GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AIRC - AIR carboxylase
Pfam: PF00731 (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. )
Length: 150
Sequences: 2121
Seq/Len: 14.14
HH_delta: -0.002 (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
52_E140_R1.021392.874
82_I112_V0.990752.788
94_L98_L0.974292.742
4_A47_F0.953322.683
6_I73_V0.862322.427
57_D131_K0.833922.347
105_S118_F0.827462.328
126_R143_R0.825612.323
45_L76_L0.806712.270
70_P100_I0.792752.231
5_I20_A0.754532.123
110_A123_L0.748552.106
52_E136_R0.747912.105
4_A56_A0.740632.084
112_V123_L0.736742.073
33_R43_R0.735042.068
26_F125_A0.733182.063
87_S90_Y0.732492.061
137_E141_A0.701341.974
16_A84_V0.699541.969
2_K57_D0.696731.961
42_E49_K0.690831.944
82_I127_I0.68781.935
128_L135_L0.678661.910
24_E30_Y0.668921.882
46_E50_E0.627941.767
50_E53_A0.61531.731
141_A145_K0.607721.710
25_E145_K0.607011.708
87_S92_G0.603451.698
87_S115_N0.577021.624
97_L101_V0.573521.614
16_A62_V0.572561.611
52_E78_T0.568621.600
125_A135_L0.549621.547
20_A30_Y0.533451.501
28_I125_A0.529351.490
78_T140_R0.527191.484
129_A135_L0.525941.480
31_E54_R0.509451.434
134_E138_K0.49771.401
20_A32_V0.497541.400
40_T43_R0.495571.395
91_L114_I0.493271.388
26_F138_K0.480271.351
35_A44_L0.460671.296
113_G116_N0.460371.295
78_T136_R0.4571.286
88_S92_G0.446061.255
17_E21_K0.443681.249
18_E118_F0.435971.227
59_I79_L0.433031.219
61_A73_V0.430711.212
82_I110_A0.426781.201
18_E21_K0.417381.175
2_K29_P0.411821.159
137_E140_R0.410461.155
14_P17_E0.408851.151
31_E56_A0.408671.150
27_G138_K0.402891.134
58_V128_L0.402111.132
21_K25_E0.392111.103
135_L138_K0.387631.091
42_E76_L0.381121.072
35_A43_R0.380541.071
139_L143_R0.378151.064
47_F56_A0.374111.053
44_L73_V0.373851.052
15_I87_S0.372191.047
57_D130_L0.37121.045
78_T139_L0.370721.043
49_K76_L0.36181.018
22_T118_F0.361271.017
22_T25_E0.353620.995
57_D132_D0.351390.989
20_A24_E0.348020.979
15_I115_N0.347630.978
21_K24_E0.344640.970
35_A72_V0.344020.968
140_R144_E0.336740.948
97_L114_I0.334460.941
136_R140_R0.326450.919
121_A125_A0.326330.918
3_V23_L0.324640.914
133_P136_R0.321950.906
48_V59_I0.321520.905
44_L48_V0.319210.898
20_A28_I0.317160.892
44_L72_V0.31410.884
94_L114_I0.313680.883
48_V51_Y0.313150.881
31_E47_F0.31150.877
82_I123_L0.31080.875
50_E54_R0.309990.872
62_V84_V0.307120.864
42_E46_E0.30430.856
42_E45_L0.299740.843
89_G96_S0.298990.841
4_A59_I0.2970.836
37_A41_P0.295860.833
22_T121_A0.295550.832
46_E49_K0.293180.825
48_V73_V0.282090.794
94_L97_L0.281940.793
10_T34_V0.281690.793
19_A60_I0.281530.792
118_F142_Y0.27830.783
43_R46_E0.2760.777
22_T26_F0.27490.774
141_A144_E0.271730.765
88_S96_S0.271160.763
72_V75_S0.271010.763
2_K132_D0.270890.762
62_V86_V0.268740.756
60_I121_A0.268490.756
15_I86_V0.265960.748
65_M89_G0.265280.746
133_P137_E0.264860.745
8_G71_G0.26240.738
121_A128_L0.262360.738
122_L125_A0.262170.738
112_V127_I0.261470.736
19_A62_V0.261080.735
133_P144_E0.259560.730
132_D135_L0.25940.730
91_L101_V0.259060.729
65_M96_S0.258830.728
133_P141_A0.256670.722
83_G100_I0.255460.719
60_I120_A0.253250.713
4_A31_E0.253150.712
57_D136_R0.2510.706
122_L143_R0.250120.704
123_L127_I0.249660.703
57_D128_L0.243440.685
90_Y94_L0.239280.673
94_L101_V0.239030.673
132_D138_K0.238820.672
7_M16_A0.238020.670
134_E137_E0.237660.669
6_I59_I0.236970.667
70_P102_Q0.236920.667
41_P75_S0.2330.656
58_V123_L0.229490.646
125_A128_L0.228380.643
73_V76_L0.226140.636
27_G137_E0.225780.635
48_V76_L0.225550.635
53_A144_E0.225180.634
107_V143_R0.224650.632
93_G98_L0.222650.627
52_E133_P0.222620.626
10_T112_V0.221150.622
22_T142_Y0.22080.621
47_F54_R0.220490.620
13_L32_V0.220290.620
91_L97_L0.220130.619
134_E144_E0.218910.616
13_L20_A0.218350.614
126_R139_L0.217970.613
134_E141_A0.217920.613
140_R145_K0.216150.608
22_T122_L0.21570.607
116_N119_N0.21560.607
53_A137_E0.215490.606
131_K136_R0.215390.606
138_K144_E0.215170.605
24_E28_I0.21490.605
127_I130_L0.21280.599
58_V127_I0.211760.596
26_F142_Y0.211210.594
123_L126_R0.210120.591
96_S99_S0.208920.588
14_P18_E0.206980.582
93_G99_S0.205330.578
15_I18_E0.203980.574
89_G115_N0.203450.573
125_A129_A0.202310.569
101_V105_S0.202240.569
129_A139_L0.201870.568
32_V43_R0.201520.567
129_A136_R0.201250.566
34_V43_R0.200790.565
18_E117_G0.200550.564
108_P118_F0.199630.562
49_K53_A0.198720.559
65_M88_S0.19730.555
51_Y59_I0.1960.552
10_T13_L0.193740.545
136_R139_L0.193150.544
21_K144_E0.192830.543
90_Y115_N0.192650.542
138_K141_A0.192070.540
57_D133_P0.191590.539
45_L48_V0.189970.535
98_L102_Q0.189430.533
78_T129_A0.188970.532
15_I117_G0.18880.531
102_Q109_V0.188560.531
10_T14_P0.188480.530
46_E53_A0.187760.528
135_L139_L0.18760.528
23_L121_A0.187320.527
7_M11_S0.186760.526
17_E134_E0.186710.525
142_Y145_K0.18670.525
33_R76_L0.185290.521
13_L17_E0.185160.521
77_T81_V0.184880.520
137_E144_E0.184840.520
121_A126_R0.18460.519
23_L125_A0.184050.518
88_S113_G0.183950.518
70_P74_A0.183690.517
105_S116_N0.183440.516
46_E141_A0.183240.516
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
3lp6A1100-0.002
4grdA1100-0.001
3orsA11000.003
3trhA11000.005
3kuuA11000.005
1o4vA11000.007
1xmpA11000.007
4b4kA11000.012
4ay3A11000.014
3oowA11000.014

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