GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UbiA - UbiA prenyltransferase family
Pfam: PF01040 (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: 257
Sequences: 2830
Seq/Len: 11.01
HH_delta: 0.932 (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
48_Y69_P0.575143.477
45_Y69_P0.562543.401
38_A80_L0.485872.937
55_P58_P0.453722.743
70_R74_I0.376512.276
68_S71_Q0.370252.238
45_Y73_L0.366122.213
91_G94_F0.348352.106
50_E179_R0.347112.098
92_P96_L0.345362.088
41_L79_L0.332662.011
47_D116_R0.313331.894
67_I72_A0.302811.831
238_D241_K0.299261.809
96_L100_L0.298211.803
221_L225_L0.28951.750
94_F138_Y0.284021.717
163_M166_N0.283851.716
162_I166_N0.283081.711
52_R63_P0.280711.697
189_K193_Y0.279241.688
171_I175_R0.270151.633
103_L107_L0.264831.601
107_L124_V0.261021.578
85_L89_L0.252991.529
34_L82_L0.250731.516
225_L228_I0.249311.507
172_E175_R0.249251.507
41_L75_F0.242981.469
197_T201_L0.242771.468
74_I78_I0.240111.452
93_W138_Y0.239871.450
171_I188_E0.238551.442
228_I232_W0.23721.434
194_L197_T0.237121.433
121_G181_T0.234421.417
190_K193_Y0.233361.411
241_K245_L0.232991.409
53_I177_A0.232081.403
31_A87_A0.231321.398
161_A164_F0.230891.396
114_L117_R0.230531.394
104_L128_V0.229291.386
77_L81_L0.22491.360
162_I165_F0.221471.339
170_D174_D0.220131.331
46_F113_R0.218691.322
41_L76_A0.21761.315
229_F233_F0.217541.315
160_F164_F0.217411.314
27_L86_L0.2161.306
103_L106_L0.215771.304
127_L152_A0.215411.302
35_L98_L0.214491.297
67_I75_F0.213471.291
27_L89_L0.211791.280
41_L67_I0.210911.275
144_P148_P0.209631.267
240_K245_L0.209561.267
168_I190_K0.208471.260
55_P172_E0.208341.259
45_Y72_A0.208061.258
50_E116_R0.207781.256
80_L102_F0.207271.253
232_W235_R0.205831.244
62_L72_A0.204841.238
94_F135_L0.203421.230
207_L216_L0.201231.217
161_A166_N0.200061.209
37_L79_L0.198911.202
155_F159_I0.198891.202
145_P148_P0.198871.202
159_I163_M0.198851.202
35_L83_G0.197961.197
158_L162_I0.197791.196
161_A165_F0.197541.194
23_P26_L0.196351.187
87_A98_L0.194261.174
130_G155_F0.19411.173
144_P149_F0.192311.163
104_L127_L0.192251.162
160_F166_N0.191471.158
27_L90_L0.19031.150
24_I140_A0.189761.147
47_D50_E0.189741.147
158_L163_M0.189371.145
149_F153_I0.187921.136
194_L198_A0.187811.135
130_G159_I0.18751.134
134_L148_P0.18721.132
243_E246_F0.186811.129
114_L124_V0.186311.126
42_L77_L0.185241.120
145_P149_F0.185211.120
78_I82_L0.184721.117
51_D60_R0.183771.111
45_Y62_L0.183291.108
206_L216_L0.182871.106
182_L186_L0.182411.103
48_Y52_R0.181151.095
160_F163_M0.18031.090
146_P149_F0.176821.069
44_D47_D0.176531.067
46_F109_S0.176471.067
159_I162_I0.175911.063
207_L217_I0.174311.054
99_L103_L0.1731.046
120_W123_L0.172051.040
171_I174_D0.171741.038
34_L83_G0.171041.034
71_Q74_I0.170821.033
189_K192_R0.169711.026
119_L180_R0.168691.020
143_D147_P0.168631.019
104_L107_L0.168311.017
47_D109_S0.16821.017
150_L209_G0.167421.012
199_G203_F0.166571.007
29_L33_F0.166461.006
171_I184_V0.165891.003
147_P210_L0.165671.002
37_L75_F0.163960.991
123_L160_F0.163440.988
47_D179_R0.16290.985
175_R184_V0.162320.981
40_Y44_D0.160950.973
147_P208_L0.16090.973
45_Y48_Y0.160390.970
217_I221_L0.159540.964
225_L229_F0.156570.947
134_L152_A0.156420.946
107_L114_L0.155940.943
23_P27_L0.155590.941
208_L211_F0.155540.940
91_G97_I0.153490.928
213_P217_I0.153270.927
226_A229_F0.151910.918
42_L76_A0.151910.918
122_E125_V0.151790.918
195_L198_A0.150870.912
39_V102_F0.150050.907
73_L77_L0.149630.905
232_W236_K0.148270.896
49_E53_I0.148140.896
198_A202_L0.148130.896
56_N173_G0.148020.895
150_L214_W0.14780.894
217_I220_L0.147620.892
45_Y76_A0.147520.892
24_I28_G0.147130.889
35_L102_F0.145810.881
37_L41_L0.145310.878
198_A230_I0.144820.875
55_P240_K0.144810.875
159_I166_N0.144470.873
121_G125_V0.144210.872
63_P72_A0.144030.871
158_L161_A0.143810.869
84_L95_L0.143630.868
207_L212_S0.143110.865
87_A135_L0.1430.864
98_L135_L0.142630.862
226_A230_I0.142430.861
88_L92_P0.142360.861
69_P73_L0.142120.859
198_A201_L0.141480.855
85_L88_L0.141450.855
