GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UCH - Ubiquitin carboxyl-terminal hydrolase
Pfam: PF00443 (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: CL0125
Length: 269
Sequences: 3471
Seq/Len: 12.9
HH_delta: 0.098 (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
145_C148_C0.780824.816
23_I214_V0.554883.422
50_E53_Q0.518153.196
19_C215_A0.489623.020
212_R233_R0.447292.759
239_K250_E0.445712.749
4_L14_N0.400712.471
21_F59_F0.393592.427
7_I10_T0.378672.335
220_Y229_V0.365242.253
19_C268_F0.360262.222
99_F103_L0.339982.097
221_G226_G0.333182.055
218_V229_V0.330762.040
219_H226_G0.328442.026
95_D98_E0.3272.017
158_L194_L0.313721.935
218_V231_Y0.304371.877
14_N18_Q0.301141.857
193_D210_K0.297341.834
100_L163_I0.296091.826
108_D129_S0.294591.817
264_A267_L0.289561.786
28_N32_S0.279521.724
163_I268_F0.277511.712
6_N11_C0.277211.710
16_V217_I0.274611.694
229_V242_K0.273851.689
55_L59_F0.270361.667
253_W257_I0.263871.627
27_R55_L0.262091.616
219_H228_Y0.260751.608
13_L99_F0.260421.606
168_R180_K0.256941.585
54_Q57_N0.256871.584
159_P162_L0.253511.564
78_I82_S0.250191.543
7_I74_P0.249541.539
58_L72_I0.247681.528
251_V256_V0.247641.527
27_R59_F0.245271.513
191_E210_K0.244671.509
11_C227_H0.244541.508
242_K249_T0.243891.504
191_E212_R0.243471.502
243_F248_V0.242421.495
58_L62_L0.242181.494
265_Y269_Y0.23951.477
162_L168_R0.23771.466
193_D196_P0.236881.461
19_C230_A0.235571.453
232_V243_F0.234861.448
100_L104_L0.231831.430
215_A232_V0.231421.427
93_Q98_E0.23071.423
21_F27_R0.22681.399
16_V96_A0.224031.382
19_C217_I0.223911.381
252_S255_E0.223241.377
23_I161_I0.223191.377
13_L78_I0.2231.375
241_Y248_V0.222761.374
144_K149_K0.221171.364
100_L266_L0.220771.362
3_G6_N0.216171.333
81_L99_F0.214411.322
94_Q98_E0.212541.311
97_H165_Q0.210711.300
2_V62_L0.210151.296
138_Q157_S0.209711.293
193_D197_Y0.208461.286
134_L161_I0.208251.284
97_H101_S0.208081.283
129_S132_S0.207631.281
56_Q60_R0.202541.249
21_F63_W0.200691.238
57_N76_D0.200051.234
231_Y251_V0.199691.232
140_E154_S0.199131.228
221_G228_Y0.198981.227
166_L185_V0.198041.221
20_L26_F0.19511.203
264_A269_Y0.194181.198
166_L267_L0.19391.196
22_H232_V0.192561.188
137_G141_S0.191041.178
16_V100_L0.190091.172
227_H245_D0.189811.171
96_A100_L0.189031.166
253_W256_V0.188891.165
180_K219_H0.187391.156
144_K151_S0.18691.153
59_F63_W0.185471.144
22_H234_D0.185321.143
158_L198_L0.183551.132
132_S136_G0.183361.131
211_Y219_H0.182981.129
52_L107_L0.182691.127
131_I137_G0.182631.126
11_C15_S0.181771.121
180_K185_V0.180261.112
21_F62_L0.17921.105
138_Q156_S0.177881.097
30_L52_L0.177151.093
142_S152_Q0.176551.089
4_L62_L0.175321.081
24_P28_N0.175191.080
50_E110_E0.174881.079
213_L267_L0.1741.073
245_D248_V0.173881.072
25_P161_I0.170341.051
52_L110_E0.170251.050
165_Q169_F0.169791.047
159_P168_R0.167811.035
251_V255_E0.167211.031
