GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VitK2_biosynth - Menaquinone biosynthesis
Pfam: PF02621 (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: CL0177
Length: 251
Sequences: 6748
Seq/Len: 26.88
HH_delta: 0.261 (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
200_Y204_N1.371484.609
204_N207_E1.184863.982
94_K119_E1.138453.826
188_K192_Q0.931563.131
210_K220_P0.88692.981
180_K184_E0.863282.901
86_P89_E0.824832.772
91_D117_K0.809312.720
47_V178_V0.791952.662
22_E196_K0.778552.616
206_D224_R0.758292.548
66_P180_K0.75652.542
64_I180_K0.752152.528
22_E192_Q0.740542.489
199_Q203_A0.728692.449
112_L116_Y0.724672.435
93_K136_D0.68092.288
85_V89_E0.673052.262
178_V183_P0.672672.261
185_E189_E0.643822.164
94_K121_V0.643652.163
220_P224_R0.636322.138
79_V82_F0.6252.100
47_V190_L0.607592.042
20_K207_E0.605742.036
123_M130_A0.582761.958
210_K214_E0.577461.941
90_L137_A0.567571.907
189_E193_A0.559931.882
219_D222_F0.559811.881
200_Y207_E0.557861.875
201_G208_I0.556451.870
182_L187_I0.551.848
207_E210_K0.548061.842
94_K136_D0.544491.830
183_P187_I0.532071.788
39_M44_E0.526051.768
209_I224_R0.524381.762
182_L186_E0.515071.731
47_V187_I0.497571.672
178_V187_I0.496281.668
88_E91_D0.489141.644
43_G181_D0.481861.619
179_R182_L0.480111.614
195_R199_Q0.47971.612
112_L115_F0.462641.555
213_A220_P0.460981.549
50_I177_V0.451651.518
95_I137_A0.447711.505
105_V109_R0.441881.485
143_D146_L0.440741.481
19_I214_E0.415931.398
221_E224_R0.41291.388
40_L45_L0.405031.361
59_A62_Y0.39571.330
193_A196_K0.39541.329
97_L120_Y0.374011.257
16_Y20_K0.372271.251
17_G197_S0.371911.250
206_D210_K0.369371.241
88_E115_F0.366621.232
185_E188_K0.360461.211
13_P198_K0.358461.205
62_Y66_P0.354081.190
22_E193_A0.351281.181
59_A180_K0.349411.174
38_Q42_E0.348981.173
111_L116_Y0.348931.173
186_E189_E0.346431.164
131_M138_A0.346151.163
23_P189_E0.343531.155
17_G21_G0.342661.152
205_P209_I0.340541.144
40_L48_A0.337121.133
85_V154_P0.333571.121
20_K200_Y0.333351.120
130_A135_A0.333151.120
129_P132_L0.332231.117
127_I138_A0.330571.111
209_I220_P0.3261.096
95_I118_P0.325841.095
111_L115_F0.32581.095
199_Q202_L0.32311.086
47_V186_E0.321821.082
16_Y211_E0.321311.080
36_L48_A0.321181.079
210_K213_A0.31921.073
35_E38_Q0.319181.073
187_I191_V0.315661.061
87_I111_L0.314771.058
126_D129_P0.313621.054
132_L151_Q0.311241.046
207_E211_E0.308641.037
198_K202_L0.307451.033
180_K183_P0.3041.022
221_E225_D0.303591.020
39_M45_L0.302771.018
190_L194_L0.302461.016
51_S54_E0.301581.014
128_P132_L0.301011.012
200_Y208_I0.298041.002
189_E192_Q0.297320.999
194_L198_K0.295830.994
74_G77_Y0.29560.993
19_I215_R0.293230.985
30_R39_M0.290490.976
156_V159_L0.286120.962
143_D147_T0.280560.943
66_P183_P0.27630.929
200_Y211_E0.275160.925
155_Y158_D0.274790.923
200_Y203_A0.274690.923
96_A131_M0.274470.922
131_M153_L0.270820.910
16_Y197_S0.269740.907
197_S201_G0.269640.906
212_A223_I0.269120.904
149_K225_D0.268190.901
96_A127_I0.26750.899
196_K199_Q0.266370.895
14_L194_L0.259320.872
84_K154_P0.25750.865
71_S74_G0.257220.864
211_E215_R0.255110.857
25_D28_I0.254960.857
24_F186_E0.254780.856
55_Y177_V0.254370.855
43_G179_R0.252880.850
147_T151_Q0.252470.848
97_L122_P0.250990.844
33_P54_E0.25070.843
129_P133_A0.248570.835
192_Q196_K0.247440.832
52_S175_V0.245840.826
154_P157_Y0.24430.821
193_A197_S0.244050.820
18_L25_D0.243750.819
192_Q195_R0.24370.819
178_V182_L0.243240.817
46_D182_L0.240760.809
63_L180_K0.240150.807
69_S191_V0.239890.806
101_S105_V0.239550.805
46_D179_R0.238370.801
181_D184_E0.236230.794
16_Y200_Y0.233780.786
53_I57_R0.23310.783
55_Y59_A0.232560.782
15_F19_I0.232190.780
196_K200_Y0.23210.780
54_E57_R0.23130.777
20_K211_E0.230590.775
