GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
T2SE - Type IIIV secretion system protein
Pfam: PF00437 (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: CL0023
Length: 270
Sequences: 5455
Seq/Len: 20.2
HH_delta: 0.094 (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
233_S236_D0.727853.153
159_V193_A0.716663.104
90_T157_R0.697313.020
131_L227_T0.684282.964
161_I189_L0.658722.853
49_I91_I0.623972.703
116_I147_L0.619692.684
102_S105_D0.619662.684
133_S229_L0.60972.641
185_S188_D0.607712.632
156_E200_V0.583642.528
17_H197_D0.540252.340
104_E117_A0.522332.262
121_R150_E0.517512.241
81_T196_Q0.485832.104
153_P172_P0.475932.061
99_K105_D0.472232.045
136_T198_P0.469882.035
117_A150_E0.469662.034
144_L226_L0.461151.997
120_L147_L0.448941.944
119_F259_S0.439631.904
41_S44_E0.433991.880
103_L117_A0.424731.840
132_I143_L0.422871.832
206_I227_T0.41651.804
136_T222_H0.402781.745
161_I193_A0.391941.698
24_V45_L0.391041.694
148_L202_I0.372441.613
86_S165_P0.371161.608
133_S231_A0.364271.578
18_I24_V0.362541.570
28_R33_V0.356761.545
49_I89_P0.352561.527
201_I217_A0.351191.521
133_S266_H0.351151.521
220_T240_R0.349251.513
114_E118_E0.347161.504
118_E121_R0.345331.496
103_L146_A0.344921.494
90_T173_N0.344741.493
46_E50_R0.340541.475
206_I212_A0.339291.470
65_P182_D0.339221.469
74_D95_K0.337461.462
101_F105_D0.329771.428
209_P213_E0.329271.426
66_I192_S0.328921.425
190_L214_A0.323431.401
213_E216_Q0.321261.391
132_I144_L0.317391.375
42_E46_E0.315471.366
191_K208_D0.314091.360
216_Q243_D0.312861.355
61_N89_P0.309121.339
229_L237_A0.305851.325
205_E230_H0.305411.323
106_L146_A0.303841.316
138_S267_L0.300781.303
231_A237_A0.300491.302
53_A67_Q0.300041.300
54_S57_G0.29931.296
152_P158_I0.298161.291
12_E29_I0.297631.289
13_V28_R0.29411.274
149_E153_P0.293811.273
17_H92_V0.291731.264
242_A250_P0.290461.258
66_I183_E0.287841.247
83_P175_I0.287461.245
36_P39_F0.285521.237
88_G176_Q0.278831.208
195_R207_R0.276481.198
130_I223_L0.273871.186
104_E150_E0.27331.184
250_P254_R0.271691.177
140_K230_H0.268481.163
149_E172_P0.268431.163
27_K197_D0.26671.155
175_I193_A0.266141.153
118_E122_S0.266041.152
25_W36_P0.265831.151
65_P84_P0.264531.146
193_A201_I0.263991.143
90_T159_V0.263931.143
212_A244_L0.263631.142
133_S237_A0.258521.120
178_Q182_D0.258241.119
111_S115_E0.257931.117
78_V93_I0.257141.114
123_A263_I0.257121.114
215_I248_M0.256351.110
129_N224_G0.255871.108
80_I91_I0.255151.105
79_R192_S0.254921.104
80_I93_I0.254711.103
151_I156_E0.253921.100
144_L202_I0.253571.098
76_I95_K0.253491.098
242_A253_L0.253231.097
141_T167_L0.251251.088
212_A248_M0.248161.075
156_E174_Q0.248041.074
143_L267_L0.246641.068
238_I257_L0.245941.065
189_L193_A0.245621.064
130_I226_L0.245251.062
216_Q219_N0.245091.062
213_E249_D0.244741.060
42_E45_L0.244681.060
18_I91_I0.244491.059
166_E205_E0.244171.058
216_Q240_R0.243941.057
140_K205_E0.243531.055
186_Y203_I0.241311.045
23_E34_R0.240971.044
90_T196_Q0.2371.027
