GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PS_pyruv_trans - Polysaccharide pyruvyl transferase
Pfam: PF04230 (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: CL0113
Length: 286
Sequences: 2524
Seq/Len: 8.83
HH_delta: 0.677 (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
135_D138_S0.37623.322
136_E140_E0.310772.744
16_K41_K0.305452.697
199_I209_I0.303672.681
101_P129_D0.283982.507
263_S268_G0.27192.401
134_R156_D0.269462.379
139_Y153_L0.268592.372
66_D103_I0.258892.286
96_K127_K0.250712.214
104_I128_A0.245432.167
262_I272_A0.23932.113
261_V277_V0.237692.099
103_I130_Y0.237572.098
140_E144_K0.219691.940
11_L105_L0.21451.894
201_R204_D0.214081.890
139_Y143_K0.213921.889
139_Y151_V0.213391.884
8_L70_G0.213271.883
14_L18_H0.212071.873
247_S250_E0.206441.823
102_V128_A0.205581.815
203_L241_I0.202321.786
96_K129_D0.20021.768
68_I105_L0.19361.709
23_E65_D0.1911.686
261_V272_A0.190261.680
256_S275_L0.189261.671
179_S258_A0.188771.667
105_L157_P0.185181.635
130_Y152_K0.183991.625
273_L279_V0.182131.608
179_S199_I0.181411.602
14_L17_K0.177641.569
67_V95_A0.17751.567
66_D101_P0.176881.562
4_D264_M0.17581.552
196_A226_F0.173671.533
67_V102_V0.165281.459
122_R126_S0.160711.419
73_G108_G0.160531.417
266_L270_I0.159561.409
19_G22_A0.159531.409
202_L207_Y0.157821.394
222_D225_D0.157251.388
245_S254_L0.155131.370
134_R267_H0.15451.364
226_F244_Y0.153221.353
128_A131_I0.152671.348
219_D222_D0.151371.337
175_R208_K0.149661.321
121_L125_L0.149421.319
7_I265_R0.146961.298
4_D71_G0.146421.293
133_V142_L0.145271.283
269_A281_A0.144921.280
212_L245_S0.144751.278
220_D223_D0.143831.270
136_E139_Y0.143381.266
258_A277_V0.142351.257
140_E143_K0.142191.256
34_F44_F0.141831.252
223_D227_N0.140851.244
260_L280_I0.140481.240
133_V138_S0.141.236
92_L102_V0.139031.228
189_E193_E0.138341.222
156_D267_H0.137751.216
114_S175_R0.136941.209
259_D277_V0.136941.209
107_Q131_I0.13641.204
71_G108_G0.134381.187
138_S267_H0.133681.180
48_L51_L0.132491.170
219_D223_D0.131111.158
95_A102_V0.130731.154
177_Y258_A0.130581.153
109_I138_S0.129771.146
176_N259_D0.129061.140
133_V139_Y0.128941.139
8_L26_I0.128431.134
70_G105_L0.12841.134
181_S209_I0.128171.132
66_D69_I0.127461.125
189_E221_E0.12721.123
71_G134_R0.126861.120
4_D72_G0.12661.118
199_I203_L0.126311.115
70_G108_G0.126151.114
4_D70_G0.125381.107
72_G266_L0.124551.100
214_F271_L0.124261.097
3_G267_H0.12361.091
109_I142_L0.123441.090
173_P176_N0.123221.088
132_S154_V0.12291.085
213_P263_S0.122671.083
119_K122_R0.121921.077
256_S277_V0.121591.074
132_S157_P0.121321.071
94_L97_K0.120291.062
53_R94_L0.119591.056
105_L154_V0.119481.055
155_P160_L0.119471.055
9_E13_K0.119211.053
93_F97_K0.118791.049
270_I274_S0.117991.042
7_I10_A0.117661.039
12_L26_I0.116931.032
106_G132_S0.116571.029
136_E153_L0.116531.029
259_D278_P0.115841.023
11_L157_P0.115691.022
114_S117_F0.115431.019
13_K16_K0.114741.013
138_S265_R0.114271.009
12_L24_I0.114241.009
82_L124_I0.114121.008
147_I151_V0.113991.007
17_K197_E0.113881.006