176_W194_L0.230450.774
41_L63_L0.229230.770
32_V35_E0.228070.766
78_S82_F0.227010.763
96_A123_M0.226020.760
108_L112_L0.224520.755
79_V83_S0.223650.752
112_L118_P0.222950.749
16_Y208_I0.221430.744
77_Y80_L0.220750.742
96_A136_D0.219950.739
37_N50_I0.218430.734
106_A109_R0.213670.718
96_A121_V0.213570.718
24_F189_E0.212380.714
39_M42_E0.212120.713
89_E93_K0.2120.712
40_L177_V0.21080.708
90_L93_K0.210140.706
197_S200_Y0.208720.701
47_V182_L0.208520.701
140_L145_A0.208260.700
218_L222_F0.208160.700
40_L179_R0.207890.699
59_A64_I0.206390.694
202_L205_P0.206290.693
31_G35_E0.204610.688
110_I114_E0.203710.685
36_L45_L0.201890.678
205_P208_I0.201410.677
94_K135_A0.199590.671
127_I131_M0.19790.665
45_L48_A0.19790.665
213_A219_D0.196640.661
178_V190_L0.196340.660
102_T105_V0.195960.659
49_L174_A0.194680.654
100_E122_P0.194370.653
149_K154_P0.194260.653
188_K191_V0.193360.650
218_L223_I0.193350.650
105_V112_L0.19280.648
12_L212_A0.192270.646
24_F193_A0.191940.645
21_G24_F0.190930.642
19_I211_E0.190270.639
98_T104_S0.189420.637
102_T172_V0.189060.635
13_P16_Y0.187330.630
206_D220_P0.186410.626
41_L179_R0.186360.626
206_D209_I0.185880.625
99_G122_P0.185730.624
35_E39_M0.185630.624
126_D130_A0.183980.618
95_I111_L0.183730.617
195_R198_K0.183260.616
13_P194_L0.183150.616
63_L66_P0.183090.615
73_D76_V0.182720.614
13_P197_S0.182150.612
127_I130_A0.181860.611
55_Y58_N0.179540.603
72_S172_V0.179510.603
33_P48_A0.179330.603
33_P51_S0.178640.600
58_N61_D0.178360.599
47_V176_W0.177930.598
184_E203_A0.177810.598
61_D64_I0.177440.596
147_T150_S0.177390.596
213_A223_I0.176980.595
211_E214_E0.176930.595
57_R61_D0.17680.594
105_V116_Y0.176140.592
15_F18_L0.175840.591
29_V39_M0.175770.591
49_L190_L0.175560.590
176_W190_L0.174640.587
30_R33_P0.174040.585
98_T102_T0.173140.582
12_L201_G0.172540.580
104_S107_L0.172450.580
93_K137_A0.172180.579
30_R35_E0.172180.579
80_L137_A0.172140.579
64_I179_R0.172090.578
56_A60_D0.171990.578
222_F225_D0.17190.578
51_S174_A0.171510.576
69_S72_S0.171390.576
109_R112_L0.171310.576
33_P36_L0.171120.575
21_G196_K0.171010.575
130_A133_A0.170630.573
87_I114_E0.170210.572
108_L120_Y0.169350.569
54_E58_N0.169310.569
49_L194_L0.168640.567
96_A138_A0.168630.567
69_S175_V0.168270.566
125_D129_P0.168070.565
109_R113_E0.167990.565
107_L120_Y0.16770.564
38_Q41_L0.167230.562
97_L101_S0.165280.555
91_D94_K0.165240.555
22_E189_E0.165180.555
58_N62_Y0.164360.552
204_N208_I0.164140.552
201_G205_P0.163810.551
36_L50_I0.163660.550
33_P102_T0.163430.549
174_A194_L0.163040.548
37_N51_S0.161670.543
16_Y19_I0.161560.543
48_A177_V0.161210.542
26_F193_A0.160790.540
85_V210_K0.160620.540
173_F223_I0.160330.539
128_P131_M0.160210.538
109_R120_Y0.159660.537
84_K134_G0.159310.535
69_S195_R0.159150.535
143_D174_A0.158930.534
41_L61_D0.158890.534
17_G193_A0.158810.534
17_G26_F0.158110.531
40_L50_I0.157990.531
18_L28_I0.156960.527
51_S55_Y0.156350.525
81_L137_A0.156180.525
75_P79_V0.155970.524
88_E185_E0.155150.521
143_D173_F0.154390.519
13_P201_G0.153710.517
128_P151_Q0.153660.516
208_I211_E0.153610.516
85_V88_E0.153270.515
102_T198_K0.152790.513
212_A216_A0.152780.513
53_I105_V0.152740.513
70_I187_I0.152690.513
191_V195_R0.152340.512
18_L215_R0.15220.512
91_D116_Y0.1520.511
98_T124_P0.151510.509
80_L83_S0.151390.509
98_T103_T0.150810.507
211_E220_P0.15070.506
53_I175_V0.150680.506
76_V80_L0.15060.506
104_S108_L0.150540.506
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
2nxoA0.9961000.261
2czlA0.98011000.269
1zbmA0.98011000.321
2i6eA0.97211000.335
3hn0A0.96411000.352
3un6A0.96811000.37
4eswA0.9881000.391
3ix1A0.98011000.394
3ksxA0.956299.90.412
2g29A0.972199.90.424

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