GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
T2SF - Type II secretion system (T2SS) protein F
Pfam: PF00482 (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: 124
Sequences: 6246
Seq/Len: 50.37
HH_delta: 0.211 (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
2_L63_V1.22383.257
41_R54_R1.162663.094
23_A36_Q1.093222.909
41_R46_G1.026872.733
3_R88_R1.025812.730
39_R43_R0.958772.551
75_D78_E0.879322.340
41_R51_A0.869472.314
20_E39_R0.8642.299
10_K81_E0.852432.268
47_S50_E0.793612.112
10_K77_S0.776772.067
5_L18_A0.749351.994
49_E71_E0.737861.963
6_S84_A0.735691.958
23_A39_R0.734091.953
46_G50_E0.73251.949
37_K55_T0.717771.910
6_S81_E0.702791.870
117_F121_I0.64331.712
19_L35_L0.639751.702
20_E43_R0.605111.610
48_L52_L0.585771.559
29_G32_R0.583731.553
113_L117_F0.53781.431
37_K41_R0.533031.418
8_L18_A0.511731.362
5_L80_L0.486981.296
103_E107_L0.482091.283
85_D89_E0.470161.251
63_V83_L0.464541.236
38_I52_L0.461851.229
17_E20_E0.454291.209
34_E55_T0.452271.203
14_P17_E0.448971.195
19_L42_L0.4461.187
40_R44_N0.443721.181
116_F120_A0.439121.169
38_I51_A0.429661.143
53_E68_Q0.427341.137
97_R101_L0.424891.131
3_R84_A0.423971.128
41_R44_N0.420661.119
109_I113_L0.419091.115
81_E85_D0.413711.101
68_Q72_S0.408241.086
50_E53_E0.404751.077
40_R43_R0.400481.066
91_E95_I0.398021.059
69_A73_G0.381711.016
32_R36_Q0.381141.014
3_R85_D0.3781.006
78_E82_Q0.375861.000
35_L38_I0.375010.998
2_L80_L0.37330.993
16_S20_E0.368590.981
15_L48_L0.366750.976
9_L18_A0.36610.974
37_K40_R0.366060.974
16_S39_R0.364830.971
30_P34_E0.363050.966
36_Q40_R0.350690.933
112_A116_F0.350220.932
2_L83_L0.346250.921
23_A32_R0.342820.912
20_E24_E0.342340.911
70_G104_P0.340110.905
4_M25_E0.339220.903
46_G51_A0.33920.903
9_L77_S0.335210.892
84_A88_R0.329350.876
62_F66_L0.327450.871
34_E37_K0.326860.870
93_L97_R0.325990.867
34_E58_E0.325320.866
5_L15_L0.325140.865
23_A35_L0.32010.852
42_L51_A0.318740.848
50_E54_R0.317160.844
16_S43_R0.31640.842
19_L39_R0.315430.839
22_L26_S0.31280.832
86_Q90_R0.312530.832
52_L67_I0.312450.831
42_L48_L0.312250.831
107_L110_V0.311530.829
46_G54_R0.310780.827
36_Q39_R0.308810.822
30_P33_E0.305160.812
95_I99_A0.304650.811
31_L34_E0.298760.795
41_R55_T0.297440.791
26_S31_L0.297220.791
26_S32_R0.296880.790
26_S35_L0.295660.787
100_E103_E0.295260.786
58_E90_R0.293590.781
60_P63_V0.293110.780
34_E59_F0.292920.779
108_I112_A0.292240.778
94_R98_A0.290460.773
97_R103_E0.289960.772
99_A102_I0.289550.770
8_L13_I0.289140.769
66_L69_A0.288360.767
52_L64_A0.287770.766
111_G115_L0.287470.765
3_R6_S0.28670.763
96_K100_E0.285840.761
53_E64_A0.284860.758
59_F64_A0.283420.754
66_L70_G0.281570.749
3_R7_S0.281120.748
6_S77_S0.280830.747
104_P109_I0.279130.743
78_E81_E0.278790.742
22_L35_L0.276940.737
98_A102_I0.276260.735
93_L96_K0.273750.728
4_M22_L0.273560.728
63_V87_L0.271910.724
92_R96_K0.266150.708
49_E68_Q0.265280.706
49_E53_E0.259520.691
15_L66_L0.25850.688
67_I80_L0.256920.684
111_G119_L0.254480.677
66_L79_V0.254070.676
94_R97_R0.25390.676
82_Q85_D0.253680.675
115_L119_L0.253080.673
70_G74_G0.25190.670
12_G45_G0.251860.670
62_F86_Q0.249920.665
91_E94_R0.248420.661
28_S31_L0.247690.659
49_E64_A0.246730.657
53_E56_G0.245460.653
87_L91_E0.243460.648
105_L109_I0.242750.646
20_E23_A0.242010.644
53_E67_I0.240860.641
6_S80_L0.238220.634
99_A115_L0.238020.633
103_E122_L0.235030.625
18_A22_L0.234090.623
2_L87_L0.232940.620
64_A68_Q0.232560.619
118_V122_L0.231850.617
22_L103_E0.230420.613
33_E37_K0.22950.611
110_V114_V0.229460.611
50_E68_Q0.229440.611
83_L87_L0.229120.610
6_S10_K0.228850.609
5_L8_L0.228060.607
89_E93_L0.226320.602
53_E61_D0.226310.602
106_I110_V0.226210.602
7_S11_S0.225810.601
71_E76_L0.225550.600
69_A87_L0.223320.594
31_L35_L0.223310.594
5_L22_L0.222490.592
19_L38_I0.220910.588
69_A72_S0.22060.587
102_I106_I0.220410.587
20_E36_Q0.219840.585
16_S23_A0.219250.583
69_A115_L0.218590.582
12_G74_G0.218250.581
87_L90_R0.217560.579
34_E54_R0.216790.577
60_P87_L0.21650.576
42_L45_G0.215360.573
33_E36_Q0.215350.573
61_D91_E0.214430.571
45_G70_G0.214020.570
71_E74_G0.212470.565
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
3c1qA0.862999.50.211
2whnA0.798499.30.261
4hhxA0.822699.30.268
3mbhA0.524234.30.846
3hd7B0.8226320.849
1w8sA0.411330.40.851
3glcA0.4597300.851
4i0uA0.830628.90.852
2iubA0.975817.70.866
3hd7A0.733917.50.866

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