GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GrpE - GrpE
Pfam: PF01025 (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: 165
Sequences: 2290
Seq/Len: 13.88
HH_delta: -0.006 (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
27_I30_L1.025083.398
19_E24_E0.918223.044
20_L23_L0.88622.938
112_E147_P0.830652.754
66_D108_N0.81962.717
73_N100_Q0.689392.285
114_E118_E0.680752.257
73_N76_R0.667532.213
146_R160_E0.664522.203
111_E150_R0.662512.196
126_E160_E0.597671.981
32_E36_R0.593541.968
66_D107_K0.588931.952
23_L27_I0.583111.933
41_F44_Y0.578931.919
22_E26_E0.571871.896
44_Y48_L0.570251.890
103_D106_E0.566251.877
106_E111_E0.547071.814
143_E162_V0.542271.798
129_E162_V0.542141.797
31_K35_L0.523041.734
26_E31_K0.516431.712
131_V142_V0.499471.656
137_E140_T0.495941.644
133_D136_K0.491511.629
75_E147_P0.490841.627
39_A43_N0.483331.602
42_E45_R0.480611.593
64_L110_V0.480241.592
64_L156_L0.475061.575
124_L150_R0.472141.565
115_P144_V0.465211.542
21_E24_E0.461661.530
61_E154_R0.448821.488
95_E99_K0.446521.480
103_D107_K0.440431.460
75_E98_L0.437581.451
72_D157_R0.435931.445
46_K50_K0.426971.415
132_P165_K0.416021.379
60_L63_F0.409691.358
113_I155_V0.388861.289
50_K54_E0.383531.271
142_V164_S0.378151.254
20_L24_E0.377321.251
49_E53_E0.373531.238
36_R39_A0.372291.234
133_D164_S0.369081.224
48_L52_K0.363511.205
105_L110_V0.363281.204
120_F127_A0.359011.190
121_D124_L0.355711.179
77_A94_L0.350041.160
85_E88_E0.349821.160
63_F108_N0.34721.151
37_L41_F0.345561.146
42_E46_K0.343741.140
136_K142_V0.34271.136
115_P118_E0.341361.132
110_V151_L0.339891.127
102_E112_E0.339681.126
27_I31_K0.33861.122
19_E22_E0.337651.119
33_R38_Q0.336891.117
26_E29_E0.335771.113
25_K28_E0.335021.111
131_V162_V0.333341.105
52_K56_K0.332861.103
57_K152_G0.331031.097
144_V159_A0.325141.078
38_Q42_E0.323561.073
68_L157_R0.323531.073
53_E57_K0.320921.064
145_V162_V0.318491.056
24_E28_E0.318391.055
116_V144_V0.318131.055
150_R153_G0.316881.050
131_V143_E0.31671.050
52_K55_A0.310181.028
30_L34_L0.309261.025
76_R79_E0.30711.018
130_T139_G0.305991.014
74_L97_I0.302151.002
21_E25_K0.29990.994
25_K29_E0.299250.992
70_V104_I0.299190.992
71_L149_Y0.29860.990
28_E32_E0.298560.990
74_L98_L0.29610.982
136_K140_T0.290670.964
61_E151_L0.290250.962
128_V160_E0.286590.950
34_L37_L0.284580.943
89_S92_E0.280040.928
58_Y152_G0.278860.924
112_E144_V0.27880.924
37_L44_Y0.277370.920
71_L105_L0.276830.918
99_K103_D0.276490.917
140_T164_S0.274960.912
29_E33_R0.272810.904
55_A59_A0.272070.902
36_R43_N0.265360.880
71_L98_L0.265270.879
34_L38_Q0.263220.873
142_V162_V0.261410.867
111_E153_G0.260810.865
23_L26_E0.256330.850
119_P140_T0.255580.847
115_P159_A0.25370.841
74_L94_L0.25140.833
