GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PPK2 - Polyphosphate kinase 2 (PPK2)
Pfam: PF03976 (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: CL0023
Length: 228
Sequences: 7178
Seq/Len: 31.48
HH_delta: 0.154 (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
54_W218_L1.055573.220
142_L203_A0.996213.039
148_E151_K0.961582.934
50_R214_A0.881042.688
205_D216_T0.872982.663
143_H200_I0.838622.559
146_K181_Q0.827012.523
145_S204_D0.767822.343
176_H180_Y0.719212.194
73_L76_P0.659182.011
50_R53_E0.658372.009
199_H220_A0.648561.979
65_F99_Y0.621341.896
181_Q185_E0.618491.887
216_T219_D0.612511.869
138_I199_H0.607281.853
216_T220_A0.601771.836
50_R211_L0.585921.788
178_D182_K0.580171.770
206_K212_A0.568121.733
150_K174_R0.558011.702
146_K178_D0.549071.675
47_T214_A0.54221.654
205_D212_A0.539371.646
54_W214_A0.523881.598
212_A215_R0.522511.594
166_V169_E0.52251.594
104_V132_D0.51831.581
55_L218_L0.508381.551
42_S144_I0.506781.546
141_F200_I0.505991.544
179_R183_A0.496111.514
212_A216_T0.490161.495
140_F217_L0.490111.495
45_G95_D0.483961.477
218_L222_E0.479361.462
144_I203_A0.471641.439
174_R178_D0.468361.429
215_R219_D0.4651.419
125_R128_R0.463551.414
185_E189_E0.462031.410
201_I213_V0.459861.403
147_K151_K0.458031.397
169_E172_E0.454891.388
61_R90_Q0.452231.380
38_G42_S0.451361.377
100_E116_W0.447811.366
145_S148_E0.447321.365
47_T217_L0.446371.362
121_E125_R0.443091.352
77_F95_D0.4391.339
54_W222_E0.434631.326
206_K211_L0.432751.320
49_N53_E0.43271.320
98_W101_D0.427731.305
74_R87_A0.422321.288
55_L222_E0.422021.288
52_I56_D0.419271.279
148_E152_R0.419071.279
187_M198_W0.415161.267
150_K154_K0.414931.266
175_K178_D0.402721.229
157_E160_P0.401771.226
148_E204_D0.401521.225
214_A218_L0.399151.218
127_E195_Y0.395311.206
128_R132_D0.394541.204
153_L173_Q0.390551.192
107_V183_A0.388861.186
139_K198_W0.383531.170
75_R87_A0.378161.154
202_P205_D0.37291.138
35_L97_S0.372491.136
170_D174_R0.37131.133
189_E200_I0.368791.125
68_P105_E0.3631.107
113_E117_E0.361791.104
155_E159_D0.359821.098
154_K157_E0.353991.080
36_F48_I0.353891.080
172_E175_K0.352191.075
203_A213_V0.349831.067
100_E125_R0.345431.054
40_D149_Q0.343891.049
103_L107_V0.340471.039
32_V138_I0.335641.024
168_P172_E0.333061.016
202_P212_A0.332861.016
124_N127_E0.331421.011
141_F198_W0.32911.004
33_L135_T0.328481.002
74_R77_F0.327410.999
122_E125_R0.323530.987
154_K158_E0.323080.986
118_R132_D0.321420.981
47_T213_V0.320430.978
49_N52_I0.31960.975
58_R106_R0.319520.975
138_I220_A0.318330.971
70_D73_L0.317010.967
190_R194_P0.313920.958
101_D105_E0.313390.956
39_W149_Q0.312380.953
186_E190_R0.311630.951
122_E126_F0.308730.942
186_E189_E0.308650.942
41_A153_L0.305790.933
146_K174_R0.305420.932
112_D115_E0.305330.932
74_R78_L0.305180.931
215_R218_L0.301810.921
147_K174_R0.299690.914
141_F188_L0.298960.912
76_P88_R0.296250.904
99_Y103_L0.294810.899
155_E158_E0.288630.881
151_K154_K0.288360.880
38_G43_G0.287470.877
95_D98_W0.286980.876
95_D99_Y0.286550.874
206_K216_T0.285930.872
182_K186_E0.285650.871
37_E188_L0.284910.869
127_E190_R0.284490.868
104_V108_E0.283220.864
175_K179_R0.282620.862
167_S170_D0.278190.849
144_I148_E0.276590.844
