GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bact_transglu_N - Bacterial transglutaminase-like N-terminal region
Pfam: PF08379 (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: 82
Sequences: 1173
Seq/Len: 14.3
HH_delta: 0.133 (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
54_D58_N0.477312.416
7_R73_T0.43532.203
23_L63_F0.414942.100
9_R71_E0.402122.035
38_W78_S0.382931.938
7_R75_E0.375721.902
11_R71_E0.369791.872
9_R73_T0.365651.851
3_R77_T0.339431.718
5_R77_T0.335481.698
37_S79_E0.33071.674
15_P70_K0.321991.630
1_R79_E0.307571.557
51_E61_H0.305111.544
3_R79_E0.303621.537
33_Q80_V0.302241.530
10_Y21_H0.293671.486
36_L79_E0.283491.435
36_L81_E0.283251.434
5_R75_E0.283221.433
2_Y82_T0.273771.386
52_Y60_V0.255391.293
17_S68_P0.254321.287
65_F69_H0.250351.267
29_S34_R0.247351.252
35_V38_W0.240211.216
26_T51_E0.239861.214
40_L61_H0.236781.198
42_I63_F0.234151.185
41_T77_T0.232421.176
26_T61_H0.231911.174
41_T75_E0.225511.141
22_R60_V0.219831.113
33_Q82_T0.215741.092
34_R81_E0.215461.090
18_L69_H0.211891.072
49_V63_F0.209681.061
23_L74_I0.206021.043
63_F69_H0.203481.030
22_R63_F0.201611.020
4_I10_Y0.201541.020
21_H55_F0.199761.011
8_T12_Y0.19690.997
26_T38_W0.196860.996
41_T45_E0.191610.970
15_P67_E0.19040.964
26_T59_R0.189990.962
16_V72_L0.188640.955
19_S69_H0.1860.941
35_V80_V0.182350.923
1_R36_L0.181860.920
35_V78_S0.179940.911
25_L56_F0.179560.909
6_H12_Y0.175940.890
1_R81_E0.173060.876
12_Y21_H0.169410.857
46_P67_E0.168390.852
6_H16_V0.166330.842
21_H72_L0.166040.840
17_S70_K0.165890.840
28_R32_G0.165740.839
39_S77_T0.164030.830
43_E75_E0.163670.828
20_P62_R0.160880.814
54_D57_G0.160720.813
18_L72_L0.159930.809
40_L74_I0.159360.807
49_V61_H0.159240.806
4_I33_Q0.158850.804
11_R36_L0.156210.791
8_T16_V0.156160.790
4_I80_V0.155650.788
14_A18_L0.154360.781
20_P64_S0.153760.778
5_R28_R0.152660.773
40_L76_A0.152390.771
2_Y62_R0.152160.770
12_Y27_P0.151980.769
23_L61_H0.151390.766
24_R60_V0.151070.765
51_E59_R0.150740.763
4_I72_L0.150240.760
62_R66_P0.149810.758
4_I78_S0.149490.757
31_P34_R0.148350.751
18_L62_R0.14490.733
5_R41_T0.144870.733
48_R66_P0.14450.731
6_H10_Y0.14380.728
48_R56_F0.143640.727
44_P60_V0.14320.725
28_R58_N0.142880.723
32_G82_T0.142710.722
12_Y81_E0.142110.719
44_P69_H0.139580.706
53_T57_G0.139510.706
50_R67_E0.139390.705
35_V72_L0.138790.702
26_T35_V0.138590.701
22_R62_R0.138350.700
24_R52_Y0.137570.696
12_Y19_S0.136630.691
26_T40_L0.13650.691
37_S77_T0.136470.691
76_A80_V0.135230.684
25_L61_H0.134640.681
2_Y52_Y0.134520.681
27_P33_Q0.134120.679
32_G55_F0.133410.675
29_S59_R0.13320.674
15_P39_S0.13310.674
69_H72_L0.132690.672
52_Y62_R0.132670.671
56_F76_A0.131580.666
42_I46_P0.130920.663
3_R37_S0.130510.661
27_P76_A0.130340.660
1_R19_S0.130150.659
6_H74_I0.129190.654
13_D53_T0.129120.653
14_A29_S0.129010.653
24_R27_P0.128840.652
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
3isrA0.93999.60.133
1dnvA0.71955.60.888
2l1aA0.40243.50.898
4e8dA0.92683.40.899
3prxB0.9393.20.9
2k9uA0.4392.80.902
3dwlD0.73172.80.903
2dj4A0.39022.60.904
3hrzA0.95122.40.906
2qh9A0.42682.40.906

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