224_D227_N0.113711.004
28_S44_F0.113421.001
106_G267_H0.112890.997
106_G157_P0.112440.993
221_E224_D0.111170.982
23_E197_E0.110930.979
194_E197_E0.110180.973
135_D267_H0.110110.972
115_E144_K0.109880.970
271_L274_S0.109830.970
7_I157_P0.109830.970
197_E200_Q0.109780.969
177_Y180_V0.10960.968
71_G156_D0.109350.966
109_I156_D0.109120.964
212_L248_P0.10910.963
135_D265_R0.108770.960
193_E204_D0.108730.960
178_I181_S0.107790.952
200_Q204_D0.107550.950
10_A14_L0.107550.950
7_I72_G0.107280.947
2_I248_P0.106050.936
6_L156_D0.106010.936
25_I45_N0.105980.936
73_G266_L0.105820.934
28_S34_F0.105030.927
237_F240_I0.104770.925
200_Q236_F0.104470.922
10_A158_A0.10440.922
157_P160_L0.104170.920
70_G73_G0.10360.915
4_D106_G0.103030.910
96_K99_G0.102760.907
107_Q265_R0.102480.905
95_A99_G0.102240.903
73_G106_G0.102170.902
199_I208_K0.102110.902
133_V151_V0.101620.897
119_K201_R0.101550.897
135_D156_D0.101290.894
45_N112_F0.101230.894
4_D107_Q0.101180.893
142_L147_I0.100950.891
111_P138_S0.100840.890
258_A261_V0.100630.889
154_V272_A0.100320.886
95_A100_K0.100250.885
177_Y257_Q0.100110.884
72_G107_Q0.099650.880
269_A279_V0.099590.879
135_D269_A0.099580.879
107_Q133_V0.099520.879
245_S251_L0.099520.879
252_L271_L0.098850.873
181_S266_L0.098840.873
67_V91_W0.09880.872
2_I266_L0.098690.871
4_D8_L0.098270.868
5_D28_S0.098110.866
114_S176_N0.097940.865
69_I102_V0.097940.865
193_E197_E0.097540.861
176_N181_S0.096880.855
73_G183_S0.09640.851
108_G158_A0.096350.851
30_D145_L0.096340.851
2_I271_L0.096320.850
4_D108_G0.096270.850
223_D226_F0.095680.845
70_G264_M0.095660.845
71_G266_L0.095650.845
109_I266_L0.094830.837
108_G214_F0.09480.837
192_I222_D0.094650.836
214_F265_R0.094470.834
177_Y181_S0.094220.832
71_G214_F0.09410.831
264_M267_H0.094010.830
112_F115_E0.093790.828
104_I107_Q0.093390.825
118_K122_R0.092840.820
53_R98_L0.092550.817
16_K22_A0.092330.815
21_D204_D0.092180.814
5_D9_E0.09210.813
176_N208_K0.091970.812
50_K54_K0.091910.812
50_K53_R0.091870.811
108_G135_D0.091810.811
200_Q203_L0.091690.810
255_I268_G0.091530.808
71_G158_A0.091340.807
196_A206_G0.091160.805
176_N207_Y0.091060.804
217_S221_E0.091050.804
4_D158_A0.091040.804
110_G141_L0.090950.803
197_E201_R0.090940.803
11_L160_L0.090780.802
4_D271_L0.090650.800
6_L135_D0.090640.800
4_D266_L0.090490.799
71_G267_H0.090470.799
18_H238_N0.090090.795
199_I207_Y0.090030.795
115_E120_L0.089870.794
10_A268_G0.089430.790
104_I142_L0.089290.788
179_S209_I0.089260.788
73_G107_Q0.089250.788
95_A98_L0.089220.788
202_L205_K0.089170.787
255_I271_L0.089160.787
106_G268_G0.089150.787
97_K197_E0.089140.787
147_I150_N0.088830.784
219_D248_P0.088570.782
218_D222_D0.088430.781
11_L107_Q0.088370.780
134_R138_S0.087790.775
73_G261_V0.087730.775
113_R175_R0.087550.773
8_L12_L0.087520.773
173_P177_Y0.087430.772
71_G106_G0.08740.772
92_L125_L0.087390.772
16_K19_G0.087310.771
23_E204_D0.087220.770
31_P34_F0.087220.770
163_P275_L0.0870.768
2_I184_P0.086670.765
115_E118_K0.086590.765
73_G158_A0.086580.764
97_K118_K0.086570.764
