GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF401 - Protein of unknown function (DUF401)
Pfam: PF04165 (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: CL0182
Length: 385
Sequences: 11466
Seq/Len: 29.78
HH_delta: 0.39 (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
277_E281_E0.762023.837
359_D362_K0.743523.744
289_P292_L0.655393.300
240_R243_E0.653113.288
72_K243_E0.527682.657
40_G43_A0.517042.603
72_K246_E0.509172.564
361_G365_K0.474012.387
295_A335_S0.461242.322
83_S87_L0.460132.317
161_S164_E0.46012.317
278_E281_E0.4552.291
121_E127_P0.449252.262
281_E284_S0.444282.237
278_E282_F0.431832.174
362_K365_K0.430312.167
128_E362_K0.429952.165
281_E285_S0.421662.123
268_E272_A0.420542.117
78_D82_E0.419262.111
145_W148_Y0.414922.089
368_L372_L0.414162.085
27_L262_G0.400422.016
173_T177_F0.388861.958
68_G250_E0.382961.928
199_K203_K0.379271.910
207_P211_I0.376081.894
105_M108_G0.35981.812
68_G71_E0.359221.809
83_S86_G0.358431.805
274_G277_E0.355451.790
243_E246_E0.347741.751
201_L204_S0.347711.751
200_D203_K0.335541.689
280_P284_S0.332121.672
242_K245_K0.331741.670
155_S162_V0.321271.618
198_L202_L0.316151.592
249_K253_E0.315621.589
202_L206_W0.314981.586
300_I304_I0.312221.572
183_F187_P0.311191.567
141_W145_W0.310941.566
288_I292_L0.306871.545
301_V311_F0.304021.531
250_E253_E0.302931.525
282_F285_S0.301961.520
146_P149_P0.298671.504
164_E167_L0.298321.502
30_A265_I0.297761.499
116_V134_N0.296711.494
43_A272_A0.295451.488
163_G167_L0.294861.485
75_G78_D0.293421.477
242_K246_E0.289181.456
97_P100_I0.285941.440
68_G72_K0.285841.439
30_A269_I0.28521.436
303_L306_G0.283811.429
198_L201_L0.283171.426
157_L312_V0.282081.420
174_L178_L0.281711.418
171_P175_L0.281271.416
194_K197_S0.280971.415
360_L364_Y0.277131.395
100_I105_M0.275521.387
141_W147_L0.275151.385
299_F302_G0.27511.385
246_E250_E0.270181.360
129_E133_I0.269661.358
184_F188_L0.269511.357
141_W146_P0.268221.350
245_K249_K0.267071.345
282_F286_L0.266651.343
246_E249_K0.265431.336
358_A363_V0.264451.331
215_S221_P0.263341.326
68_G251_A0.26241.321
268_E271_E0.261841.318
79_R83_S0.26091.314
270_L275_V0.260371.311
120_A127_P0.259681.307
112_S116_V0.259511.307
72_K247_V0.257531.297
233_I239_F0.256341.291
335_S338_A0.255661.287
170_W174_L0.255241.285
20_I25_S0.25441.281
141_W148_Y0.250191.260
103_L107_G0.248011.249
145_W149_P0.244661.232
221_P224_L0.243711.227
26_I263_I0.243451.226
201_L205_L0.241621.217
346_H350_V0.240881.213
293_I323_I0.240071.209
117_E121_E0.239681.207
244_I248_L0.239361.205
83_S201_L0.239081.204
151_I330_V0.238831.202
96_I112_S0.237921.198
183_F186_R0.236971.193
82_E122_K0.236861.193
287_G292_L0.236681.192
118_E122_K0.236251.189
320_A324_G0.236081.189
132_F366_K0.235421.185
92_S224_L0.2351.183
311_F336_G0.233681.177
148_Y172_I0.231421.165
259_L263_I0.230751.162
141_W149_P0.230091.158
132_F367_L0.229581.156
199_K202_L0.228841.152
187_P190_K0.228511.151
237_N240_R0.228091.148
324_G328_Y0.228031.148
206_W210_V0.227361.145
98_A107_G0.227341.145
361_G364_Y0.226751.142
297_I319_L0.226511.140
84_L88_F0.225981.138
