GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2320 - Uncharacterized protein conserved in bacteria (DUF2320)
Pfam: PF10082 (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: 381
Sequences: 5977
Seq/Len: 15.69
HH_delta: 0.437 (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
241_V259_P1.035914.705
95_L139_A0.912334.144
243_Y257_S0.85753.895
192_T227_V0.848413.854
273_T303_W0.778343.535
95_L137_Y0.774273.517
319_Y334_Y0.752863.420
279_A297_T0.750993.411
235_T267_W0.681793.097
281_R297_T0.662193.008
103_Y131_F0.608542.764
269_P275_V0.600952.730
197_E224_L0.588972.675
92_T95_L0.582862.648
101_G131_F0.580062.635
198_V221_Y0.576342.618
148_L182_A0.565852.570
273_T305_H0.563982.562
315_L338_L0.555532.523
237_G265_L0.547632.488
313_L340_L0.51492.339
318_G335_S0.512762.329
234_K267_W0.505752.297
96_R138_G0.504632.292
138_G145_R0.497772.261
151_G179_T0.487942.216
301_L317_A0.485682.206
276_T316_S0.483872.198
243_Y259_P0.479472.178
148_L180_A0.47372.152
98_D136_G0.473172.149
105_R129_N0.467632.124
150_A178_Y0.467522.124
144_G186_Y0.464192.109
200_Y221_Y0.459932.089
222_E242_G0.453562.060
319_Y332_D0.442562.010
311_L342_Y0.442152.008
146_L182_A0.433261.968
318_G357_E0.427911.944
94_R139_A0.422811.921
276_T302_G0.422741.920
235_T265_L0.415681.888
192_T229_W0.412841.875
97_L135_Y0.408741.857
277_L301_L0.406191.845
97_L137_Y0.402871.830
345_N348_L0.390151.772
266_T274_T0.389781.771
315_L336_A0.387981.762
239_A263_A0.387891.762
300_S316_S0.382411.737
150_A180_A0.381591.733
147_S183_R0.376421.710
344_L350_L0.37051.683
236_R268_S0.369311.678
99_L135_Y0.367961.671
230_D236_R0.360411.637
276_T304_T0.358371.628
261_W281_R0.35551.615
138_G147_S0.348511.583
261_W265_L0.348471.583
294_V322_R0.348271.582
317_A336_A0.348191.582
318_G337_G0.340331.546
222_E244_Q0.339351.541
275_V303_W0.338431.537
144_G184_L0.3371.531
88_R98_D0.335161.522
152_Y178_Y0.332971.512
318_G355_R0.332281.509
281_R295_R0.330721.502
202_D219_T0.329831.498
154_R176_D0.327441.487
305_H313_L0.325531.479
198_V223_V0.324661.475
101_G133_A0.324511.474
91_F97_L0.323721.470
264_S278_S0.318351.446
232_T235_T0.317951.444
245_R257_S0.317251.441
94_R140_R0.314351.428
188_L194_L0.313441.424
196_V225_A0.312351.419
199_R222_E0.312161.418
317_A334_Y0.31011.409
99_L133_A0.308151.400
299_V321_N0.304631.384
298_S320_E0.300561.365
193_S230_D0.298491.356
244_Q260_S0.298421.356
279_A299_V0.297631.352
258_G295_R0.296061.345
103_Y129_N0.294761.339
92_T139_A0.294471.338
88_R96_R0.293961.335
146_L184_L0.290531.320
333_T359_R0.289341.314
282_S296_T0.286151.300
334_Y358_D0.281311.278
226_G238_E0.281161.277
183_R224_L0.279881.271
237_G263_A0.27641.255
193_S228_S0.274051.245
277_L299_V0.272831.239
312_S341_T0.271341.233
102_S132_S0.270711.230
100_G134_S0.270591.229
202_D217_D0.269291.223
311_L340_L0.268591.220
313_L338_L0.268331.219
306_Q309_P0.267791.216
321_N332_D0.266891.212
320_E333_T0.265851.208
341_T349_S0.26311.195
314_S339_G0.262391.192
226_G262_D0.259731.180
83_L103_Y0.25781.171
141_F146_L0.247371.124
307_L313_L0.244161.109
238_E264_S0.239211.087
269_P273_T0.239191.086
270_T273_T0.238751.084
231_L237_G0.23851.083
234_K269_P0.233341.060
200_Y219_T0.232221.055
339_G353_G0.231671.052
336_A356_Y0.230781.048
284_E294_V0.229561.043
286_S291_G0.22921.041
152_Y176_D0.224621.020
306_Q312_S0.22371.016
195_F226_G0.223381.015
321_N330_E0.221271.005
229_W239_A0.220791.003
96_R140_R0.220141.000
181_G199_R0.219710.998
91_F137_Y0.218060.990
