GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ligase_CoA - CoA-ligase
Pfam: PF00549 (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: CL0506
Length: 153
Sequences: 3166
Seq/Len: 20.69
HH_delta: 0.241 (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
130_G134_D0.973023.497
13_D17_D0.963323.463
96_I131_A0.80512.894
66_E70_A0.672812.418
77_I107_R0.600852.160
2_Y8_A0.594812.138
76_V150_A0.58172.091
16_S35_G0.563872.027
145_Q149_A0.559752.012
78_L146_A0.54221.949
127_G130_G0.533161.916
146_A150_A0.528071.898
63_E66_E0.523241.881
139_V142_S0.517061.859
69_A108_K0.502291.805
87_S91_P0.498491.792
62_N66_E0.497681.789
93_A131_A0.494681.778
93_A97_P0.471841.696
58_P97_P0.469341.687
94_G98_A0.452171.625
38_N67_I0.421841.516
59_S64_A0.421121.514
1_L68_E0.404051.452
141_E145_Q0.395171.420
144_A148_R0.394521.418
69_A107_R0.389891.401
97_P101_E0.381731.372
11_A78_L0.379341.364
58_P93_A0.37751.357
90_D93_A0.375861.351
113_A147_A0.369951.330
14_L18_A0.367521.321
13_D39_F0.364471.310
86_G90_D0.362531.303
5_G9_M0.356161.280
66_E101_E0.354711.275
12_M36_P0.354171.273
71_D74_V0.345531.242
33_G43_G0.345011.240
127_G131_A0.337281.212
6_T9_M0.331271.191
16_S36_P0.326591.174
142_S145_Q0.326441.173
59_S63_E0.326011.172
62_N101_E0.321171.154
90_D138_I0.321021.154
4_G43_G0.312321.123
121_D127_G0.308111.107
145_Q148_R0.306011.100
118_T144_A0.302451.087
116_C120_A0.295431.062
1_L65_L0.29521.061
69_A77_I0.283791.020
58_P101_E0.27921.004
86_G91_P0.278251.000
140_A149_A0.27560.991
5_G41_D0.27360.983
97_P100_K0.270730.973
5_G44_G0.270580.973
93_A127_G0.270480.972
133_E139_V0.269850.970
13_D64_A0.268550.965
1_L64_A0.261850.941
11_A80_D0.260570.937
63_E67_I0.260480.936
47_F60_T0.260250.935
95_L99_I0.256540.922
47_F59_S0.246180.885
6_T44_G0.245950.884
38_N41_D0.242060.870
78_L112_V0.241580.868
7_L43_G0.240570.865
44_G84_G0.23940.861
129_A141_E0.239070.859
18_A148_R0.237670.854
87_S90_D0.234990.845
100_K135_A0.234040.841
121_D130_G0.230060.827
64_A67_I0.225010.809
15_I34_G0.224090.805
70_A99_I0.223360.803
15_I36_P0.2230.802
13_D38_N0.222980.801
66_E69_A0.222730.801
68_E74_V0.222670.800
5_G12_M0.222540.800
94_G97_P0.222210.799
65_L77_I0.217720.783
3_N46_A0.216690.779
12_M15_I0.216350.778
8_A12_M0.215710.775
13_D112_V0.215560.775
143_N149_A0.215510.775
142_S146_A0.21350.767
71_D109_K0.211280.759
38_N68_E0.210860.758
18_A144_A0.209150.752
69_A144_A0.208530.750
118_T141_E0.208190.748
9_M12_M0.207860.747
42_L61_R0.206990.744
6_T41_D0.206720.743
142_S149_A0.206430.742
82_V128_Q0.206080.741
120_A129_A0.205380.738
95_L107_R0.204950.737
96_I135_A0.204380.735
72_P109_K0.202960.730
11_A14_L0.202860.729
40_L64_A0.20260.728
89_E131_A0.202530.728
2_Y5_G0.202430.728
129_A138_I0.200280.720
97_P149_A0.19870.714
37_A74_V0.198190.712
130_G133_E0.197940.711
134_D137_V0.197840.711
78_L147_A0.197460.710
138_I141_E0.196220.705
141_E144_A0.195140.701
38_N64_A0.192190.691
69_A109_K0.191930.690
143_N146_A0.191340.688
7_L115_V0.189940.683
79_V95_L0.189190.680
114_R118_T0.188460.677
140_A143_N0.1880.676
138_I149_A0.186190.669
65_L92_A0.185990.669
100_K108_K0.185740.668
107_R111_V0.185660.667
89_E127_G0.185560.667
42_L64_A0.184940.665
146_A149_A0.184430.663
12_M16_S0.184380.663
99_I108_K0.1830.658
96_I100_K0.18260.656
14_L17_D0.18260.656
87_S111_V0.181810.654
62_N79_V0.181450.652
119_N127_G0.180950.650
43_G115_V0.178720.642
140_A146_A0.175870.632
81_I84_G0.173130.622
86_G120_A0.172960.622
2_Y11_A0.172720.621
66_E107_R0.170470.613
36_P40_L0.170370.612
75_K112_V0.169770.610
4_G82_V0.169250.608
70_A101_E0.169150.608
137_V148_R0.168050.604
59_S67_I0.166490.598
87_S127_G0.166430.598
3_N11_A0.166420.598
76_V112_V0.165330.594
137_V142_S0.163550.588
63_E100_K0.162380.584
38_N47_F0.162060.583
11_A15_I0.161960.582
13_D137_V0.161190.579
45_D60_T0.161010.579
41_D46_A0.160790.578
101_E107_R0.160580.577
93_A101_E0.160250.576
87_S137_V0.159990.575
128_Q131_A0.159880.575
99_I138_I0.159660.574
95_L98_A0.159420.573
112_V150_A0.159260.572
138_I142_S0.158840.571
131_A134_D0.157830.567
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
2csuA0.882499.90.241
3ufxB0.790899.80.296
3dmyA0.888999.80.307
2fp4B0.790899.80.332
2nu8B0.790899.80.344
3mwdA0.823599.60.45
3pffA0.810599.40.522
3dmyA0.73298.60.658
2fp4A0.823598.60.658
3mwdB0.803998.60.665

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