OPENSEQ.org

Archive: 2012 - 2013
SKI - Shikimate kinase
Pfam: PF01202 (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: 158
Sequences: 9963
Seq/Len: 63.06
HH_delta: 0.15 (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
97_E100_E1.49163.256
92_D138_V1.278532.791
15_R154_L1.208332.638
144_S152_E1.153462.518
11_L150_A1.091782.383
93_A98_L1.065942.327
94_D142_D1.052262.297
11_L14_K1.045532.282
9_G20_F1.014052.213
15_R150_A0.950932.076
92_D140_D0.919262.007
26_E29_E0.91331.994
94_D97_E0.90481.975
93_A141_T0.860271.878
144_S148_E0.847731.850
15_R151_E0.846081.847
139_V149_I0.831331.815
87_L137_I0.825321.802
95_P121_L0.814521.778
30_R57_E0.803551.754
145_P148_E0.788721.722
121_L125_F0.76491.670
8_V149_I0.760581.660
97_E142_D0.751411.640
93_A97_E0.721931.576
89_I137_I0.720521.573
100_E104_A0.704751.538
11_L147_E0.701171.531
144_S149_I0.698981.526
91_L141_T0.678021.480
11_L15_R0.677011.478
16_L154_L0.672891.469
151_E155_E0.663021.447
99_A115_M0.652971.425
93_A101_R0.647241.413
2_G102_L0.636141.389
12_L153_I0.633711.383
76_E80_E0.63361.383
8_V150_A0.625371.365
33_M41_E0.617221.347
95_P99_A0.614911.342
122_E126_E0.610321.332
152_E155_E0.604911.320
49_E53_E0.599931.310
8_V153_I0.586641.281
10_K14_K0.579211.264
56_R60_K0.561591.226
79_R133_Q0.555481.212
46_A49_E0.553851.209
3_S93_A0.541811.183
13_A20_F0.537461.173
52_S75_K0.528051.153
37_E40_A0.52731.151
97_E101_R0.526221.149
90_Y138_V0.523721.143
48_R51_E0.514921.124
36_S40_A0.514071.122
128_E132_E0.509471.112
10_K13_A0.507161.107
6_S24_D0.50551.103
98_L102_L0.503761.100
50_L53_E0.499421.090
115_M119_E0.491711.073
99_A103_R0.485211.059
148_E151_E0.484781.058
8_V91_L0.484651.058
57_E61_E0.482771.054
22_D25_D0.47631.040
34_S37_E0.474831.036
31_T38_I0.474621.036
42_E46_A0.471941.030
46_A50_L0.462771.010
33_M37_E0.457380.998
143_G148_E0.456440.996
6_S10_K0.453540.990
119_E122_E0.45230.987
98_L124_L0.449780.982
127_R130_L0.445860.973
143_G152_E0.444660.971
4_G101_R0.444120.969
19_P61_E0.440890.962
9_G13_A0.440490.961
27_I30_R0.439890.960
92_D128_E0.434860.949
141_T149_I0.434760.949
3_S98_L0.432690.944
58_L61_E0.43240.944
96_E100_E0.431040.941
150_A154_L0.42990.938
112_K116_E0.428220.935
35_I39_F0.424570.927
149_I152_E0.423690.925
18_R63_N0.423630.925
151_E154_L0.422510.922
119_E123_L0.417720.912
15_R147_E0.412750.901
44_E48_R0.40850.892
10_K20_F0.403520.881
39_F44_E0.400570.874
52_S56_R0.398830.871
53_E56_R0.398750.870
123_L128_E0.397820.868
127_R131_Y0.395050.862
99_A121_L0.394090.860
52_S78_N0.393380.859
7_T11_L0.392880.858
73_V76_E0.392110.856
22_D67_A0.39080.853
3_S90_Y0.390320.852
33_M42_E0.389470.850
54_A57_E0.38770.846