134_G138_S0.236991.026
151_I200_V0.236651.025
135_P138_S0.233711.012
120_L265_V0.233161.010
144_L228_T0.233091.010
100_P149_E0.232611.008
212_A241_L0.231511.003
60_I64_N0.23131.002
198_P222_H0.230941.000
232_N236_D0.229940.996
242_A254_R0.228230.989
251_E255_S0.228210.988
102_S149_E0.228020.988
82_T91_I0.22790.987
65_P184_I0.227860.987
159_V175_I0.227260.984
117_A121_R0.226490.981
53_A89_P0.225950.979
83_P177_I0.225860.978
18_I45_L0.225330.976
28_R31_G0.225170.975
194_L217_A0.224770.974
50_R62_E0.223350.967
68_D191_K0.222880.965
59_E63_R0.222460.964
223_L226_L0.221780.961
115_E118_E0.221780.961
206_I214_A0.221280.958
134_G204_G0.221080.958
68_D79_R0.21950.951
103_L150_E0.219390.950
56_A80_I0.219170.949
253_L257_L0.218390.946
68_D192_S0.218320.946
104_E110_G0.216460.938
249_D252_S0.216270.937
19_N171_G0.215250.932
81_T92_V0.214540.929
236_D259_S0.213820.926
19_N177_I0.212490.920
105_D108_E0.211730.917
127_R258_A0.211310.915
42_E89_P0.210990.914
201_I222_H0.210980.914
20_G88_G0.209890.909
219_N232_N0.209490.907
55_A59_E0.208960.905
166_E230_H0.207510.899
58_R82_T0.207220.898
202_I226_L0.207220.898
90_T175_I0.206590.895
185_S210_E0.206530.895
59_E62_E0.206410.894
140_K166_E0.20580.891
184_I189_L0.205360.889
72_P75_G0.205050.888
165_P178_Q0.204880.887
122_S258_A0.203450.881
71_L78_V0.201520.873
85_V173_N0.201250.872
209_P249_D0.200760.870
110_G114_E0.199540.864
131_L229_L0.198550.860
187_E210_E0.198480.860
50_R58_R0.198380.859
26_V35_S0.197190.854
108_E143_L0.196240.850
14_S92_V0.195750.848
107_G117_A0.195320.846
177_I196_Q0.194150.841
13_V16_I0.194020.840
45_L49_I0.193720.839
15_D92_V0.192740.835
70_E178_Q0.191730.830
134_G139_G0.191430.829
257_L260_A0.191020.827
205_E228_T0.189540.821
46_E89_P0.188380.816
51_R55_A0.188010.814
27_K37_V0.187410.812
104_E108_E0.186890.809
231_A234_A0.186380.807
163_D207_R0.186070.806
121_R154_E0.185370.803
96_F167_L0.185120.802
169_L172_P0.184710.800
192_S196_Q0.184510.799
44_E47_R0.184070.797
13_V29_I0.183990.797
151_I226_L0.183410.794
136_T220_T0.183260.794
131_L237_A0.182430.790
137_G197_D0.182250.789
165_P176_Q0.181890.788
25_W34_R0.181830.788
52_L80_I0.18110.784
179_T182_D0.181010.784
243_D252_S0.179820.779
119_F123_A0.179730.778
60_I67_Q0.179620.778
131_L206_I0.17940.777
159_V173_N0.179060.776
204_G221_G0.178740.774
99_K170_P0.178010.771
108_E116_I0.178010.771
120_L151_I0.177730.770
52_L69_G0.177560.769
254_R258_A0.177230.768
40_L44_E0.176880.766
55_A71_L0.176480.764
200_V223_L0.175690.761
94_R166_E0.175280.759
245_G253_L0.174350.755
119_F122_S0.17290.749
71_L80_I0.172070.745
166_E228_T0.171860.744
19_N157_R0.171860.744
151_I158_I0.171560.743
27_K30_G0.17150.743
149_E169_L0.170740.740
215_I219_N0.170250.737
67_Q80_I0.170130.737
92_V196_Q0.17010.737
20_G23_E0.169410.734
212_A216_Q0.168790.731
191_K210_E0.168660.731
86_S168_R0.168590.730
70_E77_R0.168220.729
11_P35_S0.167920.727
236_D239_E0.167650.726
43_E47_R0.167090.724
53_A69_G0.16680.722
