GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SWM_repeat - Putative flagellar system-associated repeat
Pfam: PF13753 (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: CL0159
Length: 317
Sequences: 1454
Seq/Len: 4.59
HH_delta: 0.516 (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
97_W200_W0.456752.716
22_D26_N0.433962.580
92_D96_N0.42892.550
200_W301_W0.401192.385
296_D300_T0.399912.378
97_W301_W0.383312.279
109_D214_D0.379032.254
101_V204_V0.378312.249
225_D229_N0.376972.241
34_I238_F0.359642.138
195_G199_T0.350552.084
93_A196_A0.349092.076
20_V223_V0.3472.063
134_F238_F0.342672.037
14_Y217_Y0.33712.004
16_V114_I0.336822.003
34_I134_F0.330281.964
121_D125_N0.326821.943
32_Q236_Q0.323321.922
168_F269_I0.320871.908
112_Y217_Y0.313931.867
18_V221_V0.297291.768
115_T220_T0.296681.764
14_Y112_Y0.295441.757
132_Q236_Q0.294031.748
102_T205_T0.290631.728
36_V240_V0.28991.724
183_V284_V0.289561.722
76_S179_D0.289511.721
80_V183_V0.288911.718
36_V136_V0.288581.716
16_V219_V0.287591.710
32_Q132_Q0.286921.706
182_T283_T0.285621.698
127_S231_A0.283761.687
114_I219_V0.282741.681
28_S127_S0.282381.679
99_V202_V0.281431.673
28_S231_A0.277681.651
20_V119_V0.277641.651
15_T218_T0.27641.643
29_T128_T0.276081.642
17_S115_T0.275331.637
18_V116_V0.273271.625
136_V240_V0.268251.595
119_V223_V0.267081.588
63_V267_V0.265551.579
23_A226_A0.263741.568
113_T218_T0.262061.558
33_S237_T0.262011.558
74_P177_A0.259621.544
72_A276_A0.259221.541
75_G279_G0.259211.541
146_V247_I0.25861.538
108_P213_A0.253661.508
75_G178_G0.252211.500
76_S280_D0.252041.499
94_D197_D0.249771.485
139_T243_T0.248961.480
126_T230_T0.247651.472
81_T184_T0.246861.468
103_P206_P0.245651.461
19_T222_T0.24251.442
190_Y291_Y0.24121.434
43_V247_I0.239841.426
92_D195_G0.238471.418
122_A226_A0.238381.417
99_V303_V0.237781.414
177_A278_A0.237761.414
293_T303_V0.235131.398
27_T230_T0.235041.397
176_D179_D0.234711.396
15_T113_T0.233521.388
23_A122_A0.233131.386
166_V267_V0.232081.380
81_T285_T0.232051.380
74_P278_A0.231121.374
107_L212_L0.229831.367
37_D125_N0.228221.357
165_T266_T0.227831.355
62_T266_T0.227451.352
178_G279_G0.226691.348
80_V284_V0.224271.333
203_T304_T0.223271.328
83_N186_N0.221351.316
72_A175_F0.220481.311
73_E76_S0.220291.310
87_G190_Y0.218561.300
167_T268_T0.217671.294
45_I249_I0.217311.292
179_D280_D0.217131.291
171_T272_T0.217021.290
79_T182_T0.21631.286
138_T242_T0.215211.280
170_G271_G0.214941.278
188_T289_N0.214551.276
39_T139_T0.213891.272
17_S220_T0.213791.271
100_T203_T0.213641.270
79_T283_T0.213191.268
19_T117_T0.213041.267
27_T126_T0.212221.262
85_T188_T0.212191.262
42_T246_T0.211121.255
175_F276_A0.210421.251
199_T300_T0.208561.240
277_E280_D0.208341.239
164_V265_T0.207291.233
135_T239_T0.205951.225
96_N199_T0.203991.213
202_V303_V0.20331.209
91_A194_V0.20291.206
96_N300_T0.20271.205
82_I286_V0.202631.205
131_S235_S0.20241.203
77_T281_T0.201821.200
175_F194_V0.201791.200
133_T237_T0.200921.195
67_G170_G0.199991.189
186_N287_N0.199891.189
65_F168_F0.199791.188
46_T250_D0.199111.184
196_A297_A0.198931.183
94_D298_D0.198521.180
212_L215_G0.197521.174
181_V282_V0.197291.173
73_E176_D0.196021.165
137_D229_N0.194731.158
