GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Uma2 - Putative restriction endonuclease
Pfam: PF05685 (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: CL0236
Length: 171
Sequences: 3907
Seq/Len: 22.85
HH_delta: 0.211 (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
37_S40_A1.611986.277
41_A44_R1.414115.507
34_R54_R1.031644.017
70_R116_L0.662942.582
38_R48_R0.645292.513
36_I101_V0.616872.402
41_A45_Q0.586512.284
37_S44_R0.556192.166
141_D146_Q0.547682.133
110_L127_I0.544962.122
156_V167_W0.54242.112
33_Q60_L0.535312.085
102_L110_L0.518232.018
94_A122_V0.507281.975
42_L48_R0.505681.969
126_W137_V0.503521.961
38_R44_R0.477151.858
110_L136_E0.463281.804
15_Y22_I0.450491.754
129_D132_R0.446761.740
41_A48_R0.446421.738
158_S167_W0.442421.723
27_P61_G0.440471.715
34_R55_V0.438441.707
62_V75_A0.4261.659
37_S57_A0.416121.620
36_I57_A0.404551.575
61_G71_A0.396121.543
108_K112_E0.388281.512
30_P56_F0.385361.501
37_S41_A0.380071.480
7_L22_I0.359931.402
59_E71_A0.35221.372
102_L106_T0.343771.339
128_V135_V0.343241.337
114_L138_Y0.334841.304
135_V157_L0.329391.283
96_D123_P0.329361.283
27_P71_A0.327071.274
76_V97_L0.325461.267
136_E147_P0.323631.260
39_L128_V0.321581.252
40_A57_A0.321581.252
107_R129_D0.316751.234
98_V122_V0.313321.220
35_I101_V0.311621.214
17_L69_R0.308531.201
140_L145_Y0.305921.191
34_R44_R0.305431.189
43_L99_V0.30341.182
139_R161_E0.302571.178
123_P145_Y0.30231.177
28_P32_H0.301171.173
35_I128_V0.29891.164
133_R153_P0.29871.163
31_R86_R0.295311.150
124_E139_R0.295091.149
99_V126_W0.289361.127
11_P15_Y0.286081.114
158_S161_E0.280741.093
30_P91_F0.280411.092
39_L74_I0.27881.086
45_Q49_P0.27811.083
129_D134_R0.277981.083
40_A74_I0.275731.074
4_F15_Y0.275531.073
48_R51_K0.274971.071
102_L129_D0.274031.067
37_S55_V0.270511.053
33_Q59_E0.268681.046
79_R82_P0.26841.045
47_L52_P0.266871.039
126_W159_L0.26351.026
19_D112_E0.263011.024
114_L125_Y0.257061.001
34_R56_F0.255480.995
53_G78_P0.254230.990
19_D119_A0.25160.980
139_R148_I0.250810.977
46_W165_G0.249530.972
2_E6_R0.248910.969
18_I116_L0.248890.969
33_Q58_S0.24860.968
17_L68_N0.248450.968
53_G76_V0.247490.964
46_W166_F0.247020.962
124_E162_L0.2470.962
5_L63_R0.246280.959
124_E159_L0.246150.959
7_L15_Y0.243910.950
78_P96_D0.240650.937
61_G69_R0.238290.928
35_I130_P0.237490.925
114_L118_A0.236670.922
36_I58_S0.236340.920
152_E155_E0.235850.918
30_P60_L0.234870.915
18_I70_R0.232660.906
106_T109_D0.231590.902
123_P162_L0.231450.901
40_A44_R0.230810.899
118_A144_G0.230630.898
159_L162_L0.227010.884
116_L120_A0.224640.875
64_L120_A0.222660.867
129_D136_E0.222550.867
107_R111_E0.220670.859
28_P33_Q0.217270.846
38_R41_A0.215730.840
44_R48_R0.211030.822
14_R28_P0.210870.821
5_L8_P0.209770.817
4_F8_P0.209290.815
4_F61_G0.209130.814
115_A118_A0.207450.808
127_I136_E0.207340.807
5_L69_R0.207150.807
43_L74_I0.207140.807
19_D67_D0.206680.805
