GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
T2SE_Nter - Type II secretion system (T2SS) protein E N-terminal domain
Pfam: PF05157 (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: 109
Sequences: 1806
Seq/Len: 16.57
HH_delta: 0.046 (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
90_A95_I0.711983.052
42_L46_R0.689552.956
63_A90_A0.62692.687
45_A103_Y0.547822.348
7_I12_L0.53022.273
9_E93_E0.49582.125
59_T86_E0.493822.117
61_V88_V0.487832.091
55_Q82_K0.466812.001
8_S11_Q0.464011.989
91_T94_D0.454561.949
17_A24_F0.419931.800
54_R61_V0.414151.775
53_L88_V0.412891.770
46_R100_E0.410611.760
66_D69_D0.406911.744
26_D94_D0.393761.688
49_R96_D0.392711.684
13_L89_L0.390161.673
37_L102_Y0.385741.654
76_L85_I0.37631.613
44_F48_N0.363591.559
65_A95_I0.360981.547
64_V87_F0.355811.525
70_P74_D0.355021.522
20_L68_L0.349441.498
49_R92_R0.346331.485
10_D24_F0.339851.457
40_L45_A0.33011.415
14_E24_F0.328361.408
53_L63_A0.31231.339
9_E13_L0.307821.320
92_R96_D0.300921.290
60_L80_L0.290591.246
53_L61_V0.29021.244
26_D29_E0.289181.240
1_L7_I0.283711.216
63_A88_V0.274671.177
73_L87_F0.268161.150
16_L19_Q0.263841.131
51_L102_Y0.263311.129
75_E78_F0.256791.101
49_R65_A0.250661.075
28_D97_Q0.250091.072
48_N72_A0.249781.071
77_E84_P0.249311.069
13_L24_F0.247831.062
9_E91_T0.246041.055
59_T84_P0.243511.044
48_N75_E0.243361.043
25_V53_L0.243161.042
56_D59_T0.242871.041
36_L55_Q0.242131.038
39_R55_Q0.239771.028
13_L91_T0.229730.985
80_L84_P0.229530.984
17_A22_L0.228660.980
27_L63_A0.2270.973
45_A99_L0.226040.969
58_G82_K0.225540.967
47_R75_E0.218140.935
75_E79_L0.218030.935
69_D72_A0.216790.929
42_L104_G0.215550.924
2_V12_L0.212380.910
40_L50_V0.204250.876
11_Q15_A0.204110.875
65_A92_R0.203080.871
33_D36_L0.202590.868
17_A23_P0.202490.868
62_V76_L0.202320.867
50_V76_L0.200360.859
41_P79_L0.199220.854
15_A18_E0.198040.849
32_V51_L0.195920.840
23_P88_V0.195210.837
7_I15_A0.1950.836
45_A50_V0.193780.831
95_I99_L0.191630.822
41_P45_A0.190.815
36_L39_R0.189680.813
10_D14_E0.187820.805
25_V90_A0.181680.779
69_D75_E0.180830.775
20_L64_V0.179870.771
16_L89_L0.178430.765
32_V36_L0.178210.764
1_L12_L0.177050.759
43_E47_R0.175880.754
20_L89_L0.174720.749
76_L80_L0.172740.741
35_E38_D0.17030.730
51_L98_L0.170240.730
10_D91_T0.170220.730
37_L105_S0.169320.726
96_D100_E0.16870.723
45_A52_P0.165620.710
32_V37_L0.165310.709
40_L52_P0.164710.706
99_L103_Y0.163970.703
22_L64_V0.162990.699
28_D101_R0.162240.696
43_E49_R0.161860.694
65_A90_A0.161730.693
19_Q74_D0.160430.688
93_E100_E0.158540.680
61_V86_E0.158140.678
18_E21_G0.158050.678
52_P55_Q0.157140.674
2_V7_I0.156420.671
72_A76_L0.154960.664
96_D99_L0.153980.660
39_R45_A0.15370.659
48_N69_D0.152950.656
74_D77_E0.152930.656
63_A98_L0.152830.655
72_A75_E0.152620.654
44_F79_L0.151420.649
8_S36_L0.150460.645
14_E17_A0.149750.642
1_L5_G0.148820.638
60_L82_K0.148060.635
65_A89_L0.14760.633
12_L77_E0.147470.632
41_P44_F0.145210.623
11_Q61_V0.142850.612
19_Q101_R0.141120.605
94_D97_Q0.140990.604
67_P89_L0.140020.600
24_F89_L0.139450.598
5_G9_E0.139420.598
50_V62_V0.139150.597
25_V88_V0.138710.595
44_F72_A0.13830.593
79_L82_K0.138190.592
69_D74_D0.136520.585
37_L43_E0.135660.582
64_V72_A0.134910.578
31_P101_R0.134680.577
5_G36_L0.134020.575
51_L91_T0.133850.574
34_P101_R0.133820.574
52_P60_L0.133390.572
9_E96_D0.132730.569
4_L29_E0.131960.566
56_D61_V0.131360.563
14_E18_E0.13130.563
27_L94_D0.130840.561
67_P85_I0.130110.558
23_P86_E0.129680.556
28_D49_R0.129650.556
49_R95_I0.129540.555
2_V6_L0.129480.555
15_A19_Q0.128670.552
39_R80_L0.128660.552
87_F99_L0.127790.548
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
2d28C0.94599.70.046
2bh1X0.7798990.373
4fu0A0.935822.20.857
3k3pA0.935814.60.868
3gvzA0.84414.30.868
2eqaA0.78912.20.872
1vkiA0.954111.70.873
3zvlA0.89918.80.88
2cwbA0.33038.60.88
1jcuA0.76158.50.88

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