33_S133_T0.193151.148
116_V221_V0.192151.142
176_D277_E0.192081.142
83_N287_N0.191661.140
137_D227_A0.191281.137
78_V181_V0.190851.135
31_T235_S0.188721.122
44_T248_T0.188561.121
82_I185_I0.188061.118
100_T304_T0.188051.118
63_V166_V0.187871.117
77_T180_T0.186761.110
117_T222_T0.185281.102
65_F269_I0.184181.095
148_I249_I0.18361.092
37_D241_D0.183081.089
73_E277_E0.182861.087
30_A234_A0.182181.083
85_T289_N0.180671.074
110_G215_G0.180381.073
60_T63_V0.179471.067
93_A297_A0.179341.066
72_A91_A0.179191.065
88_T191_T0.178381.061
50_D153_D0.177521.055
189_T290_T0.176821.051
185_I286_V0.176451.049
66_S270_S0.176181.048
90_T193_T0.175081.041
150_G251_P0.174161.036
26_N229_N0.173111.029
184_T285_T0.17281.027
89_L192_T0.172721.027
78_V282_V0.172351.025
117_T126_T0.172121.023
21_T224_T0.171441.019
120_T224_T0.171351.019
21_T120_T0.171051.017
180_T281_T0.170471.014
45_I148_I0.169821.010
39_T243_T0.168731.003
61_N164_V0.167720.997
186_N217_Y0.167420.995
137_D225_D0.167330.995
98_S201_T0.167160.994
49_A152_S0.167120.994
62_T165_T0.166990.993
149_T250_D0.165850.986
123_A227_A0.164310.977
55_N158_N0.164010.975
111_D216_T0.163030.969
68_T272_T0.161720.962
64_T268_T0.161530.960
197_D298_D0.161380.960
63_V67_G0.160470.954
169_S270_S0.159350.947
54_I157_I0.158510.942
37_D121_D0.157880.939
287_N291_Y0.156280.929
46_T149_T0.15610.928
86_T189_T0.155550.925
163_T264_N0.155360.924
50_D254_A0.154160.917
38_T138_T0.154090.916
35_T135_T0.153990.916
60_T163_T0.15390.915
68_T171_T0.152050.904
43_V146_V0.150920.897
41_P245_P0.149470.889
38_T242_T0.149380.888
89_L293_T0.146680.872
24_A123_A0.146630.872
192_T293_T0.146430.871
35_T239_T0.14270.848
255_D262_E0.142580.848
66_S169_S0.141770.843
201_T302_S0.141340.840
52_D256_N0.141140.839
64_T167_T0.138950.826
262_E267_V0.138530.824
219_V238_F0.13840.823
214_D217_Y0.138190.822
175_F179_D0.138180.822
91_A119_V0.137580.818
84_G288_G0.137530.818
164_V170_G0.137420.817
215_G238_F0.136890.814
53_I156_I0.136680.813
44_T147_T0.135940.808
21_T27_T0.135180.804
293_T301_W0.134650.801
41_P121_D0.134360.799
282_V293_T0.134260.798
16_V34_I0.134120.797
24_A227_A0.133670.795
56_G159_G0.133430.793
158_N259_N0.133320.793
22_D225_D0.132850.790
276_A280_D0.13250.788
125_N229_N0.131890.784
67_G97_W0.130650.777
43_V127_S0.129950.773
86_T290_T0.129920.772
72_A78_V0.129870.772
14_Y34_I0.127940.761
84_G187_G0.127410.758
47_S251_P0.127380.757
194_V295_V0.126410.752
264_N267_V0.126370.751
195_G296_D0.1260.749
25_G124_G0.125930.749
95_G198_G0.125180.744
89_L99_V0.125010.743
276_A295_V0.124670.741
117_T120_T0.123170.732
41_P144_P0.122220.727
92_D296_D0.12170.724
19_T27_T0.121440.722
214_D242_T0.121070.720
48_I151_I0.121030.720
144_P245_P0.120740.718
67_G271_G0.120.713
109_D138_T0.119940.713
139_T225_D0.11980.712
54_I258_I0.119780.712
183_V202_V0.119690.712
271_G279_G0.119650.711
296_D299_G0.119160.709
268_T302_S0.118470.704
295_V300_T0.118390.704
40_A244_A0.118040.702
65_F78_V0.117390.698
193_T294_T0.11680.694
195_G198_G0.116570.693
191_T292_T0.11570.688
271_G276_A0.115470.687
192_T202_V0.114670.682
45_I116_V0.114480.681
147_T248_T0.114420.680
159_G163_T0.113420.674
154_D255_D0.113090.672
72_A76_S0.112870.671
