GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1597 - Outer membrane protein family (DUF1597)
Pfam: PF07642 (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: CL0193
Length: 344
Sequences: 3542
Seq/Len: 10.3
HH_delta: 0.377 (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
268_Y292_Y0.52293.748
262_W298_L0.522533.745
312_Y334_F0.497763.568
222_L256_Y0.474783.403
57_D91_Y0.441393.164
228_Y248_Y0.401362.877
190_L210_Y0.355882.551
53_G95_K0.352142.524
46_E53_G0.337492.419
10_G64_A0.331572.377
299_N307_M0.331442.376
262_W300_Y0.330492.369
5_S42_Y0.327782.350
45_L56_F0.317792.278
153_L178_L0.310512.226
307_M341_I0.308912.214
147_F153_L0.307652.205
188_L214_A0.30562.191
270_Y292_Y0.299212.145
258_F264_L0.29482.113
230_Y248_Y0.288932.071
142_R156_G0.280562.011
194_Y208_F0.278651.997
218_P224_L0.278231.994
55_R93_S0.273751.962
8_V64_A0.273481.960
224_L254_L0.271871.949
52_V94_Y0.26721.915
55_R104_K0.26411.893
302_P308_I0.258461.853
186_L216_Y0.25711.843
308_I340_A0.255541.832
89_Q109_Y0.250611.796
44_T57_D0.250461.795
265_G297_T0.248041.778
111_P154_M0.245661.761
263_S301_K0.24561.760
4_I43_L0.237671.704
81_P87_I0.234891.684
225_G253_Y0.231541.660
145_Y153_L0.228521.638
268_Y294_L0.226781.626
310_P338_L0.225421.616
145_Y148_N0.223271.600
55_R102_S0.220491.580
255_S263_S0.215611.545
89_Q108_F0.215491.545
82_E87_I0.210961.512
4_I41_A0.210091.506
192_Y208_F0.20781.490
5_S44_T0.205471.473
192_Y210_Y0.205421.472
155_L176_G0.203851.461
291_Y315_D0.20161.445
266_V294_L0.199591.431
217_K220_D0.197581.416
267_R295_T0.197341.415
156_G175_G0.196291.407
111_P156_G0.196071.405
258_F298_L0.195581.402
5_S59_Q0.19461.395
220_D256_Y0.192371.379
186_L214_A0.191921.376
152_S179_S0.191141.370
222_L254_L0.185461.329
60_F85_F0.184951.326
314_Y334_F0.184481.322
52_V99_K0.184141.320
138_H141_V0.183521.315
104_K108_F0.183251.314
210_Y230_Y0.181981.304
60_F79_N0.181231.299
47_K54_F0.180831.296
57_D89_Q0.180061.291
226_L252_L0.179111.284
84_G87_I0.178811.282
49_A54_F0.17881.282
7_W40_Q0.177711.274
305_N342_F0.177581.273
303_T306_L0.177451.272
40_Q59_Q0.17721.270
48_P51_K0.177111.270
81_P84_G0.176721.267
306_L342_F0.174881.254
194_Y206_N0.174441.250
107_R139_T0.173881.246
316_W332_N0.173761.246
100_G145_Y0.172281.235
259_S262_W0.17111.226
217_K223_T0.1711.226
290_S318_D0.170541.222
84_G140_G0.169821.217
227_E251_A0.169381.214
310_P336_F0.169311.214
13_T337_G0.169191.213
16_F334_F0.1691.211
93_S104_K0.167421.200
185_K216_Y0.166911.196
115_E144_T0.166551.194
190_L212_L0.163951.175
291_Y317_S0.162921.168
9_D309_R0.16251.165
188_L212_L0.162481.165
111_P177_Q0.161941.161
264_L298_L0.161721.159
41_A60_F0.161571.158
297_T311_E0.161391.157
215_S223_T0.161221.156
39_N42_Y0.160931.154
59_Q88_P0.160491.150
104_K144_T0.156981.125
187_S215_S0.155651.116
215_S225_G0.155621.115
254_L266_V0.155371.114
101_L145_Y0.155231.113
40_Q88_P0.154311.106
152_S181_S0.154051.104
258_F262_W0.152851.096
299_N341_I0.152751.095
293_A313_R0.152471.093
112_I209_F0.151841.088
48_P53_G0.151691.087
270_Y290_S0.151011.082
256_Y262_W0.150331.078
295_T313_R0.150091.076
121_D125_Y0.150081.076
249_G271_F0.149231.070
100_G103_V0.148971.068
105_A143_A0.148951.068
250_A270_Y0.14861.065
265_G299_N0.148341.063
219_T222_L0.147161.055
223_T255_S0.146321.049
91_Y104_K0.146181.048
47_K303_T0.146091.047
158_V173_S0.14511.040
13_T30_T0.145091.040