68_I112_F0.086510.764
193_E225_D0.08650.764
123_R126_S0.086310.762
4_D73_G0.086280.762
92_L95_A0.086250.762
115_E119_K0.086140.761
42_S54_K0.086040.760
196_A225_D0.085930.759
69_I91_W0.085740.757
203_L207_Y0.085570.756
161_L165_Y0.085560.755
13_K168_E0.085020.751
99_G119_K0.084740.748
273_L276_G0.084710.748
213_P246_L0.084560.747
181_S199_I0.084430.745
127_K226_F0.084410.745
213_P271_L0.084390.745
208_K241_I0.084230.744
124_I141_L0.08410.743
218_D223_D0.084090.742
162_P237_F0.083960.741
107_Q110_G0.083930.741
108_G132_S0.083880.741
198_L202_L0.083820.740
252_L275_L0.083680.739
211_L244_Y0.083310.736
9_E25_I0.083140.734
252_L267_H0.082920.732
185_S216_P0.08290.732
196_A211_L0.08280.731
265_R271_L0.08280.731
143_K150_N0.082650.730
174_K206_G0.082640.730
243_D246_L0.082590.729
116_E243_D0.082520.729
122_R140_E0.082350.727
151_V201_R0.082280.727
199_I281_A0.082240.726
39_K42_S0.082140.725
119_K123_R0.082130.725
192_I218_D0.082080.725
158_A251_L0.0820.724
5_D265_R0.081970.724
84_S261_V0.08190.723
73_G214_F0.081840.723
72_G265_R0.081820.722
72_G158_A0.081740.722
45_N55_R0.081740.722
159_F270_I0.081720.722
15_L19_G0.081710.721
21_D127_K0.081570.720
34_F45_N0.081460.719
218_D221_E0.081420.719
203_L239_V0.081410.719
248_P252_L0.081360.718
178_I226_F0.081340.718
195_I209_I0.081210.717
268_G271_L0.08120.717
10_A270_I0.081050.716
29_P44_F0.080960.715
72_G106_G0.080960.715
221_E227_N0.080770.713
11_L106_G0.08070.713
216_P222_D0.08070.713
110_G266_L0.080580.712
25_I62_K0.080520.711
195_I198_L0.080480.711
170_K238_N0.080460.710
128_A281_A0.08040.710
93_F140_E0.080360.710
95_A126_S0.080240.709
185_S267_H0.08020.708
265_R270_I0.080190.708
70_G107_Q0.080160.708
152_K172_K0.080140.708
243_D254_L0.080110.707
261_V279_V0.080070.707
54_K130_Y0.080040.707
64_A100_K0.079930.706
10_A265_R0.079880.705
210_V243_D0.079710.704
9_E38_Y0.079620.703
135_D153_L0.07960.703
18_H140_E0.079590.703
243_D260_L0.079530.702
180_V267_H0.079460.702
121_L273_L0.079450.702
157_P269_A0.079420.701
218_D225_D0.079410.701
135_D254_L0.079330.700
204_D227_N0.079020.698
158_A268_G0.078990.697
125_L133_V0.078980.697
265_R268_G0.078940.697
182_N185_S0.078810.696
274_S279_V0.078630.694
157_P268_G0.078590.694
72_G156_D0.078550.694
278_P281_A0.078550.694
214_F268_G0.078520.693
44_F55_R0.078510.693
175_R261_V0.078510.693
34_F161_L0.078480.693
113_R176_N0.078480.693
49_S90_R0.078430.693
272_A279_V0.078390.692
181_S195_I0.077990.689
15_L22_A0.077960.688
114_S173_P0.07790.688
97_K200_Q0.07780.687
166_P256_S0.077770.687
204_D238_N0.077530.685
9_E37_Y0.077440.684
142_L156_D0.077160.681
22_A35_S0.076910.679
253_E257_Q0.076840.678
19_G25_I0.076660.677
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
3tovA0.895199.30.677
2gt1A0.891699.30.683
1pswA0.912699.20.695
2xciA0.870698.90.74
3oy2A0.937198.70.754
1vgvA0.933698.70.758
2gekA0.916198.60.76
3ot5A0.930198.70.76
4fkzA0.926698.70.76
3okpA0.919698.60.761
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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