172_D179_K0.166881.029
27_R31_L0.165941.023
168_R219_H0.165931.023
166_L169_F0.165281.019
221_G227_H0.161030.993
155_I158_L0.15890.980
227_H244_D0.158240.976
16_V99_F0.157060.969
215_A230_A0.155790.961
93_Q221_G0.155720.960
159_P165_Q0.155360.958
6_N14_N0.154420.952
194_L197_Y0.15380.949
231_Y242_K0.153590.947
134_L138_Q0.153440.946
217_I266_L0.152880.943
6_N18_Q0.152740.942
254_E258_K0.152260.939
168_R185_V0.152230.939
13_L17_L0.151820.936
169_F180_K0.151430.934
198_L201_N0.151220.933
195_S208_N0.149930.925
19_C163_I0.149510.922
11_C18_Q0.149410.921
51_F103_L0.149250.920
22_H215_A0.14880.918
104_L135_F0.147780.911
55_L107_L0.147440.909
141_S153_S0.147070.907
135_F139_F0.146360.903
213_L269_Y0.145240.896
96_A217_I0.145010.894
140_E156_S0.144630.892
219_H227_H0.144210.889
142_S151_S0.144020.888
26_F135_F0.142580.879
6_N245_D0.142370.878
11_C226_G0.142150.877
162_L180_K0.141580.873
20_L100_L0.141090.870
187_F267_L0.140860.869
57_N61_S0.140820.869
108_D132_S0.140310.865
229_V244_D0.14010.864
12_Y18_Q0.139950.863
241_Y250_E0.139620.861
20_L103_L0.139610.861
128_D133_D0.139560.861
5_Q73_S0.139550.861
240_W245_D0.139510.860
84_I106_W0.139440.860
158_L211_Y0.139410.860
164_I185_V0.139370.860
93_Q226_G0.139150.858
158_L209_V0.138970.857
101_S105_D0.137070.845
169_F223_A0.136310.841
256_V262_S0.135450.835
234_D241_Y0.134670.831
131_I135_F0.134440.829
234_D237_D0.134040.827
8_G11_C0.133630.824
17_L77_F0.133620.824
213_L219_H0.13330.822
56_Q63_W0.133160.821
188_P192_L0.132710.818
146_S150_N0.132670.818
155_I162_L0.131690.812
145_C149_K0.131570.811
30_L56_Q0.13120.809
42_S45_S0.131110.809
187_F264_A0.130980.808
161_I268_F0.130930.808
200_K203_S0.130620.806
111_F130_L0.130190.803
216_V231_Y0.130030.802
60_R64_S0.129830.801
256_V263_T0.129480.799
97_H266_L0.129360.798
105_D109_E0.129260.797
240_W244_D0.12810.790
23_I26_F0.127390.786
213_L216_V0.12730.785
216_V227_H0.126710.781
95_D219_H0.126470.780
237_D241_Y0.125940.777
21_F243_F0.125030.771
129_S133_D0.124990.771
93_Q225_S0.124890.770
178_S224_D0.123850.764
27_R63_W0.123430.761
74_P78_I0.123010.759
74_P81_L0.122520.756
10_T90_N0.122430.755
7_I78_I0.121690.751
165_Q168_R0.121640.750
198_L209_V0.121630.750
4_L18_Q0.121570.750
2_V65_S0.121510.749
140_E199_E0.12140.749
95_D226_G0.121320.748
95_D99_F0.121020.746
187_F192_L0.120740.745
2_V69_D0.120730.745
14_N74_P0.120690.744
169_F265_Y0.120580.744
139_F143_I0.120540.743
19_C232_V0.120520.743
100_L268_F0.120070.741
33_Y56_Q0.119860.739
191_E194_L0.119530.737
61_S72_I0.119090.734
5_Q71_S0.119010.734
136_G139_F0.118430.730
10_T13_L0.11840.730
46_K49_K0.117480.725
21_F232_V0.117040.722
180_K187_F0.116530.719
137_G187_F0.116240.717
49_K53_Q0.116090.716
6_N12_Y0.116060.716
10_T78_I0.115880.715
56_Q62_L0.115660.713
211_Y221_G0.115270.711
187_F216_V0.115190.710
55_L103_L0.114610.707
