GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Y_phosphatase - Protein-tyrosine phosphatase
Pfam: PF00102 (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: CL0031
Length: 235
Sequences: 2369
Seq/Len: 10.08
HH_delta: -0.092 (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
67_V174_V0.608223.535
46_V184_S0.511542.973
16_S33_S0.43572.532
4_K57_D0.432672.515
119_R137_H0.421692.451
5_N29_Y0.419642.439
62_V174_V0.395422.298
55_I85_D0.37352.171
189_A209_V0.359182.088
177_C184_S0.358922.086
44_F191_D0.347542.020
59_W62_V0.343491.996
98_F103_V0.341381.984
181_V218_G0.329151.913
189_A229_C0.326591.898
193_L208_I0.325741.893
87_Y176_H0.316541.840
17_R28_D0.314451.828
51_M54_T0.313951.825
63_W133_R0.308941.796
144_P147_G0.302521.758
12_P31_N0.301831.754
34_Y65_Q0.296541.724
179_D182_G0.29541.717
104_K122_E0.294891.714
120_K134_T0.293061.703
106_K122_E0.290491.688
46_V188_C0.290291.687
18_V34_Y0.287591.672
82_E85_D0.287251.670
76_F86_Q0.28481.655
61_M174_V0.28261.643
145_D179_D0.28261.643
49_A84_C0.280271.629
72_M137_H0.280041.628
190_I232_A0.274711.597
189_A212_L0.27411.593
213_R220_I0.27371.591
117_T141_T0.270721.573
204_D207_E0.269751.568
179_D221_Q0.267611.555
52_P85_D0.261061.517
66_K133_R0.260921.517
125_N128_S0.253771.475
36_D215_Q0.250371.455
116_Y158_F0.248111.442
226_Y230_Y0.244161.419
163_N191_D0.243881.417
192_I208_I0.239541.392
95_S104_K0.2381.383
62_V70_I0.23581.371
47_T174_V0.231071.343
179_D184_S0.229791.336
138_F165_S0.229261.333
17_R20_L0.227441.322
192_I212_L0.226771.318
180_G184_S0.223671.300
88_W137_H0.222431.293
193_L205_V0.222141.291
36_D43_K0.221131.285
30_I47_T0.21851.270
97_K102_T0.218231.268
46_V219_A0.218031.267
178_S183_R0.216761.260
18_V61_M0.216591.259
182_G221_Q0.214761.248
12_P33_S0.212821.237
89_P105_C0.211911.232
209_V219_A0.211431.229
196_Q208_I0.210491.223
179_D183_R0.20881.214
138_F162_V0.207671.207
118_V136_T0.204541.189
120_K136_T0.20381.185
72_M87_Y0.203031.180
176_H184_S0.202421.177
16_S215_Q0.201111.169
40_N43_K0.199091.157
83_K178_S0.197871.150
190_I229_C0.196451.142
38_Y200_E0.196261.141
121_L137_H0.195331.135
211_K214_Q0.193921.127
7_S179_D0.193881.127
212_L219_A0.19361.125
63_W101_Y0.191951.116
84_C87_Y0.191881.115
193_L233_V0.190481.107
221_Q225_Q0.190111.105
60_Q64_E0.188771.097
175_V188_C0.188511.096
213_R216_R0.188331.095
144_P148_V0.188321.095
122_E132_S0.186121.082
227_R230_Y0.186051.081
119_R139_H0.185781.080
102_T124_T0.183351.066
108_K120_K0.183341.066
104_K124_T0.18011.047
4_K27_S0.179671.044
180_G216_R0.178391.037
124_T132_S0.176791.028
98_F101_Y0.176751.027
87_Y137_H0.176571.026
77_D80_G0.176471.026
225_Q228_F0.176371.025
103_V121_L0.176231.024
83_K145_D0.175791.022
