GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CoaE - Dephospho-CoA kinase
Pfam: PF01121 (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: CL0023
Length: 180
Sequences: 7116
Seq/Len: 39.53
HH_delta: 0.001 (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
148_E152_E1.16843.186
135_I138_K0.947482.583
125_E170_F0.938242.558
51_R81_K0.890882.429
33_I36_E0.83462.276
115_F167_R0.834552.276
93_E96_K0.82232.242
78_K81_K0.767462.093
131_A136_R0.734132.002
132_P135_I0.727171.983
147_S150_E0.70821.931
137_I152_E0.701971.914
128_V168_A0.696991.900
10_G140_L0.695641.897
120_E167_R0.692421.888
138_K142_E0.671041.830
47_A50_E0.665991.816
4_G123_C0.662471.806
153_A157_S0.658451.795
5_L17_S0.655341.787
152_E156_A0.65481.785
18_K21_A0.635121.732
93_E97_F0.63351.727
127_I170_F0.625551.706
67_K70_E0.615171.677
19_I22_E0.611911.668
140_L151_A0.606271.653
86_I90_I0.596011.625
81_K84_N0.59131.612
8_G136_R0.588411.604
17_S27_V0.573951.565
149_E153_A0.569131.552
141_M148_E0.550641.501
131_A135_I0.548991.497
130_Y173_D0.547511.493
16_V129_V0.535711.461
49_K57_L0.535361.460
38_Y48_L0.524911.431
47_A89_L0.51991.418
150_E153_A0.51121.394
21_A27_V0.511021.393
44_G89_L0.503161.372
49_K54_E0.501551.368
109_V123_C0.493921.347
11_S136_R0.492271.342
130_Y171_V0.483121.317
81_K85_I0.482721.316
69_A154_R0.480581.310
18_K22_E0.472281.288
51_R78_K0.47171.286
150_E154_R0.47021.282
36_E39_E0.465251.269
4_G124_D0.463791.265
137_I141_M0.461591.259
72_V79_L0.456611.245
58_D64_D0.453871.238
71_I78_K0.451381.231
128_V171_V0.446441.217
133_E152_E0.445641.215
130_Y161_D0.443651.210
25_F108_V0.439331.198
14_S18_K0.438551.196
115_F126_V0.433361.182
32_E36_E0.427071.164
78_K83_E0.424531.158
89_L92_E0.418581.141
29_D32_E0.416611.136
47_A51_R0.411751.123
141_M151_A0.405731.106
45_Y49_K0.398461.086
46_K50_E0.395481.078
136_R155_I0.389631.062
137_I148_E0.387891.058
129_V174_N0.384471.048
133_E156_A0.383851.047
134_E138_K0.380961.039
151_A155_I0.379841.036
33_I93_E0.367771.003
94_I109_V0.366060.998
91_R94_I0.365240.996
6_T128_V0.364510.994
80_K83_E0.364250.993
26_P101_N0.362710.989
46_K49_K0.361280.985
10_G151_A0.359760.981
45_Y63_I0.359710.981
98_I107_V0.358050.976
137_I151_A0.35590.970
153_A156_A0.355620.970
146_L151_A0.354840.968
3_I127_I0.354620.967
49_K53_G0.350990.957
34_A38_Y0.350280.955
17_S110_E0.348920.951
131_A139_R0.341890.932
67_K71_I0.339680.926
125_E169_D0.339330.925
3_I125_E0.339270.925
64_D67_K0.338070.922
11_S131_A0.336720.918
56_I71_I0.335190.914
17_S21_A0.333810.910
36_E93_E0.333530.909
20_L108_V0.330550.901
131_A174_N0.329880.899
43_E47_A0.328930.897
5_L20_L0.328590.896
119_L122_L0.325410.887
80_K84_N0.323520.882
159_M167_R0.32340.882
115_F159_M0.322880.880
133_E137_I0.322140.878
97_F100_R0.322090.878
36_E97_F0.320110.873
5_L16_V0.317660.866
56_I63_I0.317240.865
96_K100_R0.314380.857
48_L52_F0.312310.852
