GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ICMT - Isoprenylcysteine carboxyl methyltransferase (ICMT) family
Pfam: PF04140 (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: CL0115
Length: 94
Sequences: 1667
Seq/Len: 17.73
HH_delta: 0.175 (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
14_W40_P0.553332.741
8_G51_G0.542822.689
46_H89_E0.470652.332
18_T40_P0.470322.330
45_R89_E0.435592.158
14_W18_T0.391691.941
24_T28_I0.383391.899
15_A48_S0.358151.774
44_V50_L0.357931.773
23_F48_S0.339831.684
29_I33_H0.315311.562
35_L45_R0.307191.522
12_R51_G0.291571.445
11_L40_P0.279531.385
8_G58_G0.27731.374
41_Y48_S0.27131.344
27_V91_A0.271041.343
11_L51_G0.269521.335
35_L89_E0.264171.309
12_R48_S0.259331.285
13_Y17_R0.256231.269
18_T38_S0.255111.264
6_I10_L0.250631.242
9_Q13_Y0.248661.232
46_H84_R0.247671.227
66_A69_T0.238321.181
27_V84_R0.238111.180
15_A51_G0.231351.146
87_E90_R0.227611.128
84_R91_A0.224721.113
57_L74_F0.22371.108
58_G61_L0.221991.100
70_A74_F0.221421.097
35_L46_H0.22071.093
23_F84_R0.21991.089
57_L71_L0.218381.082
39_G92_L0.217921.080
86_R93_I0.213461.058
76_L80_L0.212931.055
90_R93_I0.211721.049
22_Y35_L0.211161.046
82_F86_R0.209331.037
41_Y92_L0.207871.030
29_I84_R0.207751.029
59_G65_N0.205621.019
24_T48_S0.202831.005
60_Q64_F0.202691.004
53_I78_A0.200710.994
50_L85_I0.199350.988
11_L54_I0.197550.979
7_A17_R0.193140.957
5_F62_L0.192970.956
62_L65_N0.187050.927
78_A82_F0.187010.926
19_L24_T0.185350.918
73_L80_L0.184410.914
19_L55_W0.183230.908
22_Y34_K0.183210.908
10_L17_R0.180860.896
12_R84_R0.180510.894
62_L66_A0.179940.891
52_N81_L0.179570.890
23_F27_V0.178530.884
56_E70_A0.175860.871
60_Q65_N0.175240.868
46_H49_Y0.174740.866
50_L80_L0.173980.862
11_L50_L0.173230.858
16_I26_R0.172350.854
37_T93_I0.172080.853
56_E78_A0.172070.852
20_G23_F0.171430.849
48_S84_R0.169920.842
12_R52_N0.168470.835
48_S52_N0.166780.826
33_H84_R0.166620.825
15_A40_P0.166590.825
66_A75_A0.165430.820
59_G64_F0.16520.818
22_Y30_Q0.164970.817
30_Q36_V0.163690.811
10_L79_W0.162990.807
56_E81_L0.160360.794
24_T30_Q0.160290.794
7_A10_L0.160040.793
12_R16_I0.159230.789
4_L7_A0.157890.782
46_H50_L0.156340.775
55_W63_L0.155360.770
16_I89_E0.154980.768
5_F13_Y0.154920.768
26_R49_Y0.154590.766
7_A11_L0.153380.760
29_I32_G0.151980.753
45_R65_N0.151580.751
29_I91_A0.150550.746
85_I89_E0.150440.745
56_E77_V0.149760.742
27_V87_E0.149410.740
5_F42_R0.148570.736
55_W58_G0.148550.736
14_W17_R0.147770.732
23_F46_H0.146660.727
51_G54_I0.146640.726
50_L54_I0.146410.725
9_Q48_S0.146360.725
10_L86_R0.145990.723
61_L64_F0.145820.722
10_L14_W0.145580.721
61_L66_A0.144580.716
22_Y73_L0.142830.708
19_L91_A0.142320.705
22_Y52_N0.141720.702
62_L70_A0.140760.697
52_N84_R0.140330.695
77_V81_L0.140330.695
14_W86_R0.139890.693
17_R20_G0.139610.692
25_H70_A0.138520.686
24_T49_Y0.138470.686
31_P83_V0.138390.686
12_R23_F0.138340.685
5_F58_G0.137070.679
44_V84_R0.135790.673
16_I48_S0.135670.672
60_Q74_F0.135670.672
86_R90_R0.135150.670
57_L78_A0.133970.664
74_F77_V0.133510.661
71_L76_L0.133220.660
87_E91_A0.13290.658
53_I85_I0.132630.657
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
4a2nB0.989499.70.175
2jlnA115.40.887
2jp3A0.457411.60.892
2zxeG0.46814.70.909
2k1eA0.35114.20.911
3eiqC0.52133.80.913
2wjnH0.468130.916
1lddA0.43622.60.919
1vf5G0.39362.60.919
4aq5A0.36172.40.92

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