303_W315_L0.217120.986
302_G337_G0.216430.983
344_L348_L0.214630.975
204_D215_S0.213420.969
86_N98_D0.213350.969
186_Y196_V0.210140.955
224_L242_G0.208220.946
275_V301_L0.208190.946
304_T314_S0.206550.938
269_P303_W0.205480.933
302_G335_S0.204690.930
231_L265_L0.203870.926
341_T351_S0.201610.916
235_T269_P0.201250.914
184_L196_V0.200390.910
90_D96_R0.19830.901
91_F95_L0.198080.900
143_R187_R0.197810.899
307_L311_L0.197130.895
194_L225_A0.196470.892
236_R266_T0.195420.888
343_R349_S0.195360.887
299_V319_Y0.194640.884
317_A338_L0.194230.882
220_G244_Q0.193930.881
265_L269_P0.191450.870
245_R255_D0.191250.869
187_R193_S0.190690.866
295_R323_D0.189960.863
238_E266_T0.188650.857
343_R346_R0.187780.853
223_V245_R0.186170.846
316_S337_G0.186170.846
227_V239_A0.185590.843
300_S337_G0.185330.842
133_A152_Y0.185320.842
228_S236_R0.185160.841
221_Y245_R0.184060.836
280_S298_S0.183480.833
300_S335_S0.183140.832
278_S300_S0.179940.817
158_D172_D0.179510.815
134_S149_G0.179260.814
333_T357_E0.179240.814
268_S271_P0.178770.812
141_F184_L0.177470.806
145_R185_G0.177180.805
106_G128_R0.177050.804
337_G355_R0.176970.804
265_L277_L0.176750.803
340_L352_A0.176570.802
274_T304_T0.175160.796
179_T199_R0.1740.790
136_G147_S0.173690.789
296_T322_R0.171580.779
268_S274_T0.170910.776
284_E331_D0.170560.775
84_N102_S0.168660.766
143_R186_Y0.168420.765
229_W237_G0.167610.761
197_E240_K0.167130.759
322_R333_T0.167110.759
136_G149_G0.166840.758
144_G196_V0.166310.755
302_G318_G0.166250.755
239_A265_L0.166070.754
344_L347_W0.165490.752
77_D109_P0.165390.751
246_R285_E0.164740.748
139_A142_G0.16430.746
287_T291_G0.1630.740
188_L192_T0.162550.738
272_K307_L0.16250.738
262_D278_S0.162390.738
343_R347_W0.161690.734
260_S283_I0.161650.734
194_L227_V0.161350.733
229_W232_T0.161350.733
328_D361_S0.160950.731
195_F228_S0.16030.728
310_R342_Y0.160190.728
88_R91_F0.160180.728
86_N100_G0.160130.727
273_T277_L0.159440.724
226_G240_K0.159410.724
140_R145_R0.159250.723
263_A277_L0.159150.723
149_G181_G0.158990.722
246_R256_F0.158650.721
154_R174_D0.158180.719
81_H105_R0.157390.715
79_T107_H0.157350.715
191_G232_T0.156280.710
300_S304_T0.155820.708
191_G230_D0.155180.705
241_V261_W0.1550.704
147_S185_G0.154180.700
267_W270_T0.153740.698
224_L240_K0.153680.698
291_G327_S0.15350.697
323_D330_E0.153350.697
242_G359_R0.153270.696
90_D93_R0.152230.691
297_T323_D0.15180.690
302_G316_S0.150910.685
146_L150_A0.150010.681
219_T247_D0.149960.681
292_S327_S0.149920.681
173_R205_Y0.149010.677
332_D358_D0.149010.677
223_V243_Y0.148550.675
228_S238_E0.147270.669
332_D360_D0.147040.668
276_T300_S0.146370.665
315_L340_L0.145650.662
197_E242_G0.145580.661
223_V227_V0.145540.661
87_G99_L0.143690.653
132_S151_G0.141750.644
155_L175_R0.140830.640
331_D361_S0.140730.639
181_G224_L0.140060.636
337_G353_G0.140030.636
330_E360_D0.139490.634
178_Y204_D0.139090.632
188_L227_V0.138690.630
329_R361_S0.138530.629
230_D268_S0.137730.626
244_Q285_E0.137530.625
209_A212_N0.137140.623
85_A89_W0.136870.622
341_T344_L0.136010.618
142_G186_Y0.135910.617
134_S151_G0.135720.616
245_R259_P0.134670.612
220_G246_R0.134490.611
282_S337_G0.134290.610
310_R343_R0.133740.607
159_N171_S0.133720.607
178_Y182_A0.132910.604
322_R331_D0.132760.603
191_G229_W0.132620.602
294_V298_S0.132560.602
183_R195_F0.13250.602
98_D134_S0.132330.601
141_F144_G0.132210.601
242_G260_S0.131140.596
321_N334_Y0.130730.594
297_T321_N0.130430.592
270_T305_H0.130190.591
82_N86_N0.130080.591
