GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4380 - Domain of unknown function (DUF4380)
Pfam: PF14315 (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. )
Length: 274
Sequences: 1399
Seq/Len: 5.11
HH_delta: 0.55 (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
259_A262_E0.312433.463
131_R265_E0.285893.169
133_T263_S0.277133.072
114_E131_R0.254562.822
15_E30_G0.232532.577
114_E133_T0.219342.431
141_E257_T0.214342.376
118_T129_T0.20432.264
129_T265_E0.195672.169
10_S32_N0.192442.133
9_L119_L0.18812.085
112_Q133_T0.184682.047
116_T131_R0.173951.928
28_S35_E0.16711.852
11_N119_L0.166881.850
10_S15_E0.1651.829
139_P259_A0.160871.783
115_R130_H0.158541.757
16_L26_I0.157881.750
16_L29_F0.157481.746
9_L18_V0.156931.739
16_L119_L0.156431.734
17_I28_S0.154641.714
131_R263_S0.148991.651
127_E269_T0.147571.636
102_T116_T0.147151.631
14_I29_F0.145471.612
10_S91_E0.14491.606
148_T212_Y0.144261.599
7_L81_P0.140121.553
100_R116_T0.140111.553
118_T127_E0.139691.548
241_Y250_E0.139681.548
19_T27_L0.139491.546
129_T267_T0.138351.533
111_I140_V0.137061.519
78_V81_P0.135381.501
112_Q135_I0.134041.486
105_P110_G0.131921.462
104_P112_Q0.131481.457
236_C239_E0.128431.424
132_I142_W0.126411.401
58_N61_G0.124041.375
81_P90_Y0.122721.360
110_G136_G0.122371.356
102_T114_E0.121751.349
120_D127_E0.121161.343
240_V243_N0.119081.320
8_R17_I0.117051.297
142_W258_L0.116851.295
24_G101_L0.116251.289
8_R15_E0.116151.287
93_E102_T0.11581.284
24_G103_S0.112751.250
77_W145_W0.112591.248
28_S37_L0.112131.243
18_V99_V0.111981.241
137_D260_P0.111571.237
258_L262_E0.110311.223
116_T129_T0.110121.221
141_E255_L0.109741.216
82_D104_P0.109691.216
11_N14_I0.109021.208
152_P212_Y0.108281.200
14_I126_I0.107671.193
127_E267_T0.106691.183
120_D123_R0.105731.172
94_I122_D0.105651.171
98_G120_D0.104761.161
24_G52_G0.104211.155
176_L195_A0.103751.150
201_L249_L0.10371.149
256_R264_L0.10331.145
60_G138_W0.102761.139
12_G94_I0.10161.126
48_P237_S0.100961.119
106_S112_Q0.100951.119
22_V78_V0.100591.115
25_R36_N0.098671.094
39_G228_Q0.09711.076
16_L126_I0.096821.073
113_K132_I0.096661.071
171_W175_K0.096661.071
113_K144_P0.096541.070
100_R129_T0.096281.067
103_S232_P0.096031.064
14_I117_I0.095021.053
135_I261_G0.094221.044
148_T251_T0.093851.040
7_L20_P0.093751.039
145_W148_T0.093591.037
30_G35_E0.093041.031
100_R118_T0.092651.027
176_L201_L0.092271.023
133_T264_L0.091871.018
29_F126_I0.09161.015
210_L261_G0.090341.001
90_Y113_K0.090020.998
49_G78_V0.089870.996
15_E32_N0.089630.993
77_W105_P0.089360.990
114_E155_T0.089080.987
195_A200_K0.089030.987
77_W80_P0.088680.983
13_D33_G0.088430.980
43_E47_A0.088260.978
31_L209_W0.088140.977
52_G230_E0.08680.962
152_P247_L0.086280.956
191_K194_P0.086120.955
24_G115_R0.086020.953
258_L264_L0.085930.952
18_V103_S0.085820.951
152_P174_T0.085530.948
77_W81_P0.085210.944
207_A235_G0.085130.944
199_G237_S0.085030.942
14_I136_G0.084970.942
192_Q212_Y0.084810.940
53_D149_Q0.084550.937
48_P145_W0.083980.931
238_V241_Y0.083170.922
50_V228_Q0.083150.922
12_G121_A0.083110.921
262_E266_H0.082920.919
15_E139_P0.082670.916
55_G145_W0.082050.909
50_V111_I0.081620.905
152_P214_N0.081570.904
227_P253_S0.08150.903
25_R248_E0.08140.902
119_L142_W0.080530.893
81_P236_C0.080380.891
91_E102_T0.080360.891
137_D261_G0.080130.888
135_I262_E0.080070.887
143_A205_P0.079780.884
252_L255_L0.079740.884
129_T261_G0.079520.881
143_A230_E0.07950.881
111_I115_R0.079110.877
139_P257_T0.079050.876
109_T136_G0.078470.870
37_L126_I0.078230.867
145_W202_G0.078160.866
233_D236_C0.078020.865
208_G229_A0.077960.864
11_N99_V0.077880.863
30_G262_E0.07780.862
43_E236_C0.077670.861
89_P136_G0.077650.861
136_G255_L0.077490.859
35_E76_K0.077120.855
131_R262_E0.076760.851
104_P127_E0.076680.850
104_P259_A0.076590.849
136_G259_A0.076370.846
18_V88_G0.076220.845
90_Y103_S0.076150.844
40_E48_P0.075740.840
82_D114_E0.075620.838
143_A255_L0.075620.838
