GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CPSase_sm_chain - Carbamoyl-phosphate synthase small chain CPSase domain
Pfam: PF00988 (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: 131
Sequences: 1643
Seq/Len: 12.54
HH_delta: -0.046 (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
94_M102_E1.148124.371
50_I79_I0.866753.300
53_F78_L0.857423.264
28_V128_G0.812823.094
20_A104_G0.805473.066
31_N46_Y0.797683.037
8_E127_K0.761592.899
22_G106_P0.738172.810
87_P92_S0.73422.795
9_D119_K0.722022.749
40_I51_L0.645512.457
68_F99_W0.581572.214
87_P95_S0.574322.186
65_E93_E0.567482.160
77_G130_I0.54732.084
97_D101_K0.537532.046
18_F107_G0.524251.996
16_K110_G0.521271.984
47_A74_H0.519841.979
54_T117_T0.512311.950
50_I128_G0.503941.919
84_S87_P0.469611.788
31_N40_I0.440651.678
67_D91_R0.437561.666
3_A108_I0.431351.642
38_Q64_N0.419791.598
13_F119_K0.412731.571
16_K109_S0.407091.550
11_T119_K0.40631.547
50_I77_G0.406141.546
80_V83_L0.402821.534
71_D74_H0.402311.532
95_S98_E0.395851.507
41_L75_V0.388261.478
111_V116_L0.384721.465
51_L75_V0.364941.389
73_I103_H0.36071.373
11_T115_A0.360581.373
94_M98_E0.353841.347
79_I108_I0.342791.305
33_G40_I0.334441.273
21_P101_K0.332841.267
2_K14_E0.330411.258
41_L78_L0.329121.253
64_N67_D0.319651.217
6_V12_V0.31651.205
8_E126_M0.315231.200
65_E94_M0.314261.196
5_L108_I0.310241.181
57_L61_Y0.308431.174
83_L97_D0.306621.167
28_V120_L0.296561.129
22_G104_G0.292771.115
73_I105_I0.283311.079
47_A72_R0.261730.996
98_E101_K0.261330.995
63_V68_F0.260170.990
115_A119_K0.257510.980
48_G76_K0.25570.973
3_A17_S0.253490.965
25_T129_V0.251760.958
72_R103_H0.251160.956
4_Y14_E0.24950.950
53_F58_I0.248060.944
35_T38_Q0.2480.944
120_L125_S0.246320.938
100_L105_I0.242570.923
40_I53_F0.240770.917
79_I111_V0.238740.909
119_K123_K0.23650.900
63_V94_M0.235860.898
26_G50_I0.226550.862
120_L128_G0.225550.859
24_V77_G0.223160.850
6_V129_V0.222220.846
2_K16_K0.221440.843
13_F115_A0.220840.841
98_E102_E0.220540.840
47_A76_K0.218770.833
101_K104_G0.217850.829
41_L96_L0.217330.827
79_I128_G0.217130.827
7_L11_T0.215230.819
61_Y64_N0.21370.814
63_V92_S0.212630.809
19_G107_G0.209310.797
92_S95_S0.208560.794
57_L82_E0.205210.781
9_D123_K0.204340.778
4_Y12_V0.203580.775
16_K93_E0.203470.775
5_L10_G0.198860.757
17_S21_P0.198280.755
46_Y49_Q0.197080.750
31_N53_F0.197040.750
10_G15_G0.196580.748
38_Q67_D0.195630.745
55_Y99_W0.195620.745
99_W103_H0.192530.733
67_D89_H0.189980.723
7_L119_K0.189770.722
58_I80_V0.189540.722
18_F83_L0.189360.721
42_T99_W0.188080.716
21_P72_R0.1880.716
53_F80_V0.187040.712
30_F121_R0.185830.707
19_G97_D0.185760.707
18_F80_V0.184880.704
120_L126_M0.181190.690
65_E102_E0.1810.689
28_V50_I0.180140.686
31_N35_T0.179580.684
71_D85_D0.178690.680
2_K82_E0.177920.677
34_M61_Y0.176920.674
59_G62_G0.17460.665
24_V76_K0.173970.662
70_S74_H0.171750.654
117_T121_R0.17140.653
66_E91_R0.169930.647
85_D109_S0.169510.645
20_A106_P0.167080.636
100_L107_G0.165880.632
28_V108_I0.165810.631
57_L117_T0.163590.623
121_R124_G0.162480.619
82_E109_S0.161680.616
117_T124_G0.160320.610
38_Q118_R0.15970.608
50_I75_V0.157990.601
42_T68_F0.157790.601
57_L63_V0.157230.599
108_I111_V0.157120.598
64_N81_R0.156230.595
68_F103_H0.156010.594
18_F109_S0.155470.592
41_L100_L0.154980.590
127_K130_I0.154750.589
4_Y106_P0.154710.589
28_V31_N0.154010.586
40_I99_W0.153980.586
45_S121_R0.153870.586
97_D107_G0.153710.585
18_F106_P0.153210.583
64_N89_H0.153020.583
64_N90_W0.152650.581
52_V75_V0.151820.578
6_V33_G0.151460.577
119_K126_M0.151190.576
70_S73_I0.150330.572
15_G19_G0.150250.572
34_M70_S0.148310.565
55_Y61_Y0.148150.564
28_V52_V0.147930.563
75_V78_L0.147520.562
41_L55_Y0.146580.558
24_V130_I0.144870.552
33_G126_M0.144680.551
75_V105_I0.142890.544
105_I122_E0.14220.541
7_L128_G0.142030.541
21_P108_I0.141660.539
26_G51_L0.140810.536
18_F78_L0.140270.534
57_L60_N0.140230.534
14_E122_E0.140120.533
16_K94_M0.139170.530
7_L116_L0.138830.529
13_F111_V0.137440.523
52_V117_T0.135970.518
7_L10_G0.135640.516
38_Q81_R0.134760.513
26_G76_K0.134470.512
2_K92_S0.133720.509
27_E32_T0.133570.509
33_G125_S0.133060.507
24_V122_E0.132880.506
49_Q121_R0.132460.504
106_P130_I0.132250.503
45_S61_Y0.132230.503
64_N69_E0.131150.499
21_P106_P0.130470.497
29_V56_P0.130020.495
17_S97_D0.129820.494
82_E120_L0.129730.494
23_T129_V0.129660.494
30_F34_M0.129220.492
82_E85_D0.128140.488
23_T33_G0.127750.486
2_K99_W0.127570.486
51_L80_V0.126970.483
123_K130_I0.126870.483
17_S81_R0.126780.483
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
1a9xB1100-0.046
1s1mA0.870299.50.74
1vcoA0.923799.40.751
3nvaA0.91698.10.85
4eysA0.992437.90.948
4gimA0.488533.30.95
1vkmA0.465622.70.953
1sg5A0.450421.80.954
1b25A0.900821.60.954
1ftpA0.366421.50.954

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