109_A351_L0.225351.135
33_L269_I0.225091.133
196_R199_K0.225071.133
27_L265_I0.224321.129
204_S211_I0.224271.129
337_F340_V0.224171.129
36_L39_L0.221091.113
302_G306_G0.220481.110
195_P198_L0.218621.101
169_M173_T0.218511.100
75_G79_R0.218251.099
71_E78_D0.217751.096
82_E203_K0.21771.096
279_L282_F0.217691.096
155_S165_F0.216911.092
93_L214_L0.215521.085
96_I100_I0.215181.083
347_L351_L0.214831.082
321_P324_G0.214781.081
131_T358_A0.21411.078
127_P362_K0.213861.077
311_F315_A0.213661.076
311_F316_F0.21351.075
181_W184_F0.213451.075
168_A171_P0.21331.074
208_I211_I0.213211.073
21_N25_S0.212311.069
202_L205_L0.211731.066
261_I265_I0.211651.066
203_K206_W0.210731.061
167_L171_P0.210081.058
78_D238_R0.209941.057
96_I105_M0.209831.056
143_F146_P0.209731.056
296_L300_I0.209681.056
204_S207_P0.209431.054
25_S29_G0.208831.051
267_K314_I0.208491.050
131_T356_F0.207131.043
30_A262_G0.207061.043
271_E277_E0.206971.042
239_F247_V0.205811.036
92_S221_P0.20571.036
348_C351_L0.205681.036
210_V213_L0.204451.029
82_E86_G0.203891.027
29_G33_L0.203591.025
52_S261_I0.20331.024
71_E77_L0.203051.022
186_R189_K0.202741.021
158_S320_A0.202191.018
156_A159_G0.20021.008
30_A34_G0.199531.005
171_P174_L0.198811.001
29_G34_G0.198430.999
65_F248_L0.196950.992
28_L32_I0.196930.992
69_L233_I0.196630.990
94_A105_M0.196330.988
79_R82_E0.196060.987
240_R247_V0.195920.986
26_I266_F0.195640.985
353_A360_L0.192230.968
93_L221_P0.191920.966
181_W185_L0.191780.966
160_I164_E0.191270.963
135_Y352_T0.191220.963
146_P337_F0.190410.959
50_S53_S0.190320.958
20_I24_I0.19020.958
366_K369_P0.189560.954
323_I328_Y0.189520.954
114_P118_E0.189430.954
98_A102_L0.188980.951
153_L309_Q0.188190.948
184_F187_P0.187260.943
185_L189_K0.186430.939
200_D204_S0.186380.938
167_L222_L0.185990.936
214_L224_L0.185340.933
128_E358_A0.185320.933
102_L106_P0.185260.933
182_L186_R0.18510.932
153_L312_V0.185010.932
126_S129_E0.184940.931
369_P372_L0.184530.929
21_N24_I0.184380.928
334_A338_A0.183480.924
94_A97_P0.183450.924
364_Y368_L0.183190.922
211_I232_A0.183080.922
201_L211_I0.182990.921
270_L276_V0.182630.920
341_M348_C0.182360.918
131_T363_V0.182340.918
185_L188_L0.18180.915
158_S316_F0.181740.915
67_M77_L0.181570.914
129_E132_F0.181550.914
151_I155_S0.181380.913
337_F341_M0.180960.911
40_G44_F0.180660.910
205_L208_I0.179550.904
84_L87_L0.179460.904
97_P101_G0.179370.903
96_I103_L0.17860.899
342_L368_L0.178560.899
86_G90_R0.178510.899
32_I36_L0.177990.896
345_V350_V0.177940.896
81_V115_M0.177920.896
23_G262_G0.177720.895
317_P322_L0.177490.894
206_W211_I0.177410.893
291_F295_A0.177270.893
93_L329_L0.176790.890
100_I108_G0.176720.890
154_A158_S0.175980.886
140_I143_F0.175660.884
83_S205_L0.175580.884
248_L252_L0.175130.882
367_L371_A0.175130.882
140_I341_M0.174910.881
277_E280_P0.174830.880
274_G278_E0.174540.879
359_D364_Y0.174450.878
351_L354_E0.174380.878
225_G228_I0.174070.876
311_F339_G0.173420.873
116_V356_F0.173350.873
287_G290_P0.173230.872
349_L353_A0.172440.868
312_V316_F0.172160.867
340_V348_C0.172160.867
33_L36_L0.171950.866
