GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PTR - Phage tail repeat like
Pfam: PF12789 (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: 60
Sequences: 292
Seq/Len: 4.87
HH_delta: 0.888 (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_T57_D0.685852.829
10_S13_D0.59112.438
13_D16_G0.509832.103
3_A6_S0.431441.780
32_T35_D0.430961.778
12_S15_T0.401391.656
47_A50_N0.384981.588
22_D25_A0.33461.380
40_Q44_N0.331081.366
21_L24_K0.325451.342
10_S16_G0.313951.295
18_Q22_D0.309991.279
20_A23_G0.304661.257
34_A37_T0.298121.230
44_N47_A0.297561.227
43_L46_K0.291281.201
35_D38_G0.286051.180
12_S16_G0.274811.134
11_I17_L0.270541.116
38_G42_T0.267291.103
22_D28_N0.266521.099
44_N50_N0.256781.059
39_L43_L0.249611.030
25_A28_N0.249531.029
23_G26_D0.248861.027
52_T55_I0.246681.018
15_T37_T0.246341.016
42_T45_A0.24611.015
10_S15_T0.244961.010
3_A7_H0.242511.000
22_D27_K0.239980.990
21_L25_A0.239020.986
45_A48_D0.238890.985
17_L21_L0.237270.979
39_L46_K0.235490.971
11_I21_L0.234520.967
31_H36_I0.232260.958
38_G41_T0.231840.956
18_Q23_G0.231720.956
33_I40_Q0.230190.949
51_H54_T0.227780.940
52_T56_S0.225680.931
45_A49_K0.220450.909
45_A50_N0.215960.891
51_H55_I0.215450.889
19_E23_G0.212790.878
11_I18_Q0.210620.869
29_H36_I0.209480.864
29_H39_L0.207660.857
47_A53_H0.20110.830
32_T38_G0.197740.816
3_A8_T0.196630.811
5_K8_T0.194970.804
39_L42_T0.194520.802
44_N49_K0.19390.800
29_H33_I0.192670.795
18_Q21_L0.190030.784
47_A51_H0.189870.783
42_T50_N0.188670.778
14_I17_L0.187660.774
53_H56_S0.187550.774
40_Q45_A0.187330.773
49_K57_D0.187270.772
50_N53_H0.185960.767
13_D18_Q0.182490.753
8_T15_T0.175970.726
30_T36_I0.174850.721
41_T45_A0.174130.718
40_Q46_K0.167810.692
23_G28_N0.167790.692
4_K8_T0.165810.684
52_T57_D0.164280.678
9_H17_L0.163550.675
43_L47_A0.162720.671
3_A14_I0.160130.661
16_G20_A0.159860.659
18_Q24_K0.158210.653
33_I39_L0.157690.650
41_T44_N0.156320.645
35_D46_K0.156210.644
31_H39_L0.155260.640
40_Q47_A0.154130.636
31_H34_A0.152990.631
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:
PDB Cov Prob HH_delta
3p57A0.754.10.888
4h0cA0.38333.40.892
1wlxA12.60.898
1sseB0.68331.90.904
2z4sA0.73331.80.905
3j20M0.41671.70.906
3uq8A0.81671.20.914
4glwA0.81.20.915
3nbxX0.93331.10.916
3uo9A0.88331.10.916
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