83_K221_Q0.174751.016
206_F210_K0.174461.014
50_P54_T0.174411.014
209_V220_I0.172561.003
182_G225_Q0.172521.003
182_G220_I0.17211.000
180_G185_G0.172041.000
115_H142_N0.17170.998
13_Y31_N0.171320.996
48_Q54_T0.170990.994
14_D17_R0.170640.992
109_I119_R0.170610.992
180_G183_R0.170240.989
140_Y149_P0.169990.988
48_Q51_M0.16920.983
162_V187_F0.168350.978
29_Y32_A0.167030.971
45_I67_V0.166530.968
228_F232_A0.166080.965
188_C219_A0.165710.963
57_D60_Q0.165270.961
35_V219_A0.164840.958
209_V213_R0.164720.957
205_V229_C0.162160.943
206_F226_Y0.161970.941
7_S10_I0.161590.939
30_I61_M0.160970.936
12_P219_A0.160720.934
137_H176_H0.160640.934
48_Q57_D0.16060.933
32_A45_I0.160430.932
62_V135_V0.160430.932
78_E83_K0.160360.932
207_E210_K0.160360.932
116_Y161_K0.160340.932
59_W70_I0.159640.928
12_P217_P0.15780.917
208_I212_L0.15710.913
105_C121_L0.157070.913
78_E183_R0.156940.912
67_V171_G0.156830.912
36_D41_G0.155740.905
36_D40_N0.155560.904
183_R213_R0.154830.900
185_G220_I0.154660.899
45_I61_M0.154550.898
10_I181_V0.153940.895
205_V230_Y0.153860.894
49_A74_C0.153680.893
74_C84_C0.152750.888
60_Q101_Y0.152640.887
72_M139_H0.152420.886
149_P228_F0.15230.885
225_Q230_Y0.152240.885
145_D177_C0.151740.882
196_Q200_E0.151670.882
52_P82_E0.151430.880
105_C109_I0.151260.879
72_M84_C0.151160.879
209_V229_C0.150440.874
5_N9_D0.149240.867
35_V188_C0.148850.865
69_I138_F0.148770.865
61_M72_M0.148540.863
5_N10_I0.147890.860
146_D179_D0.147740.859
175_V187_F0.147440.857
115_H154_S0.147410.857
47_T58_F0.146750.853
226_Y229_C0.145470.846
58_F70_I0.145330.845
59_W72_M0.143480.834
56_E99_G0.143390.833
7_S178_S0.143340.833
186_T190_I0.14270.829
21_N64_E0.142290.827
37_G43_K0.1420.825
21_N24_P0.141920.825
209_V226_Y0.141750.824
44_F173_I0.141340.822
59_W123_V0.140910.819
155_F158_F0.140590.817
140_Y158_F0.139970.814
78_E178_S0.13820.803
129_K132_S0.137660.800
143_W183_R0.137150.797
229_C233_V0.13710.797
71_V162_V0.136970.796
182_G186_T0.136960.796
16_S212_L0.136610.794
177_C180_G0.136330.792
155_F228_F0.135440.787
189_A193_L0.135390.787
101_Y125_N0.13490.784
195_E199_K0.13490.784
35_V46_V0.13470.783
49_A178_S0.134660.783
75_S141_T0.134410.781
151_S154_S0.134160.780
83_K179_D0.133650.777
5_N14_D0.133350.775
176_H179_D0.132930.773
122_E134_T0.132740.772
159_I187_F0.131880.767
8_P11_L0.131790.766
178_S221_Q0.131770.766
110_E122_E0.131490.764
105_C119_R0.131390.764
125_N129_K0.131150.762
5_N13_Y0.130830.760
67_V173_I0.130780.760
145_D221_Q0.130680.760
178_S182_G0.130650.759
14_D19_K0.130150.756
71_V158_F0.129370.752
220_I225_Q0.129320.752
95_S102_T0.12920.751
145_D178_S0.128630.748
6_R9_D0.128620.748
182_G185_G0.12860.747
72_M76_F0.128590.747
14_D29_Y0.128290.746
