GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PGP_phosphatase - Mitochondrial PGP phosphatase
Pfam: PF09419 (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: CL0137
Length: 168
Sequences: 851
Seq/Len: 5.07
HH_delta: 0.507 (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
153_G160_T0.583934.901
120_F152_M0.37053.110
143_G149_D0.290182.436
140_A161_I0.26412.217
42_K138_E0.259722.180
99_E103_K0.248682.087
124_L139_I0.227231.907
20_H154_N0.227161.907
69_N73_K0.216921.821
142_I161_I0.210271.765
48_K82_I0.190521.599
118_G122_E0.187891.577
31_F71_L0.184291.547
82_I102_E0.182131.529
45_I141_V0.180721.517
47_D51_T0.179821.509
17_L151_L0.173571.457
65_A69_N0.173551.457
86_S98_A0.17041.430
123_I152_M0.169481.423
43_A129_C0.168921.418
31_F67_W0.168861.417
129_C139_I0.167141.403
124_L136_P0.165921.393
41_I140_A0.159241.337
85_N117_P0.156821.316
23_V29_I0.155481.305
66_E70_E0.152051.276
48_K120_F0.151681.273
46_F142_I0.151391.271
24_P28_D0.150081.260
30_D33_A0.14741.237
46_F80_V0.146431.229
151_L155_R0.143941.208
43_A127_F0.143721.206
106_G128_K0.142341.195
150_V160_T0.141011.184
120_F141_V0.140611.180
122_E126_Y0.140511.179
37_K74_Q0.136071.142
69_N72_K0.135241.135
62_P66_E0.135061.134
68_L107_I0.133541.121
37_K42_K0.133461.120
80_V115_K0.133321.119
21_L140_A0.133081.117
86_S102_E0.132781.115
69_N103_K0.130811.098
26_I64_Y0.12921.084
38_K73_K0.128461.078
70_E73_K0.128161.076
57_E60_I0.127531.070
80_V107_I0.127421.070
48_K98_A0.12661.063
48_K145_R0.12611.058
95_G99_E0.125641.055
33_A39_K0.125261.051
141_V158_S0.122671.030
54_P61_P0.12241.027
33_A107_I0.120531.012
29_I44_L0.120221.009
95_G113_R0.119931.007
77_K127_F0.119251.001
73_K125_K0.118280.993
33_A140_A0.1180.990
95_G112_H0.117850.989
38_K128_K0.117790.989
103_K137_S0.117210.984
121_R125_K0.116310.976
68_L80_V0.116030.974
117_P153_G0.115630.971
73_K136_P0.115320.968
60_I101_L0.114720.963
36_L160_T0.114410.960
145_R148_T0.114240.959
26_I162_L0.114040.957
82_I156_M0.114030.957
32_E74_Q0.114020.957
62_P73_K0.113910.956
125_K137_S0.113820.955
50_N145_R0.112990.948
19_P50_N0.11280.947
45_I127_F0.11280.947
54_P57_E0.112410.944
32_E38_K0.111690.938
126_Y137_S0.111520.936
102_E107_I0.110760.930
121_R139_I0.110360.926
72_K137_S0.109940.923
58_D101_L0.109220.917
97_R114_A0.10920.917
86_S145_R0.108190.908
21_L33_A0.107790.905
44_L140_A0.107470.902
112_H118_G0.106540.894
38_K69_N0.105940.889
81_L110_L0.104460.877
76_G145_R0.10430.875
38_K63_E0.104010.873
120_F123_I0.103230.867
70_E74_Q0.102660.862
31_F41_I0.10230.859
33_A38_K0.10210.857
53_T101_L0.102070.857
37_K73_K0.101970.856
86_S97_R0.101540.852
61_P65_A0.10150.852
154_N160_T0.100940.847
62_P108_P0.100280.842
153_G159_Y0.099510.835
62_P104_A0.099430.835
86_S114_A0.099310.834
71_L139_I0.099180.833
96_E103_K0.098860.830
136_P157_G0.098670.828
19_P47_D0.09770.820
83_V146_L0.0970.814
45_I51_T0.096510.810
118_G125_K0.095520.802
50_N148_T0.095440.801
140_A159_Y0.095050.798
32_E106_G0.094690.795
85_N144_D0.094130.790
64_Y156_M0.093970.789
96_E113_R0.09390.788
75_F145_R0.093010.781
20_H159_Y0.092910.780
124_L156_M0.092810.779
72_K99_E0.092730.778
141_V152_M0.092640.778
49_D148_T0.092570.777
32_E72_K0.092390.776
27_R75_F0.092210.774
73_K106_G0.091940.772
28_D137_S0.091740.770
47_D52_L0.091690.770
47_D50_N0.091580.769
46_F67_W0.091370.767
118_G155_R0.09120.766
85_N149_D0.091160.765
62_P65_A0.091060.764
21_L159_Y0.091050.764
53_T60_I0.090860.763
24_P164_T0.090520.760
107_I113_R0.090120.756
129_C138_E0.089950.755
51_T145_R0.089910.755
97_R111_R0.089010.747
47_D145_R0.088970.747
119_C153_G0.088830.746
83_V143_G0.088580.744
61_P82_I0.087940.738
80_V102_E0.08780.737
30_D38_K0.087750.737
97_R152_M0.087710.736
126_Y129_C0.087710.736
28_D128_K0.08770.736
67_W114_A0.087190.732
57_E96_E0.086680.728
36_L40_G0.086510.726
81_L160_T0.086430.725
103_K125_K0.086420.725
72_K80_V0.08630.724
49_D144_D0.086140.723
44_L71_L0.085840.721
42_K139_I0.085690.719
55_P86_S0.085680.719
20_H164_T0.085370.717
69_N106_G0.084780.712
28_D73_K0.084710.711
18_L157_G0.084040.705
68_L100_A0.083730.703
105_L150_V0.083670.702
98_A102_E0.083430.700
48_K51_T0.0830.697
119_C126_Y0.082440.692
85_N148_T0.082340.691
44_L51_T0.082090.689
148_T154_N0.082020.688
57_E103_K0.081710.686
58_D139_I0.081660.685
84_S98_A0.080650.677
67_W86_S0.080490.676
84_S145_R0.080440.675
38_K65_A0.080270.674
80_V105_L0.080260.674
83_V123_I0.080240.674
150_V161_I0.080220.673
73_K76_G0.080010.672
81_L126_Y0.080.672
102_E109_V0.079980.671
40_G54_P0.079930.671
77_K122_E0.079920.671
36_L51_T0.079910.671
110_L120_F0.079740.669
141_V150_V0.079730.669
51_T97_R0.079590.668
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
3l8hA0.714399.70.507
3ib6A0.708399.70.509
2o2xA0.892999.70.517
2odaA0.702499.70.528
2pr7A0.666799.70.531
2fprA0.791799.70.539
2gmwA0.857199.70.54
3nvbA0.886999.70.541
4jdpA0.845299.70.544
2wm8A0.815599.60.55
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