154_R158_Q0.311120.848
92_E96_K0.310880.848
72_V82_L0.309970.845
7_G13_K0.308860.842
168_A171_V0.307110.837
86_I89_L0.306920.837
48_L56_I0.306560.836
19_I23_L0.302470.825
4_G114_L0.301160.821
5_L108_V0.300310.819
14_S31_D0.300030.818
34_A37_L0.29990.818
43_E46_K0.299890.818
8_G155_I0.296260.808
38_Y63_I0.296030.807
136_R161_D0.294730.804
15_T18_K0.292730.798
79_L82_L0.292170.797
63_I68_L0.291510.795
137_I155_I0.28980.790
79_L83_E0.289560.790
3_I106_V0.289510.789
95_E99_K0.288730.787
43_E51_R0.288380.786
2_I109_V0.285690.779
146_L154_R0.285510.779
17_S29_D0.285360.778
30_A94_I0.284930.777
159_M162_E0.282610.771
92_E95_E0.280840.766
2_I123_C0.278430.759
133_E155_I0.277270.756
119_L123_C0.276220.753
66_K70_E0.275370.751
91_R95_E0.275090.750
158_Q162_E0.273670.746
29_D110_E0.271760.741
151_A154_R0.27140.740
2_I98_I0.26980.736
30_A111_I0.269620.735
48_L82_L0.268760.733
6_T126_V0.266020.725
8_G133_E0.264750.722
85_I88_P0.262470.716
35_H38_Y0.262020.714
97_F101_N0.261920.714
52_F78_K0.260740.711
28_I33_I0.260530.710
7_G12_G0.257480.702
11_S161_D0.257290.702
20_L23_L0.25580.697
56_I67_K0.252680.689
108_V111_I0.252490.688
32_E35_H0.250250.682
140_L144_D0.249980.682
117_S120_E0.249020.679
45_Y57_L0.248070.676
146_L150_E0.246990.673
83_E87_H0.246710.673
16_V19_I0.246570.672
37_L86_I0.246540.672
149_E152_E0.24580.670
35_H65_R0.245560.670
83_E86_I0.245480.669
37_L89_L0.244650.667
111_I119_L0.24330.663
156_A160_P0.241460.658
49_K56_I0.240580.656
9_I154_R0.238390.650
158_Q161_D0.238020.649
9_I155_I0.237080.646
48_L51_R0.236870.646
72_V78_K0.234630.640
28_I97_F0.234380.639
20_L127_I0.232160.633
29_D112_P0.229990.627
98_I109_V0.229730.626
137_I140_L0.227280.620
135_I139_R0.226880.619
9_I140_L0.226660.618
156_A159_M0.226380.617
138_K148_E0.225290.614
14_S110_E0.219790.599
25_F106_V0.217450.593
148_E151_A0.217120.592
56_I59_E0.216210.590
79_L157_S0.214990.586
7_G11_S0.213990.583
95_E122_L0.213480.582
13_K139_R0.213460.582
14_S29_D0.213190.581
48_L72_V0.211510.577
102_K105_K0.211290.576
8_G11_S0.209940.572
11_S128_V0.209270.571
133_E162_E0.209030.570
82_L85_I0.208960.570
12_G139_R0.208130.568
52_F56_I0.2070.564
112_P115_F0.206540.563
38_Y45_Y0.206530.563
44_G47_A0.205830.561
38_Y56_I0.20360.555
96_K99_K0.203020.554
38_Y44_G0.203020.554
20_L25_F0.202010.551
55_E71_I0.20050.547
4_G7_G0.198010.540
115_F120_E0.197150.538
55_E59_E0.196640.536
35_H90_I0.196610.536
65_R69_A0.196440.536
2_I107_V0.1950.532
38_Y52_F0.194990.532
134_E148_E0.19460.531
94_I97_F0.194540.530
37_L44_G0.194080.529
138_K141_M0.193380.527
89_L93_E0.192060.524
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
4i1uA0.99441000.001
2f6rA199.90.151
1jjvA0.994499.90.175
2grjA0.888999.90.182
2if2A0.994499.90.209
1vhtA0.994499.90.213
1uf9A0.955699.90.269
1a7jA0.988999.80.349
1uj2A0.911199.80.381
3akeA0.977899.80.392

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