95_P122_V0.206520.804
124_E137_V0.205420.800
102_L105_S0.205330.800
30_P92_P0.204480.796
47_L76_V0.203390.792
7_L11_P0.202840.790
112_E115_A0.20230.788
33_Q57_A0.201540.785
107_R110_L0.198940.775
111_E115_A0.198130.772
46_W49_P0.19760.770
131_E134_R0.194730.758
13_Y24_E0.194340.757
31_R34_R0.193540.754
144_G147_P0.190240.741
30_P34_R0.190130.740
36_I74_I0.190.740
28_P59_E0.187660.731
37_S74_I0.186960.728
45_Q48_R0.185890.724
41_A49_P0.185590.723
46_W163_L0.184710.719
64_L70_R0.184580.719
121_G143_G0.183730.715
37_S42_L0.183520.715
38_R54_R0.182690.711
16_E113_K0.181420.706
3_E6_R0.181010.705
34_R37_S0.18040.703
42_L45_Q0.180170.702
15_Y24_E0.180160.702
28_P57_A0.179970.701
38_R42_L0.179270.698
136_E150_V0.179110.698
114_L144_G0.178960.697
82_P85_P0.176420.687
45_Q74_I0.176370.687
13_Y17_L0.174780.681
31_R133_R0.174250.679
127_I138_Y0.174020.678
33_Q36_I0.172770.673
4_F7_L0.171570.668
141_D144_G0.171530.668
64_L116_L0.171470.668
111_E114_L0.171360.667
14_R25_M0.171220.667
113_K117_Y0.169870.662
47_L51_K0.169790.661
43_L47_L0.169530.660
115_A144_G0.168950.658
30_P84_I0.166870.650
144_G148_I0.166860.650
117_Y122_V0.166610.649
103_S106_T0.16420.639
17_L70_R0.164060.639
77_V92_P0.163630.637
106_T111_E0.163510.637
28_P61_G0.162630.633
60_L91_F0.161880.630
159_L163_L0.161840.630
61_G91_F0.161630.629
62_V95_P0.161180.628
48_R54_R0.160910.627
35_I38_R0.16040.625
16_E103_S0.160090.623
116_L119_A0.159590.621
118_A122_V0.159070.619
7_L13_Y0.158090.616
63_R69_R0.158030.615
30_P85_P0.158020.615
47_L55_V0.157020.611
8_P11_P0.156980.611
158_S165_G0.156150.608
54_R57_A0.156070.608
44_R47_L0.156030.608
163_L166_F0.155610.606
57_A75_A0.154380.601
102_L145_Y0.15430.601
140_L147_P0.154260.601
47_L163_L0.15420.600
134_R149_E0.153590.598
139_R142_D0.15340.597
64_L68_N0.153070.596
43_L97_L0.152930.596
143_G149_E0.152560.594
98_V125_Y0.150950.588
32_H73_D0.150860.587
46_W124_E0.150770.587
126_W135_V0.149810.583
115_A119_A0.149710.583
55_V74_I0.148530.578
24_E78_P0.148260.577
118_A140_L0.147580.575
114_L127_I0.147520.574
32_H109_D0.147410.574
3_E7_L0.147140.573
4_F22_I0.146950.572
92_P95_P0.146480.570
118_A145_Y0.146390.570
80_E83_P0.145950.568
136_E148_I0.145940.568
102_L127_I0.145740.568
107_R131_E0.145740.568
107_R114_L0.145560.567
31_R104_P0.145270.566
28_P36_I0.145050.565
134_R152_E0.144360.562
31_R85_P0.144240.562
30_P42_L0.144090.561
77_V85_P0.143940.561
98_V114_L0.143610.559
14_R71_A0.143070.557
109_D113_K0.142970.557
14_R24_E0.142650.556
34_R57_A0.142240.554
103_S113_K0.141880.553
2_E5_L0.140970.549
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
1wdjA0.95911000.211
3ot2A0.95321000.215
3ijmA0.865595.10.854
3dnxA0.713518.10.929
2ixsA0.8489.70.937
2p64A0.23396.70.941
1i7nA0.60824.30.946
3fhkA0.29824.10.946
3nt1A0.60823.50.948
1pk8A0.63743.30.949

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