129_A234_A0.112840.671
297_A300_T0.112580.669
128_T233_T0.112570.669
170_G200_W0.112440.669
217_Y238_F0.111630.664
47_S150_G0.110560.657
194_V223_V0.110260.656
224_T230_T0.110210.655
52_D155_N0.109810.653
175_F223_V0.10960.652
20_V28_S0.109310.650
80_V99_V0.108240.644
76_S79_T0.108160.643
88_T292_T0.108160.643
121_D225_D0.108040.642
87_G291_Y0.107980.642
18_V30_A0.107480.639
284_V303_V0.107270.638
98_S302_S0.106870.635
37_D137_D0.106840.635
185_I219_V0.106730.635
19_T23_A0.106040.630
283_T291_Y0.106020.630
186_N190_Y0.10580.629
99_V114_I0.105790.629
44_T68_T0.105750.629
267_V301_W0.105730.629
120_T126_T0.105160.625
145_T246_T0.104490.621
74_P91_A0.10420.620
110_G134_F0.103780.617
22_D121_D0.103270.614
258_I262_E0.103270.614
38_T125_N0.103150.613
166_V212_L0.103150.613
61_N265_T0.10270.611
41_P127_S0.101640.604
271_G301_W0.101550.604
26_N125_N0.101320.602
46_T68_T0.10120.602
42_T145_T0.100640.598
91_A94_D0.100520.598
178_G181_V0.100390.597
83_N112_Y0.099730.593
117_T127_S0.099660.593
151_I154_D0.099210.590
55_N229_N0.09880.587
285_T290_T0.098660.587
222_T231_A0.09840.585
45_I48_I0.09790.582
44_T127_S0.097570.580
90_T294_T0.097020.577
37_D123_A0.0970.577
157_I258_I0.096540.574
188_T205_T0.096270.572
258_I261_A0.095880.570
137_D241_D0.095760.569
26_N37_D0.095710.569
82_I87_G0.09570.569
51_D54_I0.095040.565
241_D277_E0.094990.565
179_D223_V0.094850.564
19_T28_S0.094650.563
64_T134_F0.094440.562
175_F178_G0.094380.561
103_P106_D0.094340.561
91_A96_N0.094080.559
283_T290_T0.093560.556
216_T239_T0.093170.554
59_A63_V0.093110.554
286_V291_Y0.093020.553
154_D158_N0.092890.552
278_A295_V0.092870.552
87_G101_V0.092580.550
226_A229_N0.092450.550
73_E78_V0.092190.548
167_T201_T0.092120.548
217_Y240_V0.091860.546
55_N259_N0.091770.546
296_D302_S0.091560.544
177_A196_A0.091520.544
168_F183_V0.091170.542
31_T131_S0.090980.541
48_I114_I0.090970.541
48_I65_F0.090910.541
267_V271_G0.090690.539
241_D244_A0.090580.539
40_A143_A0.090520.538
286_V289_N0.090510.538
222_T230_T0.09050.538
30_A129_A0.090440.538
154_D157_I0.090210.536
212_L217_Y0.090130.536
181_V192_T0.090060.535
177_A192_T0.089620.533
184_T221_V0.089560.533
51_D255_D0.08860.527
258_I263_A0.088490.526
119_V127_S0.088070.524
159_G165_T0.087960.523
112_Y134_F0.087820.522
125_N241_D0.087750.522
37_D41_P0.087020.517
78_V89_L0.087020.517
166_V170_G0.086920.517
43_V119_V0.08680.516
60_T67_G0.086510.514
60_T264_N0.086420.514
263_A267_V0.086350.513
182_T224_T0.086320.513
281_T294_T0.086240.513
36_V39_T0.085990.511
109_D112_Y0.085550.509
51_D154_D0.085220.507
215_G299_G0.084830.504
15_T18_V0.084570.503
271_G282_V0.084380.502
290_T294_T0.084340.501
272_T302_S0.084270.501
83_N86_T0.084210.501
76_S119_V0.08390.499
283_T292_T0.083880.499
26_N241_D0.083510.497
18_V34_I0.083280.495
290_T293_T0.082590.491
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
2yn5A0.703599.90.516
2yn5A0.77699.90.538
3pddA0.593199.50.689
3pddA0.504799.20.745
4ak1A0.9369980.839
4ak1A0.949597.90.842
1xf1A0.400697.80.845
3tkvA0.914897.80.846
1xf1A0.709897.50.859
3tkvA0.798197.40.86
If you are interested in a protein containing this domain,
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