27_L31_L0.171750.865
26_I259_L0.171340.863
308_T340_V0.171230.862
22_I26_I0.170580.859
241_R245_K0.170030.856
284_S325_G0.169710.854
162_V165_F0.169510.853
340_V347_L0.169470.853
287_G293_I0.169420.853
298_P302_G0.169310.852
97_P105_M0.169250.852
85_K123_M0.169220.852
61_L65_F0.168880.850
150_G308_T0.168620.849
263_I310_A0.167970.846
269_I273_T0.167010.841
207_P232_A0.166550.839
96_I102_L0.166390.838
81_V85_K0.166360.838
120_A130_K0.166240.837
233_I244_I0.165930.835
125_L130_K0.164680.829
142_E147_L0.164520.828
334_A337_F0.164340.827
298_P315_A0.16390.825
29_G32_I0.16370.824
128_E131_T0.163150.821
234_L237_N0.162930.820
295_A299_F0.162560.818
31_L35_L0.162530.818
142_E348_C0.162210.817
96_I99_L0.162060.816
52_S58_V0.161920.815
129_E370_P0.161550.813
57_I60_I0.160840.810
231_L234_L0.160780.810
182_L185_L0.16050.808
243_E247_V0.160370.807
295_A298_P0.16030.807
241_R244_I0.160040.806
301_V306_G0.160040.806
34_G44_F0.159940.805
82_E85_K0.159840.805
205_L209_L0.159690.804
142_E149_P0.159650.804
209_L213_L0.159350.802
362_K366_K0.159320.802
65_F69_L0.159210.802
146_P339_G0.159170.801
202_L209_L0.159020.801
130_K134_N0.158840.800
72_K250_E0.158670.799
79_R238_R0.158640.799
82_E197_S0.158010.796
211_I214_L0.157760.794
214_L328_Y0.157710.794
297_I302_G0.157670.794
240_R245_K0.157110.791
157_L316_F0.156650.789
56_T60_I0.155710.784
150_G309_Q0.155180.781
41_L45_L0.153820.774
306_G371_A0.153450.773
358_A362_K0.153280.772
154_A160_I0.153170.771
41_L44_F0.153070.771
30_A266_F0.152940.770
277_E321_P0.152510.768
90_R193_K0.152460.768
39_L43_A0.15230.767
102_L105_M0.152280.767
353_A363_V0.152270.767
302_G305_T0.151990.765
93_L96_I0.151870.765
233_I243_E0.151850.765
34_G38_G0.151820.764
28_L31_L0.151720.764
32_I35_L0.151660.764
93_L328_Y0.15160.763
208_I212_I0.151570.763
69_L232_A0.15020.756
275_V278_E0.150070.756
186_R190_K0.149880.755
204_S208_I0.149690.754
209_L212_I0.149660.754
107_G110_L0.149590.753
23_G30_A0.149470.753
310_A313_G0.149420.752
35_L42_D0.149380.752
100_I106_P0.149070.751
81_V158_S0.149030.750
352_T358_A0.148830.749
95_F99_L0.148740.749
81_V262_G0.148710.749
108_G352_T0.148640.748
280_P283_L0.148430.747
364_Y367_L0.148410.747
172_I175_L0.14840.747
306_G310_A0.148260.746
67_M73_L0.148040.745
162_V166_V0.147570.743
309_Q313_G0.147520.743
206_W214_L0.147490.743
306_G347_L0.147370.742
301_V305_T0.147340.742
214_L329_L0.147210.741
310_A346_H0.146740.739
108_G111_F0.146330.737
363_V367_L0.145630.733
297_I301_V0.145350.732
78_D118_E0.145310.732
103_L106_P0.145270.731
108_G223_A0.145130.731
97_P103_L0.144710.729
326_L329_L0.144570.728
87_L90_R0.14430.727
301_V304_I0.144290.726
93_L107_G0.143790.724
346_H369_P0.143770.724
341_M367_L0.143570.723
75_G238_R0.143490.722
263_I346_H0.143380.722
185_L190_K0.143160.721
73_L77_L0.143030.720
316_F320_A0.142890.719
207_P212_I0.142780.719
64_Y254_P0.142770.719
168_A330_V0.142350.717
343_S348_C0.142160.716
310_A347_L0.142110.716
63_I67_M0.142040.715
257_L260_I0.142040.715
260_I309_Q0.141960.715
348_C352_T0.141720.714
331_L334_A0.141580.713
92_S327_P0.141530.713
