GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
T2SM - Type II secretion system (T2SS) protein M
Pfam: PF04612 (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: CL0331
Length: 160
Sequences: 1160
Seq/Len: 7.25
HH_delta: 0.549 (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
91_A98_I0.461884.047
74_P133_G0.22761.994
29_A33_L0.224661.968
85_S103_P0.21591.891
31_L36_W0.215441.887
83_L134_I0.20331.781
46_L49_Q0.202611.775
50_L54_Q0.195521.713
117_S120_Q0.193011.691
90_S124_W0.187641.644
94_A127_Q0.184051.612
30_L34_L0.181491.590
49_Q52_Q0.177261.553
95_G106_E0.174591.530
32_Y37_Q0.16741.467
80_P84_A0.165771.452
18_L22_L0.165431.449
83_L96_L0.165041.446
52_Q56_Q0.162431.423
59_W63_Q0.16021.404
91_A96_L0.158791.391
35_L39_L0.158561.389
91_A124_W0.158151.386
55_Q59_W0.157681.381
17_R21_V0.154311.352
100_R112_W0.153881.348
44_D47_Q0.150971.323
125_L129_E0.1471.288
42_R46_L0.14431.264
41_E45_Q0.143341.256
35_L38_P0.142911.252
37_Q134_I0.140931.235
95_G120_Q0.140121.228
57_L60_L0.139871.225
74_P107_G0.139711.224
20_L24_V0.139011.218
57_L61_Q0.137441.204
45_Q49_Q0.136021.192
38_P41_E0.135761.189
39_L85_S0.133191.167
87_I136_V0.130441.143
73_A78_L0.129331.133
25_V62_Q0.128851.129
20_L27_L0.128551.126
44_D48_Q0.126341.107
36_W92_R0.124761.093
104_Q110_Q0.124251.089
65_Q100_R0.122991.078
48_Q51_Q0.120411.055
90_S94_A0.119861.050
46_L102_Q0.119281.045
96_L124_W0.119141.044
62_Q89_Q0.118891.042
80_P131_Q0.118691.040
81_Q128_L0.118491.038
89_Q140_S0.116651.022
43_R46_L0.11541.011
102_Q110_Q0.114050.999
110_Q141_L0.113950.998
31_L35_L0.113480.994
67_I84_A0.113420.994
52_Q71_Q0.11320.992
39_L124_W0.112610.987
69_A127_Q0.111860.980
53_L133_G0.111280.975
23_G123_Q0.110810.971
122_L129_E0.110560.969
24_V70_L0.11020.965
96_L115_N0.110070.964
67_I71_Q0.110.964
32_Y82_S0.108790.953
80_P101_I0.108610.952
25_V38_P0.108390.950
121_L125_L0.108080.947
19_L140_S0.107830.945
108_R118_F0.107440.941
55_Q58_A0.107380.941
43_R47_Q0.107140.939
37_Q41_E0.106680.935
82_S119_D0.106660.934
47_Q51_Q0.106640.934
30_L140_S0.106110.930
99_S114_E0.105420.924
65_Q123_Q0.104750.918
56_Q59_W0.104530.916
106_E119_D0.104150.912
40_L47_Q0.103690.908
53_L56_Q0.103590.908
83_L86_L0.103190.904
24_V31_L0.102970.902
81_Q88_Q0.102490.898
88_Q134_I0.102240.896
28_L36_W0.101830.892
87_I124_W0.101640.890
53_L57_L0.101630.890
40_L44_D0.101060.885
102_Q138_Q0.100690.882
122_L126_Q0.100570.881
90_S127_Q0.100040.876
45_Q117_S0.09950.872
88_Q138_Q0.099470.871
73_A133_G0.099290.870
125_L137_T0.099080.868
30_L47_Q0.098380.862
79_S131_Q0.098350.862
54_Q140_S0.098320.861
68_Q97_T0.098250.861
109_V118_F0.097830.857
25_V82_S0.09780.857
112_W144_A0.097680.856
50_L53_L0.096710.847
28_L59_W0.096560.846
126_Q129_E0.096160.842
73_A83_L0.096090.842
89_Q141_L0.095590.837
83_L88_Q0.095490.837
121_L127_Q0.095430.836
88_Q101_I0.095350.835
81_Q118_F0.094990.832
54_Q57_L0.094490.828
46_L130_Q0.093980.823
85_S89_Q0.093670.821
62_Q68_Q0.093550.820
136_V141_L0.093120.816
61_Q72_Q0.093030.815
76_N105_G0.092610.811
124_W132_H0.092280.808
92_R118_F0.092270.808
91_A109_V0.09220.808
50_L60_L0.091560.802
46_L56_Q0.091450.801
59_W105_G0.091240.799
32_Y54_Q0.091160.799
47_Q140_S0.091060.798
32_Y97_T0.090890.796
52_Q68_Q0.090750.795
67_I118_F0.090540.793
121_L141_L0.089930.788
98_I101_I0.089920.788
53_L96_L0.08990.788
109_V126_Q0.089890.788
27_L107_G0.089840.787
51_Q59_W0.08980.787
51_Q56_Q0.089550.785
119_D134_I0.089530.784
40_L87_I0.08950.784
119_D122_L0.089470.784
73_A107_G0.089430.783
26_L87_I0.089090.781
27_L76_N0.088930.779
17_R24_V0.088710.777
41_E111_V0.088680.777
88_Q132_H0.088630.776
84_A103_P0.088540.776
112_W128_L0.088520.776
113_L138_Q0.088460.775
126_Q130_Q0.088330.774
94_A125_L0.088050.771
33_L110_Q0.087560.767
18_L102_Q0.087350.765
83_L107_G0.087130.763
34_L73_A0.087090.763
61_Q101_I0.086850.761
90_S93_Q0.086660.759
80_P108_R0.086440.757
86_L90_S0.086430.757
30_L139_L0.086230.755
37_Q71_Q0.086220.755
28_L123_Q0.086060.754
97_T137_T0.085760.751
19_L130_Q0.085570.750
32_Y136_V0.085560.750
96_L113_L0.085440.749
114_E132_H0.085390.748
104_Q142_T0.084590.741
56_Q63_Q0.084470.740
29_A32_Y0.084460.740
49_Q117_S0.084330.739
99_S112_W0.084180.737
129_E134_I0.084180.737
88_Q124_W0.084070.737
86_L135_S0.084010.736
45_Q72_Q0.083980.736
23_G26_L0.083790.734
96_L101_I0.083710.733
16_R62_Q0.083620.733
61_Q137_T0.083420.731
107_G119_D0.08330.730
69_A130_Q0.083240.729
18_L99_S0.083040.728
101_I129_E0.083040.728
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
1uv7A0.62599.10.549
2rjzA0.768898.70.621
3trgA0.606283.90.853
4g9iA0.57580.60.858
1ulrA0.543775.70.864
3vthA0.6188750.865
3ne5A0.931374.90.865
1w2iA0.562571.90.868
2fhmA0.562570.80.869
2w7vA0.5375670.872
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0285 seconds.