GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Prok-JAB - Prokaryotic homologs of the JAB domain
Pfam: PF14464 (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: CL0366
Length: 104
Sequences: 1406
Seq/Len: 13.52
HH_delta: 0.196 (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
22_G65_W0.38032.029
16_Y70_S0.375252.002
35_V38_N0.373311.992
11_H20_A0.373161.991
77_S80_I0.369191.970
47_F51_R0.359151.916
25_L54_A0.355221.895
11_H15_A0.352141.879
15_A20_A0.3321.771
75_P93_I0.312511.667
46_S50_E0.311921.664
15_A18_N0.301851.611
12_A20_A0.286841.530
8_I94_V0.278431.486
64_I83_M0.254421.358
26_G62_V0.251361.341
11_H65_W0.248741.327
19_E66_H0.24281.296
8_I12_A0.239461.278
75_P83_M0.233421.245
34_I39_V0.233211.244
21_C64_I0.230911.232
51_R55_R0.228841.221
32_R37_P0.227811.216
35_V40_N0.227261.213
77_S81_R0.225561.204
83_M91_Y0.222491.187
7_Q10_A0.221891.184
19_E68_H0.221571.182
4_V7_Q0.220191.175
76_S79_D0.21841.165
78_T82_S0.216991.158
46_S49_R0.212171.132
10_A14_A0.21141.128
20_A65_W0.209691.119
9_I13_R0.208421.112
44_R51_R0.208381.112
30_D38_N0.207661.108
4_V24_L0.206511.102
54_A61_I0.206181.100
41_P45_D0.205891.099
34_I38_N0.205361.096
26_G63_G0.204821.093
32_R40_N0.200851.072
17_P67_S0.199211.063
91_Y94_V0.192671.028
30_D35_V0.192361.026
17_P20_A0.191221.020
29_D32_R0.190481.016
53_E57_R0.191.014
64_I91_Y0.189191.009
8_I65_W0.18911.009
49_R67_S0.18761.001
24_L63_G0.18660.996
45_D49_R0.186040.993
18_N23_L0.18350.979
90_S94_V0.18320.978
7_Q37_P0.183060.977
4_V31_Q0.181290.967
10_A13_R0.179880.960
44_R47_F0.177440.947
16_Y20_A0.174750.932
41_P46_S0.174380.930
88_P93_I0.173680.927
25_L55_R0.173640.926
63_G69_P0.173440.925
37_P40_N0.171220.914
88_P91_Y0.170820.911
12_A67_S0.170020.907
46_S51_R0.169650.905
25_L61_I0.167920.896
5_L9_I0.166990.891
37_P57_R0.166730.890
90_S93_I0.164750.879
4_V8_I0.163890.874
64_I89_P0.163880.874
36_V59_L0.159160.849
64_I82_S0.158860.848
25_L34_I0.157160.839
21_C61_I0.156840.837
66_H76_S0.156320.834
31_Q39_V0.156310.834
49_R61_I0.155420.829
42_D45_D0.153910.821
68_H76_S0.153190.817
36_V40_N0.153170.817
8_I22_G0.152430.813
53_E56_E0.14990.800
44_R56_E0.147340.786
47_F50_E0.145750.778
14_A18_N0.145630.777
33_F36_V0.145420.776
67_S83_M0.145370.776
32_R38_N0.144840.773
45_D50_E0.143020.763
49_R54_A0.141840.757
23_L61_I0.140870.752
21_C38_N0.140690.751
25_L58_G0.139940.747
33_F38_N0.139920.747
6_E9_I0.139910.747
41_P49_R0.137330.733
5_L8_I0.136250.727
61_I64_I0.136190.727
11_H14_A0.135530.723
65_W91_Y0.135450.723
63_G75_P0.133670.713
34_I58_G0.133170.711
4_V27_R0.132880.709
43_P46_S0.13270.708
67_S75_P0.131390.701
74_F93_I0.130620.697
35_V63_G0.130260.695
21_C49_R0.130240.695
6_E31_Q0.129960.693
9_I73_A0.129670.692
31_Q34_I0.129640.692
23_L69_P0.12940.690
23_L64_I0.128410.685
30_D33_F0.128360.685
45_D72_P0.127790.682
48_R51_R0.127760.682
68_H79_D0.126010.672
66_H79_D0.125720.671
20_A67_S0.125390.669
89_P94_V0.125310.669
72_P75_P0.123780.660
6_E48_R0.123580.659
42_D46_S0.12310.657
37_P60_E0.122240.652
64_I86_L0.121780.650
43_P50_E0.121690.649
21_C45_D0.121510.648
32_R36_V0.121270.647
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
2kksA0.980899.70.196
2kcqA0.980899.70.213
1oi0A0.961599.60.245
2znrA0.990499.50.315
3rzvA0.990499.50.334
4b4tV199.40.347
4f7oA199.30.407
2o95A0.961598.70.54
2p8rA0.980898.20.616
4b4tU0.961598.20.617

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