309_R339_D0.144991.039
10_G31_D0.144341.035
314_Y332_N0.14421.034
224_L252_L0.144061.033
266_V296_L0.143831.031
158_V161_W0.143491.029
37_N341_I0.143291.027
17_N333_Q0.143121.026
211_D229_D0.142931.025
150_K180_Y0.142511.022
151_W180_Y0.141191.012
261_K300_Y0.140541.007
103_V143_A0.13951.000
142_R158_V0.13930.998
154_M177_Q0.139190.998
230_Y246_S0.138210.991
88_P109_Y0.136850.981
217_K257_Q0.136710.980
10_G337_G0.136130.976
47_K305_N0.135970.975
4_I45_L0.135510.971
113_G135_P0.134950.967
257_Q263_S0.13410.961
263_S299_N0.134070.961
55_R95_K0.133770.959
12_Y334_F0.133590.958
167_D172_P0.132630.951
42_Y88_P0.132510.950
11_Y35_E0.132160.947
53_G93_S0.131650.944
42_Y59_Q0.130970.939
185_K218_P0.130290.934
259_S298_L0.13010.933
189_Y213_V0.129920.931
124_N297_T0.129250.926
61_G87_I0.129230.926
260_D300_Y0.128630.922
219_T264_L0.128370.920
177_Q191_N0.12770.915
297_T337_G0.127660.915
220_D257_Q0.127630.915
246_S290_S0.127540.914
153_L176_G0.126550.907
47_K306_L0.125950.903
95_K102_S0.125830.902
183_N214_A0.125540.900
52_V100_G0.12520.897
87_I90_A0.12380.887
222_L226_L0.123470.885
93_S101_L0.121830.873
294_L316_W0.121160.868
155_L178_L0.120940.867
146_A152_S0.120830.866
266_V269_E0.120640.865
290_S316_W0.120310.862
181_S187_S0.119580.857
292_Y316_W0.119280.855
14_Y314_Y0.118570.850
46_E55_R0.11830.848
5_S57_D0.117810.844
13_T313_R0.116990.839
55_R91_Y0.116280.833
294_L314_Y0.116220.833
38_L61_G0.115490.828
301_K307_M0.115010.824
52_V98_G0.114960.824
302_P306_L0.114750.823
253_Y267_R0.114620.822
308_I338_L0.114270.819
157_V172_P0.114120.818
61_G88_P0.114070.818
118_F121_D0.113720.815
293_A315_D0.113570.814
48_P306_L0.113490.813
5_S88_P0.113450.813
248_Y272_D0.113270.812
94_Y306_L0.113240.812
108_F142_R0.1130.810
312_Y336_F0.112270.805
119_A125_Y0.110840.794
261_K301_K0.110690.793
173_S195_G0.110350.791
232_W246_S0.110310.791
58_L90_A0.110240.790
147_F150_K0.110080.789
79_N85_F0.109990.788
50_D305_N0.109950.788
41_A45_L0.109810.787
36_F181_S0.109290.783
14_Y336_F0.108980.781
118_F123_F0.108950.781
4_I316_W0.108580.778
12_Y34_N0.108570.778
262_W302_P0.108520.778
118_F124_N0.107880.773
2_I58_L0.107850.773
115_E118_F0.107690.772
112_I191_N0.107540.771
56_F86_A0.107450.770
32_R200_D0.106740.765
232_W316_W0.106530.764
159_N175_G0.106520.764
256_Y259_S0.106350.762
121_D124_N0.106030.760
4_I90_A0.105870.759
256_Y260_D0.105120.753
104_K142_R0.105090.753
10_G13_T0.104720.751
302_P310_P0.104720.751
47_K50_D0.104610.750
42_Y47_K0.104430.749
218_P222_L0.104370.748
163_T166_F0.10420.747
151_W178_L0.104120.746
43_L90_A0.103650.743
214_A217_K0.103530.742
307_M310_P0.103450.742
143_A159_N0.103360.741
249_G269_E0.103280.740
112_I133_Y0.103070.739
251_A267_R0.102720.736
158_V162_D0.10260.735
111_P146_A0.102390.734
50_D303_T0.101820.730
306_L340_A0.10170.729
63_D80_N0.101660.729
92_V143_A0.101650.729
36_F341_I0.101530.728
172_P196_P0.10150.728
296_L312_Y0.101060.724
129_Y132_N0.100780.722
39_N62_T0.100530.721
38_L41_A0.100430.720
302_P340_A0.100150.718
123_F265_G0.099830.716
298_L314_Y0.099740.715
11_Y337_G0.099350.712
271_F291_Y0.098990.710
143_A155_L0.098960.709
177_Q189_Y0.09880.708
147_F155_L0.098730.708
119_A122_N0.098520.706
292_Y318_D0.09840.705
7_W341_I0.09770.700
40_Q341_I0.097540.699
49_A94_Y0.097460.699
179_S187_S0.097440.698
168_N172_P0.096990.695
298_L310_P0.096910.695
101_L141_V0.096810.694