57_N69_D0.114450.706
11_C98_E0.114010.703
137_G142_S0.114010.703
11_C228_Y0.113770.702
245_D265_Y0.113430.700
230_A243_F0.113360.699
228_Y245_D0.113020.697
169_F181_I0.112760.695
76_D79_N0.112730.695
157_S198_L0.112440.693
144_K150_N0.112410.693
226_G245_D0.111880.690
140_E143_I0.111240.686
242_K251_V0.111180.686
77_F81_L0.110770.683
54_Q80_A0.110740.683
61_S69_D0.110590.682
28_N31_L0.110550.682
88_F104_L0.110370.681
180_K226_G0.110370.681
130_L137_G0.110230.680
20_L217_I0.110020.679
16_V266_L0.109940.678
159_P211_Y0.109430.675
262_S266_L0.10940.675
83_S87_S0.109210.674
101_S163_I0.109150.673
255_E258_K0.10890.672
6_N226_G0.108710.670
29_Y130_L0.108630.670
15_S230_A0.108570.670
82_S94_Q0.108380.668
213_L240_W0.108320.668
52_L56_Q0.10830.668
61_S76_D0.108110.667
145_C227_H0.108080.667
180_K221_G0.108050.666
129_S136_G0.107870.665
26_F31_L0.107850.665
7_I88_F0.107810.665
47_K110_E0.107550.663
43_N46_K0.106860.659
92_E102_F0.106850.659
15_S19_C0.106770.659
30_L55_L0.10670.658
133_D151_S0.106370.656
3_G10_T0.106320.656
65_S69_D0.106250.655
133_D160_P0.1060.654
94_Q97_H0.105680.652
44_P48_I0.105190.649
93_Q227_H0.105110.648
220_Y242_K0.104980.647
108_D112_N0.104950.647
174_E179_K0.104460.644
174_E203_S0.10440.644
70_S149_K0.104370.644
61_S65_S0.104350.644
85_N106_W0.104180.643
127_E132_S0.103840.640
81_L87_S0.103830.640
23_I135_F0.103580.639
139_F153_S0.10320.636
58_L77_F0.103070.636
98_E227_H0.102980.635
182_N263_T0.102720.634
199_E202_N0.102530.632
96_A226_G0.102270.631
137_G157_S0.102250.631
127_E134_L0.102020.629
51_F54_Q0.101950.629
216_V221_G0.101710.627
11_C93_Q0.101540.626
227_H230_A0.10150.626
226_G265_Y0.101490.626
126_S133_D0.101450.626
62_L70_S0.101160.624
77_F84_I0.101140.624
113_S128_D0.101120.624
95_D221_G0.100950.623
3_G18_Q0.100930.622
159_P180_K0.100910.622
193_D209_V0.100490.620
26_F211_Y0.100430.619
4_L58_L0.100320.619
182_N187_F0.099960.617
8_G18_Q0.099940.616
17_L85_N0.099850.616
82_S88_F0.09980.616
2_V71_S0.099760.615
93_Q219_H0.099510.614
28_N33_Y0.099240.612
174_E201_N0.099160.612
165_Q217_I0.098970.610
12_Y21_F0.098870.610
49_K110_E0.098820.609
89_S92_E0.098710.609
176_G244_D0.098710.609
10_T88_F0.098020.605
164_I192_L0.097950.604
93_Q228_Y0.097880.604
74_P88_F0.097620.602
220_Y246_S0.097570.602
143_I146_S0.097460.601
86_P107_L0.097220.600
178_S223_A0.09720.599
153_S167_K0.096860.597
53_Q57_N0.09620.593
25_P160_P0.096080.593
42_S47_K0.096060.592
95_D228_Y0.096040.592
87_S90_N0.096030.592
128_D132_S0.095910.592
43_N47_K0.095790.591
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
2y6eA0.96281000.098
2aynA0.9741000.106
2gfoA0.96281000.111
1vjvA0.98141000.113
3nheA0.95541000.121
1nb8A0.90331000.137
3i3tA0.94421000.138
2f1zA0.90331000.139
3mhsA0.96651000.149
3ihpA0.95911000.182

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