230_D233_G0.129940.590
105_R174_D0.129810.590
109_P125_P0.12970.589
294_V335_S0.129670.589
240_K262_D0.129540.588
258_G283_I0.129490.588
280_S300_S0.12920.587
94_R142_G0.128680.585
177_E203_R0.128480.584
286_S324_Y0.128110.582
349_S352_A0.127970.581
281_R299_V0.127690.580
334_Y356_Y0.127560.579
310_R344_L0.127260.578
201_T220_G0.126870.576
220_G285_E0.126710.576
98_D138_G0.126360.574
256_F293_Y0.126150.573
145_R187_R0.125950.572
282_S286_S0.124540.566
315_L319_Y0.124540.566
166_T210_D0.124080.564
307_L310_R0.123610.561
202_D245_R0.123590.561
190_P326_G0.122990.559
243_Y261_W0.122990.559
286_S294_V0.122230.555
114_D212_N0.122120.555
268_S272_K0.122050.554
102_S153_D0.121390.551
179_T201_T0.121320.551
338_L354_Y0.121120.550
296_T320_E0.120750.548
206_D215_S0.120580.548
225_A241_V0.119640.543
226_G280_S0.119580.543
197_E222_E0.119560.543
282_S285_E0.119250.542
94_R141_F0.119180.541
80_D106_G0.119090.541
244_Q262_D0.118860.540
340_L344_L0.118620.539
149_G179_T0.118530.538
264_S280_S0.117790.535
120_D208_R0.117380.533
336_A340_L0.117160.532
261_W297_T0.117050.532
137_Y148_L0.116960.531
99_L103_Y0.11690.531
220_G294_V0.116680.530
241_V263_A0.116370.529
105_R127_E0.115980.527
331_D359_R0.115780.526
260_S281_R0.115530.525
262_D282_S0.115390.524
89_W92_T0.115350.524
178_Y202_D0.114970.522
267_W271_P0.11480.521
242_G335_S0.114720.521
304_T316_S0.114440.520
328_D331_D0.114210.519
342_Y350_L0.113860.517
149_G183_R0.113670.516
81_H85_A0.113510.516
77_D126_V0.112570.511
272_K306_Q0.112360.510
130_T181_G0.112280.510
163_S211_P0.112070.509
84_N100_G0.111990.509
298_S302_G0.111780.508
86_N296_T0.111730.508
262_D280_S0.111690.507
84_N179_T0.111590.507
270_T275_V0.111590.507
181_G222_E0.111530.507
354_Y357_E0.111370.506
272_K309_P0.111310.506
171_S250_D0.111280.505
271_P274_T0.110930.504
223_V257_S0.110760.503
169_S209_A0.110560.502
117_G170_T0.109990.500
140_R208_R0.109940.499
240_K261_W0.109810.499
182_A186_Y0.10970.498
238_E262_D0.10970.498
99_L136_G0.109530.498
345_N349_S0.109270.496
276_T318_G0.109250.496
242_G302_G0.109150.496
102_S130_T0.108610.493
93_R346_R0.108530.493
318_G359_R0.108520.493
192_T230_D0.10850.493
300_S318_G0.10850.493
312_S343_R0.108390.492
96_R136_G0.108150.491
204_D247_D0.108090.491
83_L288_D0.108020.491
286_S293_Y0.107890.490
294_V318_G0.107840.490
294_V328_D0.107780.490
137_Y146_L0.107570.489
112_S157_Y0.107240.487
237_G241_V0.107160.487
242_G337_G0.106790.485
155_L261_W0.106590.484
244_Q283_I0.106510.484
278_S298_S0.106340.483
120_D125_P0.105990.481
135_Y150_A0.105950.481
348_L352_A0.105880.481
249_D253_R0.105850.481
316_S355_R0.105520.479
313_L317_A0.105220.478
121_V173_R0.104820.476
144_G194_L0.104690.476
276_T335_S0.104650.475
190_P229_W0.104230.473
243_Y258_G0.104140.473
81_H103_Y0.103970.472
298_S318_G0.103730.471
242_G318_G0.10370.471
310_R345_N0.103690.471
312_S315_L0.103680.471
78_Y171_S0.103330.469
82_N106_G0.10330.469
118_G141_F0.103120.468
338_L342_Y0.103080.468
324_Y331_D0.103020.468
77_D172_D0.102910.467
244_Q282_S0.102790.467
186_Y194_L0.102690.466
110_R157_Y0.102220.464
262_D298_S0.102120.464
128_R157_Y0.102020.463
203_R264_S0.101920.463
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
3efmA0.97641000.437
3qlbA0.97381000.449
4epaA0.97641000.452
1xkwA0.9791000.465
2w16A0.97641000.475
1qfgA0.97641000.476
1kmoA0.97999.90.483
3fhhA0.973899.90.49
3cslA0.984399.90.497
2hdiA0.934499.90.498

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