50_D54_F0.096660.693
38_L87_I0.09640.691
295_T311_E0.0960.688
141_V147_F0.095980.688
120_P137_T0.095790.687
56_F90_A0.095340.683
58_L300_Y0.095220.683
222_L258_F0.095070.681
127_R227_E0.094840.680
127_R134_G0.09470.679
303_T342_F0.094660.679
48_P305_N0.094470.677
144_T156_G0.094450.677
101_L339_D0.094280.676
3_T44_T0.094260.676
53_G98_G0.094050.674
41_A90_A0.093980.674
228_Y250_A0.093730.672
94_Y100_G0.093510.670
311_E337_G0.093510.670
219_T260_D0.093440.670
2_I47_K0.093040.667
101_L143_A0.092660.664
37_N307_M0.092630.664
111_P191_N0.092430.663
259_S301_K0.092370.662
157_V161_W0.09230.662
258_F263_S0.092250.661
231_G247_W0.091970.659
105_A141_V0.091950.659
44_T55_R0.091930.659
122_N135_P0.091740.658
49_A304_P0.091570.656
113_G137_T0.091410.655
49_A101_L0.091410.655
105_A108_F0.091380.655
45_L101_L0.091360.655
98_G101_L0.091240.654
32_R35_E0.091190.654
173_S255_S0.091020.652
174_F196_P0.091010.652
226_L250_A0.090810.651
52_V275_D0.090780.651
214_A226_L0.090760.651
93_S102_S0.09040.648
58_L86_A0.090380.648
161_W168_N0.090370.648
87_I101_L0.090230.647
217_K256_Y0.089890.644
46_E95_K0.089810.644
147_F178_L0.089610.642
155_L158_V0.089130.639
298_L302_P0.089080.639
273_D289_F0.08890.637
104_K146_A0.088860.637
154_M179_S0.088820.637
60_F87_I0.08880.637
41_A85_F0.088790.636
122_N125_Y0.088770.636
13_T32_R0.088680.636
260_D319_D0.088640.635
191_N211_D0.088520.635
128_S131_F0.088510.634
13_T193_Y0.088440.634
9_D34_N0.08830.633
88_P137_T0.087950.630
93_S108_F0.087880.630
128_S138_H0.087820.629
2_I6_G0.08780.629
262_W310_P0.087770.629
119_A123_F0.087670.628
127_R132_N0.087660.628
142_R175_G0.087520.627
162_D166_F0.087440.627
226_L313_R0.08730.626
142_R146_A0.087250.625
149_D287_N0.087220.625
310_P339_D0.087170.625
134_G222_L0.087050.624
188_L210_Y0.086870.623
118_F128_S0.08670.621
152_S155_L0.086640.621
3_T304_P0.086220.618
80_N87_I0.086060.617
173_S194_Y0.086060.617
251_A269_E0.085820.615
88_P309_R0.085810.615
35_E337_G0.085730.615
148_N153_L0.085680.614
94_Y101_L0.085590.614
246_S318_D0.085580.613
160_G234_D0.085450.613
95_K296_L0.085440.612
138_H160_G0.085360.612
124_N131_F0.085320.612
144_T154_M0.08530.611
217_K259_S0.085160.610
120_P131_F0.085110.610
42_Y89_Q0.085010.609
272_D290_S0.08490.609
93_S309_R0.084810.608
248_Y274_K0.084690.607
101_L309_R0.084490.606
136_F234_D0.084240.604
181_S185_K0.084140.603
89_Q137_T0.083980.602
50_D306_L0.083940.602
88_P101_L0.08370.600
117_I227_E0.083650.600
147_F183_N0.083350.597
214_A227_E0.083260.597
108_F144_T0.083220.597
16_F250_A0.083130.596
151_W252_L0.083080.596
253_Y309_R0.082990.595
212_L226_L0.082970.595
171_G179_S0.082970.595
15_N30_T0.082880.594
40_Q81_P0.082780.593
258_F266_V0.082690.593
33_A37_N0.082650.592
117_I191_N0.08260.592
227_E267_R0.082390.591
247_W291_Y0.082360.590
111_P175_G0.082210.589
207_R231_G0.082110.589
95_K146_A0.081880.587
91_Y108_F0.081850.587
60_F86_A0.081580.585
257_Q260_D0.081570.585
293_A317_S0.081570.585
111_P142_R0.081550.585
6_G106_G0.081530.584
201_G245_A0.081410.584
294_L332_N0.081290.583
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
2o4vA0.9071000.377
3nsgA0.904199.90.475
2fgqX0.889599.90.49
2j1nA0.892499.90.49
2zfgA0.904199.90.498
1phoA0.880899.90.501
4auiA0.860599.90.502
3vy8X0.898399.90.505
3a2sX0.904199.90.542
2porA0.799499.60.657

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