32_E40_E0.251280.833
138_P165_K0.246290.816
71_L102_E0.245390.813
126_E146_R0.244640.811
43_N46_K0.244580.811
41_F48_L0.243630.808
136_K164_S0.242990.806
92_E95_E0.242460.804
98_L102_E0.236830.785
78_L91_L0.235510.781
130_T165_K0.233190.773
58_Y154_R0.229630.761
75_E102_E0.229510.761
62_K66_D0.226860.752
86_E89_S0.226520.751
49_E52_K0.221640.735
60_L108_N0.221310.734
100_Q103_D0.220960.732
138_P164_S0.220450.731
40_E44_Y0.218790.725
93_G96_M0.218490.724
70_V101_L0.217920.722
51_E55_A0.21640.717
114_E144_V0.214540.711
48_L51_E0.214060.710
30_L33_R0.212530.705
119_P137_E0.209910.696
22_E25_K0.209520.695
53_E56_K0.208720.692
58_Y61_E0.20830.691
129_E143_E0.20790.689
35_L42_E0.207880.689
26_E30_L0.207810.689
19_E23_L0.206490.685
55_A58_Y0.204750.679
96_M99_K0.204360.677
129_E145_V0.203130.673
155_V158_P0.20270.672
151_L156_L0.202680.672
83_S86_E0.200810.666
64_L151_L0.199210.660
32_E35_L0.197210.654
76_R146_R0.196890.653
70_V100_Q0.195530.648
61_E65_K0.193080.640
115_P141_I0.192520.638
85_E89_S0.191320.634
88_E92_E0.191030.633
39_A46_K0.189860.629
125_H141_I0.189030.627
154_R158_P0.188760.626
82_K87_E0.187140.620
104_I108_N0.18670.619
71_L112_E0.186450.618
90_L97_I0.18570.616
79_E143_E0.185090.614
59_A63_F0.18380.609
57_K61_E0.183610.609
51_E54_E0.183390.608
38_Q41_F0.180710.599
41_F74_L0.180210.597
54_E57_K0.180140.597
89_S96_M0.179920.596
139_G142_V0.177690.589
88_E95_E0.177580.589
81_A91_L0.175480.582
119_P139_G0.175440.582
60_L152_G0.17440.578
84_N88_E0.174190.577
42_E109_G0.17410.577
20_L27_I0.174050.577
58_Y151_L0.173540.575
92_E99_K0.173430.575
76_R80_A0.172840.573
40_E47_R0.172480.572
137_E164_S0.172440.572
113_I150_R0.171560.569
144_V147_P0.170720.566
41_F52_K0.169580.562
102_E106_E0.169510.562
69_P100_Q0.169250.561
37_L40_E0.169130.561
120_F141_I0.168860.560
37_L48_L0.165140.547
122_P125_H0.163560.542
71_L75_E0.16340.542
41_F45_R0.160620.532
83_S87_E0.159860.530
118_E124_L0.159580.529
81_A87_E0.159570.529
19_E26_E0.158910.527
47_R51_E0.157110.521
28_E31_K0.157020.521
127_A158_P0.156690.519
135_D140_T0.156520.519
108_N149_Y0.155580.516
132_P164_S0.154720.513
118_E150_R0.15410.511
59_A108_N0.15410.511
113_I159_A0.154050.511
100_Q105_L0.153380.508
88_E91_L0.153070.507
36_R47_R0.151990.504
76_R100_Q0.150980.501
74_L90_L0.150770.500
113_I158_P0.150650.499
26_E33_R0.150270.498
84_N87_E0.149020.494
24_E27_I0.148940.494
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
4aniA1100-0.006
1dkgA11000.031
3a6mA0.96971000.033
3swyA0.278863.60.911
3vkgA0.872762.80.911
2j69A0.987960.60.912
3hnwA0.4485590.913
1i6zA0.70356.10.915
2dfsA0.654549.50.918
2yy0A0.230349.30.918

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