GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TnpB_IS66 - IS66 Orf2 like protein
Pfam: PF05717 (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: 107
Sequences: 687
Seq/Len: 6.42
HH_delta: 0.929 (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
37_L50_I0.408262.796
15_K19_G0.40492.773
15_K23_L0.348522.387
65_L70_F0.342052.343
18_D64_R0.318942.184
51_L58_F0.312.123
52_Y61_Y0.307942.109
39_V50_I0.303022.075
59_W63_K0.272881.869
89_L93_L0.267191.830
41_C45_R0.260411.784
17_I58_F0.252411.729
31_D34_S0.25161.723
53_W66_E0.251121.720
16_G55_G0.244951.678
5_Y36_D0.241061.651
37_L63_K0.230361.578
34_S38_F0.227361.557
41_C72_W0.225071.542
90_S94_E0.215041.473
5_Y8_C0.211611.449
47_R62_Y0.210911.445
91_W96_I0.197091.350
88_Q91_W0.193761.327
96_I103_R0.192821.321
100_R103_R0.188761.293
11_V20_L0.187691.286
22_A26_E0.181871.246
43_R65_L0.181121.241
28_L97_D0.178361.222
42_N59_W0.173111.186
53_W58_F0.172821.184
58_F62_Y0.172571.182
17_I91_W0.17131.173
18_D62_Y0.167071.144
52_Y59_W0.164181.125
88_Q92_L0.164131.124
7_A11_V0.163291.118
87_E91_W0.163291.118
72_W92_L0.158531.086
46_D53_W0.158471.085
4_I19_G0.154961.061
42_N51_L0.148851.020
9_G13_M0.14861.018
26_E29_G0.145971.000
92_L95_G0.145320.995
28_L41_C0.140270.961
44_R47_R0.139450.955
27_E36_D0.136910.938
39_V53_W0.135480.928
47_R67_R0.135260.926
46_D66_E0.134220.919
17_I62_Y0.133430.914
29_G38_F0.13290.910
13_M68_G0.131730.902
85_T94_E0.130570.894
54_D86_W0.129780.889
4_I39_V0.129250.885
82_V99_R0.128910.883
16_G20_L0.128230.878
18_D38_F0.128150.878
13_M43_R0.127240.871
57_G95_G0.127080.870
18_D23_L0.127030.870
89_L103_R0.126850.869
42_N46_D0.126270.865
2_V35_G0.124140.850
7_A28_L0.12340.845
43_R70_F0.122150.837
54_D59_W0.120930.828
37_L61_Y0.120920.828
35_G63_K0.119650.820
48_I70_F0.119570.819
18_D51_L0.119460.818
84_L88_Q0.119370.818
88_Q98_W0.11920.816
24_V56_D0.119150.816
17_I51_L0.117470.805
42_N61_Y0.117470.805
49_K64_R0.117440.804
3_R36_D0.117350.804
53_W56_D0.11710.802
6_L9_G0.1160.795
43_R77_E0.115930.794
24_V39_V0.11590.794
9_G49_K0.114730.786
55_G63_K0.113610.778
56_D63_K0.113250.776
29_G67_R0.113180.775
24_V28_L0.111730.765
11_V53_W0.111140.761
27_E103_R0.110650.758
44_R67_R0.110040.754
32_P55_G0.109870.753
5_Y30_L0.109820.752
43_R48_I0.109630.751
7_A39_V0.109220.748
48_I65_L0.109220.748
27_E31_D0.109190.748
4_I56_D0.108990.746
18_D28_L0.108810.745
10_P29_G0.108780.745
53_W62_Y0.108460.743
10_P42_N0.108280.742
91_W103_R0.108190.741
20_L40_F0.107830.739
7_A18_D0.107560.737
44_R97_D0.107520.736
68_G90_S0.107520.736
45_R71_K0.107310.735
16_G47_R0.106860.732
63_K66_E0.106720.731
22_A69_R0.106230.728
50_I78_E0.105360.722
47_R55_G0.104710.717
3_R35_G0.104640.717
22_A25_R0.104560.716
11_V19_G0.104420.715
53_W65_L0.104120.713
10_P78_E0.10340.708
6_L23_L0.103190.707
9_G21_A0.10290.705
35_G41_C0.102710.703
10_P70_F0.10250.702
24_V30_L0.102220.700
2_V37_L0.101970.698
46_D62_Y0.101920.698
42_N101_V0.10150.695
85_T90_S0.101170.693
23_L27_E0.10090.691
25_R33_F0.100470.688
30_L47_R0.10010.686
25_R31_D0.099890.684
92_L98_W0.099780.683
17_I20_L0.099420.681
34_S59_W0.099380.681
36_D59_W0.098810.677
96_I99_R0.098530.675
27_E39_V0.098360.674
23_L83_E0.097830.670
72_W98_W0.097680.669
71_K82_V0.097590.668
78_E83_E0.097540.668
51_L62_Y0.097220.666
15_K33_F0.09710.665
6_L44_R0.097070.665
51_L57_G0.096850.663
17_I38_F0.09660.662
71_K98_W0.096470.661
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
3zh9B0.934623.80.929
3lyvA0.607521.40.93
3ka5A0.598118.80.932
3vtvA0.598116.70.933
3k2tA0.532716.70.933
3vtwA0.598116.60.933
2nqwA0.598115.20.934
1eo6A0.616814.70.935
2rk5A0.626213.70.936
1oegA0.24312.80.936
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.016 seconds.