793
22_V39_Q0.14820.786
1_G30_Y0.147830.784
39_Q47_P0.147510.782
76_L82_S0.145180.770
19_S106_I0.145080.769
91_I108_L0.144480.766
60_L116_Y0.144160.765
33_Q91_I0.142980.758
17_S50_P0.142820.757
2_I32_V0.142620.756
60_L74_S0.142130.754
30_Y58_F0.14190.753
8_R81_E0.141670.751
113_P117_R0.140940.747
33_Q85_R0.140540.745
22_V61_E0.140290.744
25_N106_I0.140120.743
85_R113_P0.139580.740
78_I99_E0.139520.740
44_E119_A0.139430.739
103_G119_A0.139130.738
30_Y60_L0.138030.732
64_E101_K0.1380.732
35_W111_S0.137850.731
7_T117_R0.13770.730
10_I117_R0.137170.727
34_V70_V0.137170.727
43_D47_P0.136980.726
45_D96_A0.136860.726
49_D53_V0.136520.724
33_Q57_I0.135530.719
82_S118_P0.135120.717
4_I9_I0.134380.713
57_I91_I0.134380.713
108_L121_L0.133640.709
63_G68_V0.133290.707
74_S100_S0.133140.706
75_K78_I0.132960.705
7_T10_I0.132240.701
2_I30_Y0.131990.700
95_E100_S0.131710.698
34_V93_P0.130990.695
77_P118_P0.130790.694
84_Y107_A0.130280.691
4_I66_Q0.129650.688
76_L80_R0.129620.687
87_S91_I0.129540.687
43_D49_D0.129380.686
53_V74_S0.128920.684
37_Y109_R0.128350.681
26_S109_R0.127980.679
8_R113_P0.127570.677
55_P69_R0.127460.676
14_S71_Y0.12710.674
25_N72_R0.127070.674
21_T67_T0.126860.673
32_V66_Q0.126730.672
92_P113_P0.126160.669
67_T108_L0.125820.667
85_R115_F0.125530.666
8_R86_L0.125480.665
23_T64_E0.124670.661
10_I104_V0.124630.661
8_R117_R0.12440.660
39_Q45_D0.124210.659
11_F15_Q0.123330.654
18_A71_Y0.12310.653
16_R23_T0.122760.651
52_I106_I0.122610.650
50_P82_S0.122030.647
85_R109_R0.121040.642
22_V54_S0.12080.641
14_S120_G0.120570.639
83_L120_G0.120220.638
31_L56_P0.120190.637
84_Y116_Y0.119840.636
30_Y116_Y0.119560.634
27_D119_A0.119510.634
6_P89_R0.118710.630
13_E119_A0.118560.629
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
3q48A0.983699.90.097
1klfA0.967299.90.109
2co7B0.967299.90.112
4djmA0.967299.90.117
2xg5A0.950899.90.119
4ay0A0.967299.90.12
1l4iA0.967299.90.12
3gfuC0.942699.90.145
1rowA0.827996.40.782
1wicA0.926295.40.801

Page generated in 0.0309 seconds.