GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OTCace_N - Aspartateornithine carbamoyltransferase carbamoyl-P binding domain
Pfam: PF02729 (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: 142
Sequences: 3263
Seq/Len: 22.98
HH_delta: -0.06 (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
35_Q38_K1.318313.801
92_S116_S1.01862.937
5_S127_E0.992962.863
61_A66_G0.982252.832
25_K141_E0.972692.804
22_K140_R0.964252.780
85_E110_E0.95992.767
19_D140_R0.935442.697
42_V61_A0.908022.618
43_A95_V0.890052.566
15_E140_R0.871862.514
62_N67_H0.735332.120
10_S13_E0.729332.103
99_V122_A0.701482.022
22_K137_F0.701012.021
47_F107_A0.67571.948
11_P15_E0.673321.941
104_S107_A0.610791.761
88_A111_L0.592331.708
55_L91_L0.554611.599
18_L137_F0.549231.583
22_K141_E0.538351.552
72_D75_T0.53281.536
20_L23_E0.524991.514
51_T87_T0.503051.450
18_L140_R0.50031.442
1_R13_E0.49881.438
26_A30_K0.496151.430
51_T81_G0.494521.426
42_V97_A0.494431.425
42_V99_V0.488121.407
85_E114_H0.484581.397
21_A137_F0.480781.386
106_G110_E0.480481.385
77_S80_K0.455991.315
109_E113_E0.455851.314
54_R58_E0.451251.301
51_T77_S0.450881.300
23_E27_A0.44671.288
98_I117_V0.446151.286
2_H112_A0.445781.285
57_F130_T0.440931.271
3_L133_L0.433391.249
58_E70_Y0.427241.232
18_L22_K0.419141.208
41_T67_H0.414481.195
102_H124_D0.410581.184
61_A68_V0.407411.175
5_S8_D0.406891.173
47_F78_L0.404381.166
49_P79_G0.403611.164
15_E19_D0.400111.154
9_L17_L0.400021.153
28_P63_R0.396121.142
20_L24_L0.389461.123
35_Q65_G0.386691.115
3_L9_L0.386011.113
41_T63_R0.384771.109
25_K137_F0.37991.095
6_I14_I0.377131.087
42_V66_G0.37071.069
48_E123_G0.368781.063
62_N68_V0.364761.052
89_R92_S0.363551.048
85_E89_R0.360051.038
56_S94_Y0.360031.038
98_I111_L0.356531.028
136_L139_I0.356291.027
6_I132_A0.354951.023
92_S117_V0.35461.022
100_I111_L0.353961.020
4_L112_A0.353061.018
57_F122_A0.353041.018
105_H125_D0.351041.012
105_H109_E0.33930.978
77_S87_T0.339270.978
2_H115_S0.338470.976
37_L66_G0.334940.966
110_E114_H0.329860.951
102_H107_A0.323270.932
93_R142_H0.316810.913
56_S130_T0.31630.912
16_A20_L0.315920.911
23_E26_A0.314460.907
88_A115_S0.313350.903
97_A120_I0.31230.900
22_K26_A0.311190.897
27_A34_S0.310630.896
44_L70_Y0.309540.892
134_A137_F0.308650.890
104_S125_D0.308510.889
57_F99_V0.306120.883
58_E68_V0.303130.874
89_R114_H0.300810.867
108_L124_D0.297380.857
137_F141_E0.296920.856
12_E15_E0.295370.852
7_K127_E0.294080.848
8_D13_E0.289970.836
51_T76_S0.289840.836
127_E132_A0.289440.834
84_L107_A0.28930.834
81_G87_T0.287750.830
77_S81_G0.286430.826
82_E86_D0.284890.821
132_A136_L0.283240.817
28_P31_G0.282660.815
4_L109_E0.282650.815
106_G124_D0.279960.807
59_A63_R0.278860.804
106_G126_H0.277080.799
100_I107_A0.2770.799
44_L61_A0.275540.794
106_G109_E0.274480.791
18_L21_A0.273420.788
6_I127_E0.273090.787
44_L68_V0.270340.779
2_H92_S0.269440.777
58_E62_N0.266440.768
109_E112_A0.264030.761
46_F53_T0.263480.760
41_T59_A0.26250.757
12_E16_A0.260960.752
49_P81_G0.259490.748
19_D26_A0.259350.748
60_A130_T0.255860.738
19_D23_E0.255530.737
30_K34_S0.255390.736
76_S81_G0.253750.732
98_I115_S0.253290.730
110_E113_E0.251650.726
91_L95_V0.251640.725
34_S39_G0.251540.725
40_K96_D0.250720.723
55_L71_L0.249080.718
76_S80_K0.248020.715
18_L133_L0.24780.714
48_E103_P0.242680.700
52_R101_R0.238010.686
27_A30_K0.237810.686
111_L115_S0.235150.678
90_V94_Y0.231770.668
88_A98_I0.230620.665
90_V93_R0.230290.664
46_F50_S0.227890.657
51_T80_K0.227890.657
54_R70_Y0.227260.655
92_S115_S0.226880.654
103_P107_A0.226690.654
49_P75_T0.226290.652
84_L100_I0.225750.651
59_A69_I0.22420.646
2_H116_S0.223840.645
23_E30_K0.223020.643
87_T91_L0.222950.643
91_L98_I0.222920.643
24_L36_L0.222670.642
31_G38_K0.220570.636
49_P70_Y0.218930.631
3_L14_I0.216440.624
43_A98_I0.216430.624
47_F102_H0.215860.622
34_S38_K0.214780.619
80_K83_S0.213520.616
50_S53_T0.213370.615
105_H126_H0.212860.614
73_P76_S0.210730.608
75_T78_L0.209930.605
17_L20_L0.209590.604
53_T131_Q0.209410.604
19_D22_K0.20810.600
22_K25_K0.207070.597
26_A29_K0.205960.594
36_L64_L0.205410.592
41_T62_N0.203990.588
14_I133_L0.203740.587
44_L99_V0.203130.586
135_D138_T0.201940.582
138_T142_H0.201890.582
121_N129_P0.201510.581
136_L140_R0.20130.580
46_F52_R0.201030.580
59_A91_L0.200590.578
27_A31_G0.200470.578
82_E101_R0.19930.575
48_E77_S0.199260.574
49_P94_Y0.199120.574
47_F100_I0.198330.572
49_P80_K0.198220.571
76_S87_T0.198030.571
53_T101_R0.195910.565
24_L27_A0.194050.559
95_V117_V0.193690.558
12_E19_D0.192560.555
76_S132_A0.192060.554
56_S90_V0.190410.549
6_I136_L0.19040.549
35_Q64_L0.190180.548
63_R96_D0.190010.548
88_A114_H0.189290.546
52_R82_E0.18610.537
124_D130_T0.185990.536
13_E16_A0.183290.528
5_S126_H0.182470.526
10_S14_I0.181340.523
62_N95_V0.1810.522
59_A62_N0.180180.519
50_S54_R0.179980.519
53_T56_S0.178880.516
88_A119_V0.17830.514
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
4am8A1100-0.06
4a8pA1100-0.059
4a8tA1100-0.058
4f2gA1100-0.056
1dxhA1100-0.055
1duvG1100-0.055
4amuA1100-0.055
1pvvA1100-0.053
1vlvA1100-0.052
4h31A1100-0.051

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