12_L154_L0.387110.845
140_D143_G0.386380.843
14_K150_A0.386030.843
91_L153_I0.385370.841
90_Y135_A0.383620.837
11_L154_L0.383230.837
116_E119_E0.38030.830
56_R81_L0.378580.826
145_P150_A0.373270.815
23_L72_I0.370120.808
126_E130_L0.368270.804
75_K134_A0.368090.803
39_F47_F0.366940.801
37_E41_E0.365750.798
92_D132_E0.364640.796
77_E80_E0.363160.793
68_C73_V0.362030.790
99_A120_I0.353590.772
100_E103_R0.353010.771
57_E60_K0.352310.769
148_E152_E0.352290.769
102_L106_D0.351620.768
20_F67_A0.35030.765
21_I64_C0.345650.754
21_I26_E0.344910.753
78_N81_L0.344760.753
96_E99_A0.343580.750
102_L120_I0.34190.746
124_L128_E0.341710.746
150_A153_I0.339890.742
87_L136_D0.339440.741
64_C67_A0.338570.739
101_R141_T0.336810.735
147_E150_A0.336790.735
13_A19_P0.333760.729
91_L149_I0.331580.724
52_S55_L0.331450.723
36_S39_F0.330590.722
80_E83_K0.330330.721
141_T144_S0.329370.719
31_T46_A0.327370.715
95_P124_L0.326830.713
25_D28_E0.322570.704
90_Y132_E0.322290.703
38_I46_A0.319180.697
130_L133_Q0.318250.695
56_R59_L0.317270.693
88_V136_D0.3140.685
116_E120_I0.312970.683
16_L150_A0.311190.679
28_E31_T0.310870.679
50_L54_A0.310720.678
90_Y131_Y0.307080.670
26_E54_A0.305910.668
7_T145_P0.305780.667
53_E57_E0.304940.666
47_F50_L0.304920.666
34_S38_I0.302930.661
27_I31_T0.301650.658
82_L88_V0.301530.658
31_T50_L0.297790.650
5_K24_D0.296430.647
112_K115_M0.294840.644
35_I38_I0.292930.639
52_S77_E0.291240.636
132_E138_V0.29120.636
1_M123_L0.291190.636
8_V11_L0.29040.634
120_I124_L0.28960.632
58_L62_N0.288780.630
75_K78_N0.28820.629
33_M36_S0.287160.627
139_V153_I0.287010.626
82_L86_G0.286790.626
83_K136_D0.284830.622
114_K119_E0.283730.619
90_Y128_E0.281610.615
47_F51_E0.280610.613
122_E125_F0.280050.611
89_I139_V0.27990.611
44_E47_F0.278940.609
25_D29_E0.273020.596
125_F128_E0.272120.594
144_S147_E0.271380.592
76_E79_R0.271310.592
95_P98_L0.270670.591
27_I38_I0.270250.590
104_A107_N0.268520.586
72_I75_K0.267930.585
12_L150_A0.263850.576
92_D141_T0.263450.575
18_R64_C0.261570.571
43_G78_N0.261550.571
1_M39_F0.261490.571
19_P62_N0.261390.571
126_E131_Y0.261160.570
40_A43_G0.254230.555
23_L26_E0.253270.553
23_L54_A0.251760.550
4_G7_T0.245930.537
22_D98_L0.243360.531
27_I72_I0.243360.531
145_P149_I0.243310.531
113_G119_E0.242050.528
93_A149_I0.241910.528
135_A138_V0.240990.526
45_E49_E0.24010.524
74_L126_E0.239690.523
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
3trfA199.80.15
3vaaA0.993799.80.156
2iyvA0.993799.80.192
3nwjA0.987399.80.2
1zuhA0.949499.80.221
1e6cA0.987399.80.226
1viaA0.955799.70.237
1kagA199.70.24
2pt5A0.974799.70.241
3fdiA0.936799.60.322

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