137_D267_T0.075560.838
143_A252_L0.075330.835
78_V145_W0.075250.834
17_I27_L0.075240.834
102_T131_R0.075030.832
59_Y141_E0.074950.831
136_G140_V0.074920.830
239_E242_T0.074850.830
25_R230_E0.074690.828
135_I265_E0.074320.824
36_N76_K0.073870.819
90_Y130_H0.073490.815
229_A232_P0.073350.813
106_S111_I0.073110.810
116_T259_A0.073040.810
28_S47_A0.073010.809
98_G116_T0.07290.808
258_L266_H0.072680.806
77_W154_G0.072480.803
152_P192_Q0.07220.800
82_D204_N0.071950.797
185_D188_I0.071380.791
92_V99_V0.071210.789
179_P182_H0.071090.788
35_E47_A0.070890.786
136_G260_P0.070810.785
93_E96_D0.070790.785
244_D252_L0.070780.785
19_T175_K0.070750.784
173_Y269_T0.070680.783
54_S58_N0.070640.783
31_L34_G0.070630.783
60_G67_S0.070620.783
161_A243_N0.070620.783
207_A234_F0.070430.781
115_R149_Q0.070230.778
150_V230_E0.070190.778
142_W228_Q0.069880.775
14_I119_L0.069850.774
110_G132_I0.069770.773
187_Y214_N0.069740.773
230_E250_E0.069710.773
123_R127_E0.069670.772
138_W262_E0.06940.769
134_N260_P0.069330.768
19_T32_N0.069310.768
186_G191_K0.069170.767
25_R148_T0.069080.766
238_V242_T0.069060.765
23_G55_G0.068950.764
92_V139_P0.068930.764
107_P211_A0.068850.763
234_F244_D0.06870.761
80_P104_P0.068660.761
24_G53_D0.068640.761
206_S237_S0.068560.760
25_R76_K0.068530.760
97_D100_R0.068510.759
143_A237_S0.068350.758
171_W209_W0.068320.757
174_T192_Q0.068270.757
190_L195_A0.068110.755
18_V25_R0.068070.754
135_I258_L0.06790.753
175_K195_A0.067840.752
77_W90_Y0.06710.744
153_G235_G0.067030.743
91_E137_D0.066970.742
228_Q250_E0.066910.742
8_R104_P0.066780.740
67_S240_V0.066750.740
237_S243_N0.066720.740
138_W258_L0.066650.739
179_P212_Y0.066630.739
13_D139_P0.066530.737
37_L80_P0.066530.737
115_R229_A0.066470.737
17_I245_P0.066460.737
112_Q263_S0.066420.736
60_G66_P0.066390.736
97_D121_A0.066350.735
91_E204_N0.066340.735
133_T155_T0.066320.735
206_S259_A0.066320.735
16_L99_V0.066290.735
154_G267_T0.06610.733
176_L249_L0.066070.732
97_D120_D0.065990.731
61_G67_S0.065960.731
42_N47_A0.065950.731
138_W193_D0.065930.731
188_I191_K0.065920.731
119_L127_E0.065890.730
29_F148_T0.065870.730
81_P89_P0.065870.730
227_P245_P0.065420.725
27_L41_A0.065380.725
30_G267_T0.065190.723
105_P113_K0.065140.722
199_G266_H0.064990.720
199_G202_G0.064930.720
26_I117_I0.064590.716
26_I171_W0.064560.716
81_P104_P0.064440.714
81_P103_S0.064430.714
117_I128_V0.064390.714
133_T265_E0.064370.713
17_I30_G0.064240.712
82_D235_G0.06390.708
28_S40_E0.063850.708
49_G111_I0.063830.707
155_T174_T0.063760.707
41_A51_S0.063750.707
8_R89_P0.063670.706
260_P263_S0.063660.706
250_E254_P0.063650.705
53_D243_N0.063520.704
202_G231_Y0.06350.704
110_G211_A0.063440.703
25_R250_E0.063320.702
24_G251_T0.06330.702
31_L226_D0.063280.701
133_T261_G0.063250.701
107_P110_G0.063010.698
26_I96_D0.062960.698
133_T137_D0.062920.697
60_G75_S0.062890.697
14_I31_L0.062880.697
236_C263_S0.062870.697
182_H230_E0.062740.695
212_Y235_G0.06270.695
174_T214_N0.062640.694
187_Y251_T0.062640.694
29_F152_P0.062620.694
131_R253_S0.062510.693
13_D112_Q0.062490.693
142_W264_L0.062440.692
175_K179_P0.062430.692
96_D262_E0.06240.692
192_Q230_E0.062360.691
118_T206_S0.062350.691
109_T145_W0.062320.691
227_P231_Y0.06230.691
61_G155_T0.062270.690
32_N205_P0.062240.690
107_P113_K0.062140.689
195_A234_F0.062130.689
107_P137_D0.062080.688
188_I202_G0.0620.687
132_I243_N0.061920.686
202_G258_L0.06190.686
24_G193_D0.061830.685
99_V173_Y0.061830.685
91_E194_P0.061820.685
185_D242_T0.061820.685
154_G247_L0.061740.684
48_P79_W0.061690.684
54_S66_P0.061680.684
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
3ty1A0.941699.90.55
3k25A0.897899.90.559
3dcdA0.912499.80.578
3bs6A0.886999.80.579
3q1nA0.908899.80.584
3mwxA0.948999.80.592
3blcA0.890599.80.593
1jovA0.828599.80.596
3os7A0.956299.80.6
3nreA0.92799.80.608
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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