193_K196_R0.14140.712
94_A329_L0.141380.712
258_L261_I0.141330.712
58_V62_L0.141270.711
59_L256_I0.141130.711
23_G258_L0.141070.710
343_S350_V0.141070.710
127_P358_A0.141050.710
30_A45_L0.140820.709
169_M172_I0.14060.708
143_F147_L0.14050.707
111_F115_M0.140470.707
203_K232_A0.140270.706
228_I232_A0.140170.706
155_S160_I0.140110.705
112_S355_Y0.140030.705
37_F40_G0.139720.703
51_S261_I0.139640.703
339_G346_H0.139570.703
65_F230_L0.139030.700
143_F148_Y0.138960.700
264_M268_E0.138940.700
222_L305_T0.138830.699
65_F251_A0.138610.698
99_L156_A0.138610.698
92_S105_M0.138560.698
273_T276_V0.138560.698
32_I37_F0.138530.697
319_L323_I0.138420.697
93_L327_P0.138380.697
245_K248_L0.138330.696
166_V222_L0.138040.695
94_A176_A0.137960.695
93_L168_A0.137940.695
283_L322_L0.137920.694
80_M111_F0.137890.694
67_M110_L0.137590.693
149_P302_G0.137570.693
183_F369_P0.137360.692
339_G343_S0.137320.691
201_L207_P0.136870.689
193_K197_S0.13670.688
256_I259_L0.136340.686
40_G272_A0.136310.686
100_I107_G0.136220.686
127_P131_T0.135690.683
305_T308_T0.135110.680
332_A335_S0.13510.680
79_R203_K0.134560.677
168_A329_L0.134460.677
210_V214_L0.134440.677
351_L355_Y0.134340.676
260_I270_L0.134320.676
256_I274_G0.134010.675
73_L76_Q0.133870.674
159_G163_G0.133710.673
367_L370_P0.13370.673
106_P223_A0.133640.673
239_F243_E0.133620.673
303_L342_L0.132750.668
298_P332_A0.132670.668
249_K252_L0.132520.667
203_K207_P0.132450.667
69_L244_I0.132340.666
185_L224_L0.13230.666
54_W60_I0.132120.665
79_R201_L0.132120.665
267_K274_G0.132110.665
299_F306_G0.132030.665
309_Q316_F0.13190.664
108_G135_Y0.131870.664
143_F340_V0.131770.663
54_W57_I0.13160.663
207_P236_Y0.131320.661
276_V280_P0.13120.661
57_I309_Q0.131090.660
342_L371_A0.131070.660
191_S194_K0.1310.660
310_A339_G0.130920.659
93_L108_G0.130880.659
93_L105_M0.130860.659
254_P263_I0.130850.659
211_I215_S0.130820.659
105_M309_Q0.130730.658
306_G339_G0.130630.658
112_S118_E0.130440.657
344_P349_L0.130370.656
298_P301_V0.129560.652
344_P364_Y0.129250.651
363_V366_K0.12910.650
196_R202_L0.129020.650
173_T176_A0.128960.649
128_E365_K0.128950.649
141_W341_M0.128930.649
273_T317_P0.128820.649
152_I172_I0.128690.648
276_V313_G0.128540.647
64_Y67_M0.128490.647
79_R236_Y0.128340.646
237_N241_R0.128230.646
31_L50_S0.127980.644
57_I260_I0.127980.644
111_F146_P0.127880.644
106_P109_A0.127870.644
59_L64_Y0.127860.644
262_G266_F0.127850.644
61_L257_L0.127790.643
59_L63_I0.127780.643
252_L267_K0.127750.643
177_F180_G0.127680.643
343_S347_L0.127490.642
226_L229_A0.127480.642
39_L42_D0.127460.642
214_L327_P0.127360.641
160_I329_L0.127280.641
19_K24_I0.127030.640
284_S322_L0.127010.639
306_G346_H0.126980.639
210_V228_I0.126960.639
166_V170_W0.126950.639
166_V275_V0.126880.639
180_G187_P0.126790.638
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
4f35D0.97141000.39
4f35D0.4727990.794
2m67A0.194824.80.953
3qnqA0.490912.20.959
2rddB0.09617.90.962
3w9iA0.4267.90.962
4apsA0.49877.50.962
2kncA0.14036.80.963
4iu9B0.483160.964
3ne5A0.36625.60.965

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