32_A61_M0.128040.744
179_D225_Q0.127620.742
102_T106_K0.126820.737
220_I223_P0.126560.736
74_C83_K0.126320.734
143_W180_G0.126130.733
186_T225_Q0.125870.732
76_F88_W0.125380.729
166_K173_I0.125110.727
13_Y33_S0.125030.727
83_K87_Y0.124730.725
49_A83_K0.12430.722
14_D18_V0.124270.722
49_A59_W0.123880.720
57_D61_M0.123730.719
181_V185_G0.123710.719
49_A179_D0.123690.719
184_S216_R0.12340.717
162_V173_I0.12330.717
181_V192_I0.123290.717
49_A78_E0.123050.715
182_G213_R0.122010.709
12_P119_R0.121860.708
181_V220_I0.121820.708
10_I218_G0.121070.704
87_Y119_R0.120990.703
99_G103_V0.120660.701
75_S139_H0.120470.700
45_I65_Q0.120230.699
190_I233_V0.120110.698
56_E100_D0.120090.698
210_K217_P0.119740.696
67_V120_K0.119670.696
10_I13_Y0.118990.692
113_S161_K0.118460.689
185_G219_A0.118350.688
17_R29_Y0.118070.686
37_G192_I0.117950.686
164_K214_Q0.117760.684
170_N189_A0.117320.682
54_T57_D0.117230.681
158_F163_N0.117080.680
49_A72_M0.1170.680
227_R231_M0.116950.680
220_I229_C0.116820.679
50_P58_F0.116680.678
70_I169_P0.116670.678
162_V165_S0.116640.678
152_P156_L0.116630.678
69_I215_Q0.116590.678
179_D186_T0.116380.676
193_L196_Q0.116370.676
171_G195_E0.116180.675
60_Q63_W0.116070.675
140_Y154_S0.116060.675
137_H177_C0.115850.673
186_T220_I0.115640.672
163_N198_K0.115470.671
112_N117_T0.115410.671
29_Y34_Y0.115120.669
178_S184_S0.1150.668
13_Y16_S0.11490.668
140_Y155_F0.114760.667
159_I190_I0.114450.665
104_K121_L0.114430.665
5_N31_N0.114260.664
100_D126_G0.114210.664
7_S83_K0.114190.664
97_K127_K0.114160.664
71_V187_F0.113890.662
152_P232_A0.113770.661
177_C225_Q0.113450.659
189_A208_I0.112640.655
48_Q216_R0.11240.653
24_P39_K0.111770.650
200_E203_V0.111690.649
63_W135_V0.111420.648
69_I166_K0.1110.645
32_A47_T0.110880.644
59_W89_P0.110640.643
117_T139_H0.110530.642
41_G101_Y0.110440.642
13_Y217_P0.110330.641
63_W123_V0.110180.640
6_R12_P0.110010.639
42_K69_I0.110.639
5_N18_V0.10990.639
58_F62_V0.109790.638
62_V67_V0.10960.637
213_R219_A0.109560.637
106_K120_K0.109160.634
157_D160_R0.108970.633
29_Y48_Q0.108890.633
183_R186_T0.108470.630
5_N12_P0.108330.630
13_Y158_F0.107870.627
156_L190_I0.107470.625
72_M176_H0.107280.624
213_R221_Q0.106860.621
73_L187_F0.106480.619
144_P149_P0.106380.618
158_F162_V0.106170.617
145_D225_Q0.10610.617
31_N219_A0.105990.616
110_E118_V0.105980.616
23_S26_D0.105680.614
7_S145_D0.10560.614
66_K171_G0.105550.613
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
4ge6A0.9872100-0.092
1ygrA0.9915100-0.058
3ps5A0.9872100-0.058
3s3eA0.9745100-0.054
2b3oA0.9872100-0.052
2shpA0.9872100-0.051
3i36A0.9787100-0.051
1yfoA0.983100-0.047
1ygrA0.9745100-0.046
2p6xA0.9787100-0.044

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