GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytidylate_kin2 - Cytidylate kinase-like family
Pfam: PF13189 (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: 179
Sequences: 7223
Seq/Len: 40.35
HH_delta: 0.16 (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
126_F129_E1.468283.589
139_E143_E1.451273.547
129_E133_E1.087612.658
4_I16_A0.953172.330
138_S141_E0.936952.290
132_M139_E0.929752.273
88_I91_E0.885232.164
123_P126_F0.849082.075
143_E147_K0.828212.024
18_R21_E0.806831.972
18_R22_K0.789671.930
128_V143_E0.768121.878
31_E34_E0.741161.812
131_I142_A0.737171.802
84_A87_E0.732141.790
144_K148_K0.726221.775
87_E91_E0.694041.696
128_V132_M0.688271.682
122_A127_R0.681161.665
76_P79_D0.6711.640
124_L143_E0.661471.617
84_A88_I0.653821.598
137_I142_A0.649651.588
46_E49_E0.649561.588
80_K83_R0.620181.516
47_F55_P0.608381.487
124_L147_K0.599851.466
87_E90_R0.589651.441
132_M142_A0.585181.430
141_E144_K0.584811.429
144_K147_K0.578031.413
11_G130_R0.575341.406
9_G131_I0.574821.405
17_E21_E0.568971.391
85_Q89_I0.560951.371
15_I120_I0.554921.356
47_F51_D0.537021.313
79_D83_R0.524981.283
128_V139_E0.522891.278
122_A126_F0.520821.273
81_I85_Q0.50971.246
51_D55_P0.5091.244
10_S122_A0.498081.217
6_R12_G0.497721.217
35_E39_E0.493751.207
75_H78_D0.492871.205
26_P96_G0.488731.195
49_E52_E0.473391.157
16_A27_Y0.469591.148
17_E20_A0.46711.142
86_S90_R0.456521.116
2_I116_L0.451491.104
35_E38_K0.445541.089
90_R94_A0.429811.051
2_I118_V0.427581.045
49_E76_P0.425931.041
7_Q10_S0.423991.036
137_I145_L0.421421.030
7_Q127_R0.420331.027
45_E48_E0.418521.023
13_R17_E0.408630.999
14_E18_R0.407840.997
25_Y100_I0.400020.978
6_R11_G0.399630.977
47_F80_K0.393560.962
79_D82_F0.39240.959
16_A20_A0.392250.959
86_S89_I0.388970.951
6_R10_S0.388890.951
47_F52_E0.387340.947
137_I141_E0.38420.939
15_I19_L0.384090.939
78_D83_R0.383210.937
141_E145_L0.382520.935
88_I92_L0.380670.930
124_L128_V0.379540.928
31_E35_E0.378030.924
9_G142_A0.376270.920
82_F85_Q0.375530.918
125_E129_E0.372710.911
33_I36_A0.371850.909
132_M137_I0.369970.904
125_E143_E0.369660.904
20_A27_Y0.367610.899
10_S127_R0.36420.890
28_Y100_I0.36230.886
51_D54_K0.35980.879
5_S119_F0.359760.879
4_I19_L0.359670.879
44_E48_E0.358730.877
124_L146_I0.357870.875
25_Y97_N0.356920.872
34_E38_K0.353830.865
40_S59_F0.353640.864
142_A146_I0.353610.864
76_P80_K0.352880.863
129_E139_E0.35280.862
11_G14_E0.346170.846
107_Y110_R0.344990.843
105_A108_I0.34430.842
125_E139_E0.34410.841
34_E105_A0.342720.838
5_S117_H0.340770.833
142_A145_L0.338380.827
44_E47_F0.337020.824
35_E105_A0.331950.811
7_Q146_I0.331170.809
102_G115_V0.330850.809
140_E144_K0.330550.808
12_G130_R0.328260.802
3_T115_V0.327570.801
15_I18_R0.326480.798
43_S46_E0.324950.794
3_T108_I0.323860.792
38_K41_G0.323140.790
2_I98_C0.3230.790
128_V142_A0.322270.788
18_R23_L0.321430.786
38_K46_E0.318880.779
39_E42_I0.317760.777
128_V146_I0.317020.775
6_R13_R0.316710.774
16_A104_C0.314710.769
91_E95_K0.314660.769
54_K62_D0.311550.762
32_I36_A0.308950.755
32_I85_Q0.308050.753
82_F86_S0.307930.753
140_E143_E0.30620.748
78_D148_K0.305780.747
78_D81_I0.305760.747
19_L23_L0.304890.745
16_A102_G0.30480.745
129_E132_M0.301450.737
52_E55_P0.300410.734
109_L117_H0.297590.727
28_Y33_I0.297320.727
29_D32_I0.296840.726
33_I85_Q0.296760.725
76_P81_I0.295510.722
40_S45_E0.293070.716
92_L95_K0.289050.707
47_F78_D0.287620.703
26_P92_L0.286540.700
106_N110_R0.286340.700
10_S13_R0.285890.699
77_D81_I0.285180.697
91_E94_A0.284760.696
4_I15_I0.284280.695
48_E51_D0.282610.691
29_D104_C0.281820.689
53_K58_S0.277410.678
83_R86_S0.277030.677
131_I134_R0.275590.674
36_A40_S0.274260.670
100_I109_L0.273970.670
86_S111_D0.270470.661
34_E37_A0.270130.660
6_R30_R0.268990.657
13_R102_G0.268610.657
104_C115_V0.267390.654
131_I135_E0.267190.653
59_F62_D0.265140.648
32_I35_E0.263270.644
58_S61_Y0.262340.641
78_D82_F0.261610.639
106_N109_L0.261270.639
55_P58_S0.260410.637
125_E128_V0.258230.631
51_D81_I0.257740.630
93_A109_L0.256720.628
17_E27_Y0.256620.627
92_L100_I0.252850.618
8_Y146_I0.251370.614
13_R104_C0.250210.612
139_E142_A0.24870.608
33_I86_S0.248270.607
26_P95_K0.247680.605
89_I93_A0.247470.605
6_R16_A0.246850.603
8_Y145_L0.24650.603
20_A32_I0.244760.598
92_L112_I0.243870.596
36_A88_I0.242520.593
77_D80_K0.242240.592
46_E54_K0.241480.590
124_L127_R0.241180.590
126_F130_R0.237730.581
39_E59_F0.237030.579
105_A109_L0.23630.578
131_I145_L0.235940.577
135_E141_E0.23530.575
36_A39_E0.235290.575
110_R117_H0.234940.574
45_E49_E0.234780.574
75_H79_D0.233460.571
38_K60_L0.232580.568
41_G44_E0.231470.566
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
3hdtA0.994499.90.16
3fdiA0.966599.90.184
3r20A0.938599.80.384
4i1uA0.916299.80.391
4e22A0.949799.70.441
3akeA0.927499.60.475
2grjA0.849299.60.481
1jjvA0.916299.60.489
1vhtA0.916299.60.494
2f6rA0.916299.60.497

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