31_A34_L0.141140.853
130_G156_F0.140990.852
92_P95_L0.140890.852
206_L210_L0.140790.851
227_L230_I0.140670.850
167_D170_D0.140190.848
75_F79_L0.140190.848
214_W218_I0.140120.847
129_F159_I0.140060.847
228_I231_L0.139780.845
230_I245_L0.139620.844
23_P30_L0.139130.841
195_L199_G0.138730.839
219_A223_A0.138650.838
51_D115_K0.138260.836
157_L196_L0.13740.831
202_L227_L0.137180.829
81_L85_L0.137060.829
168_I188_E0.136960.828
26_L30_L0.136510.825
91_G142_G0.136420.825
231_L234_F0.136090.823
83_G131_L0.135810.821
90_L94_F0.135280.818
32_V98_L0.134880.815
133_I155_F0.13470.814
61_P66_R0.134470.813
118_P182_L0.134350.812
62_L66_R0.134340.812
143_D148_P0.134070.811
88_L95_L0.133290.806
202_L223_A0.133150.805
167_D183_P0.132880.803
242_P245_L0.132580.801
156_F160_F0.131990.798
199_G202_L0.131150.793
212_S215_P0.130540.789
34_L79_L0.130460.789
87_A90_L0.13030.788
89_L92_P0.129610.784
101_G128_V0.129230.781
31_A98_L0.129010.780
63_P80_L0.128950.780
51_D61_P0.128250.775
109_S183_P0.12810.774
43_N51_D0.128040.774
235_R238_D0.127980.774
159_I164_F0.127740.772
153_I205_L0.127390.770
70_R82_L0.127310.770
93_W141_G0.127130.769
233_F245_L0.127080.768
68_S72_A0.1270.768
197_T200_L0.126750.766
62_L67_I0.126410.764
93_W97_I0.126380.764
44_D54_H0.126360.764
137_A148_P0.126250.763
109_S121_G0.126120.762
73_L106_L0.125780.760
28_G32_V0.12560.759
195_L231_L0.12550.759
85_L103_L0.125480.759
62_L65_G0.125420.758
69_P74_I0.125190.757
23_P238_D0.124980.756
114_L118_P0.124220.751
82_L92_P0.123890.749
194_L230_I0.123720.748
24_I27_L0.12360.747
97_I144_P0.123460.746
56_N60_R0.123460.746
41_L52_R0.123180.745
44_D61_P0.122240.739
55_P59_N0.122150.738
78_I99_L0.122060.738
101_G135_L0.121780.736
50_E177_A0.121580.735
70_R85_L0.121460.734
137_A141_G0.121260.733
213_P221_L0.12120.733
219_A222_L0.12090.731
168_I171_I0.120830.730
174_D197_T0.120280.727
26_L85_L0.12010.726
130_G135_L0.119830.724
214_W217_I0.119620.723
48_Y62_L0.119620.723
188_E192_R0.119370.722
101_G105_G0.119280.721
236_K240_K0.118790.718
125_V129_F0.118190.715
158_L166_N0.118040.714
138_Y144_P0.117770.712
119_L184_V0.11760.711
197_T203_F0.117450.710
50_E53_I0.11740.710
63_P66_R0.117240.709
108_Y115_K0.116680.705
122_E164_F0.116660.705
119_L185_L0.116380.704
128_V159_I0.116030.701
159_I201_L0.115990.701
205_L209_G0.115660.699
90_L95_L0.115540.698
172_E239_P0.115530.698
93_W96_L0.115430.698
26_L244_R0.115430.698
231_L235_R0.115360.697
73_L100_L0.115190.696
32_V135_L0.115060.696
217_I224_A0.114850.694
36_Q170_D0.114520.692
93_W142_G0.114340.691
70_R176_K0.113980.689
207_L213_P0.11380.688
68_S74_I0.11370.687
161_A201_L0.11370.687
121_G166_N0.113580.687
36_Q40_Y0.113490.686
160_F165_F0.113360.685
56_N125_V0.113270.685
239_P245_L0.113180.684
137_A145_P0.113020.683
65_G71_Q0.112930.683
100_L103_L0.112750.682
107_L193_Y0.112530.680
98_L104_L0.112480.680
146_P208_L0.112280.679
224_A228_I0.11180.676
28_G139_A0.111510.674
186_L190_K0.111390.673
122_E160_F0.111260.673
56_N167_D0.111030.671
122_E163_M0.110960.671
152_A158_L0.110910.670
239_P243_E0.11080.670
242_P246_F0.110620.669
34_L37_L0.110520.668
55_P90_L0.110520.668
125_V174_D0.110350.667
27_L30_L0.109680.663
133_I136_G0.10950.662
87_A101_G0.109450.662
70_R73_L0.10930.661
147_P150_L0.109060.659
239_P242_P0.108950.659
103_L217_I0.108270.655
33_F37_L0.108130.654
193_Y196_L0.108080.653
85_L92_P0.107990.653
106_L197_T0.107750.651
43_N108_Y0.107630.651
150_L153_I0.107550.650
57_K125_V0.107440.650
35_L44_D0.107370.649
114_L140_A0.107080.647
35_L131_L0.106860.646
141_G146_P0.106780.646
35_L84_L0.106740.645
30_L33_F0.106540.644
169_R172_E0.106340.643
140_A143_D0.106270.642
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
2xq2A0.891155.10.932
3ze3A0.338544.60.935
3dh4A0.805443.90.936
2kdcA0.338536.10.939
1fftA0.260719.70.946
3o7qA0.883318.50.946
4j05A0.260712.30.95
4f35D0.9312.30.95
1pw4A0.91444.40.959
3ne5A0.47473.50.961
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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