101_D104_V0.276270.843
65_F69_T0.273920.836
173_Q177_Y0.268160.818
97_S101_D0.267620.816
140_F199_H0.266590.813
176_H179_R0.261580.798
207_R211_L0.259340.791
48_I64_A0.25820.788
151_K155_E0.257360.785
51_L217_L0.256890.784
131_A196_A0.256280.782
100_E103_L0.255540.780
171_W175_K0.255040.778
213_V216_T0.254820.777
36_F47_T0.254310.776
118_R122_E0.253450.773
140_F201_I0.253060.772
34_I138_I0.252030.769
74_R88_R0.251270.767
179_R182_K0.250170.763
63_H92_G0.249080.760
143_H185_E0.247910.756
149_Q153_L0.24750.755
128_R131_A0.247350.755
47_T51_L0.244350.745
53_E56_D0.244140.745
143_H202_P0.243090.742
121_E190_R0.242850.741
142_L217_L0.241410.737
172_E176_H0.24010.733
139_K197_P0.238910.729
32_V137_I0.238270.727
48_I52_I0.237560.725
32_V91_I0.237280.724
115_E118_R0.237050.723
104_V133_D0.236780.722
37_E139_K0.23610.720
39_W181_Q0.235510.719
50_R54_W0.234780.716
95_D100_E0.234250.715
131_A134_G0.23360.713
60_F91_I0.233490.712
202_P216_T0.232620.710
178_D181_Q0.232110.708
77_F90_Q0.232030.708
129_M133_D0.231640.707
131_A195_Y0.231020.705
54_W215_R0.229990.702
154_K170_D0.22970.701
63_H90_Q0.228830.698
43_G152_R0.228360.697
99_Y197_P0.228330.697
146_K150_K0.228050.696
72_E76_P0.227170.693
169_E173_Q0.224370.685
91_I98_W0.224190.684
140_F216_T0.223520.682
35_L136_L0.223040.680
121_E124_N0.220480.673
51_L221_L0.220370.672
117_E190_R0.22030.672
219_D222_E0.219150.669
157_E171_W0.218410.666
68_P71_E0.218370.666
144_I149_Q0.216680.661
108_E133_D0.216590.661
201_I217_L0.215950.659
165_K168_P0.214930.656
207_R214_A0.214110.653
124_N190_R0.21360.652
131_A135_T0.213020.650
205_D213_V0.211610.646
38_G44_K0.20910.638
199_H216_T0.208990.638
153_L157_E0.208940.637
47_T50_R0.208190.635
39_W184_Y0.206270.629
141_F181_Q0.206210.629
141_F184_Y0.205990.628
120_L190_R0.205070.626
55_L214_A0.204140.623
173_Q176_H0.20410.623
146_K149_Q0.203630.621
37_E100_E0.202990.619
140_F220_A0.202670.618
68_P170_D0.201910.616
214_A217_L0.200280.611
52_I64_A0.198130.604
113_E116_W0.196920.601
39_W143_H0.196830.601
100_E104_V0.195560.597
35_L198_W0.194870.595
147_K168_P0.194690.594
126_F129_M0.194530.593
124_N128_R0.193020.589
56_D61_R0.192950.589
132_D195_Y0.192840.588
185_E200_I0.192070.586
38_G41_A0.190110.580
52_I59_G0.190080.580
97_S102_V0.189730.579
204_D216_T0.189550.578
89_G92_G0.188980.577
123_I190_R0.188960.577
61_R64_A0.188790.576
98_W102_V0.188710.576
201_I220_A0.188660.576
180_Y184_Y0.188570.575
36_F51_L0.18840.575
39_W146_K0.188250.574
168_P173_Q0.187870.573
102_V187_M0.187820.573
77_F122_E0.187630.572
146_K177_Y0.18760.572
39_W42_S0.187320.571
99_Y139_K0.187030.571
114_A118_R0.185320.565
122_E132_D0.185310.565
182_K185_E0.18490.564
100_E107_V0.184430.563
68_P102_V0.183370.559
211_L215_R0.183070.559
69_T137_I0.182840.558
47_T207_R0.181370.553
129_M132_D0.181190.553
96_R99_Y0.181070.552
142_L184_Y0.18060.551
142_L213_V0.180020.549
35_L99_Y0.1790.546
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
3czqA11000.154
3czpA11000.16
3czpA11000.165
3rhfA11000.191
4hlcA0.785199.90.444
3v9pA0.850999.90.457
4tmkA0.785199.90.458
4edhA0.802699.90.466
3hjnA0.754499.90.466
3sr0A0.815899.80.475

Page generated in 0.0203 seconds.