135_P232_N0.165920.719
103_L143_L0.165850.718
150_E153_P0.165210.716
150_E154_E0.165010.715
103_L108_E0.164530.713
95_K98_S0.16440.712
128_G221_G0.163710.709
184_I188_D0.163670.709
40_L48_L0.163610.709
81_T90_T0.163490.708
186_Y227_T0.163360.708
163_D195_R0.163220.707
45_L91_I0.163010.706
134_G205_E0.162960.706
17_H27_K0.162680.705
59_E64_N0.162540.704
161_I183_E0.16140.699
43_E46_E0.161320.699
78_V95_K0.160960.697
29_I35_S0.160950.697
101_F146_A0.160740.696
77_R96_F0.160610.696
81_T85_V0.16050.695
161_I186_Y0.160430.695
69_G82_T0.160140.694
149_E152_P0.159420.690
11_P29_I0.158520.687
139_G166_E0.157670.683
148_L151_I0.157210.681
207_R230_H0.157150.681
219_N252_S0.157130.681
68_D207_R0.157090.680
16_I26_V0.156770.679
179_T185_S0.156580.678
164_P207_R0.15650.678
39_F43_E0.156160.676
158_I171_G0.155110.672
179_T184_I0.154380.669
139_G204_G0.15430.668
159_V196_Q0.154080.667
119_F130_I0.153990.667
159_V198_P0.153880.666
208_D211_A0.15310.663
240_R244_L0.153060.663
72_P78_V0.152770.662
244_L249_D0.152260.659
49_I82_T0.152130.659
148_L169_L0.152130.659
64_N184_I0.151720.657
83_P92_V0.15150.656
162_E207_R0.15140.656
94_R205_E0.151350.656
12_E28_R0.151320.655
11_P33_V0.15120.655
141_T169_L0.151150.655
68_D195_R0.151010.654
79_R164_P0.15070.653
140_K228_T0.150690.653
139_G221_G0.150430.652
234_A266_H0.149940.649
235_E239_E0.149830.649
102_S146_A0.14960.648
193_A203_I0.149040.646
134_G221_G0.148950.645
76_I93_I0.148940.645
119_F258_A0.148770.644
56_A69_G0.148640.644
188_D192_S0.147750.640
36_P154_E0.147460.639
166_E195_R0.147430.639
79_R196_Q0.146140.633
79_R128_G0.145980.632
218_A224_G0.145730.631
233_S266_H0.145590.631
123_A130_I0.145580.631
69_G78_V0.145330.629
38_R44_E0.145080.628
15_D186_Y0.144750.627
211_A241_L0.144610.626
134_G137_G0.144160.624
139_G205_E0.144090.624
187_E213_E0.144040.624
78_V90_T0.143770.623
254_R257_L0.143540.622
179_T186_Y0.143230.620
187_E209_P0.143060.620
187_E191_K0.142950.619
39_F42_E0.142950.619
96_F100_P0.142520.617
24_V48_L0.142390.617
44_E48_L0.142320.616
133_S264_I0.141980.615
129_N223_L0.141540.613
71_L93_I0.141510.613
175_I196_Q0.14150.613
174_Q267_L0.141050.611
114_E150_E0.141020.611
129_N218_A0.140870.610
35_S40_L0.140740.610
23_E39_F0.140650.609
238_I242_A0.140540.609
15_D137_G0.140350.608
214_A217_A0.140130.607
186_Y211_A0.140070.607
137_G208_D0.139570.605
206_I241_L0.13920.603
39_F48_L0.138960.602
53_A82_T0.138790.601
101_F109_S0.138730.601
195_R205_E0.138670.601
250_P253_L0.138650.601
81_T192_S0.137950.598
265_V268_K0.13730.595
95_K99_K0.137110.594
136_T195_R0.136840.593
206_I257_L0.136780.592
187_E217_A0.136780.592
231_A238_I0.136650.592
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
4ihqA0.97041000.094
2oap10.96671000.252
3jvvA0.96671000.38
2gzaA0.99261000.391
2pt7A0.98891000.395
1p9rA0.95931000.409
2ewvA0.97041000.421
2eyuA0.618599.80.636
3ec2A0.592698.50.836
2r8rA0.53798.40.842

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