GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LytR_C - LytR cell envelope-related transcriptional attenuator
Pfam: PF13399 (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: 90
Sequences: 1102
Seq/Len: 12.24
HH_delta: 0.849 (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_E58_R0.485592.710
64_L82_V0.44612.489
49_Y57_A0.417032.327
12_T17_L0.396642.213
30_F60_L0.351351.960
6_V25_L0.349151.948
60_L80_V0.332511.855
10_N16_G0.299461.671
14_V17_L0.289641.616
13_G17_L0.283921.584
7_E81_V0.277941.551
11_G38_A0.26411.474
22_A32_V0.255091.423
25_L30_F0.255031.423
10_N18_A0.251161.401
13_G41_S0.247921.383
7_E33_V0.245481.370
5_R33_V0.241071.345
22_A35_V0.239741.338
22_A26_R0.238891.333
11_G42_D0.231431.291
11_G83_V0.230991.289
9_L38_A0.228781.277
28_R63_A0.224181.251
53_D56_A0.222931.244
45_T67_A0.220371.230
13_G86_K0.21831.218
50_G81_V0.215071.200
48_Y83_V0.214931.199
49_Y69_I0.212841.188
23_D27_N0.210771.176
30_F63_A0.210121.172
50_G53_D0.207811.160
9_L36_G0.207161.156
11_G48_Y0.203491.135
18_A37_N0.200731.120
45_T66_G0.199721.114
8_V22_A0.195611.091
60_L82_V0.194671.086
9_L81_V0.192381.073
58_R61_A0.190071.061
49_Y71_V0.189451.057
57_A61_A0.188881.054
47_I82_V0.188041.049
49_Y54_E0.183971.027
7_E79_D0.182381.018
38_A83_V0.182071.016
5_R79_D0.181161.011
23_D26_R0.180191.005
12_T41_S0.179381.001
45_T87_D0.178360.995
72_D75_R0.17480.975
5_R31_T0.173370.967
17_L84_L0.172160.961
50_G79_D0.168450.940
10_N37_N0.166040.926
16_G19_A0.165670.924
59_E63_A0.163510.912
30_F59_E0.162610.907
5_R48_Y0.160520.896
17_L88_F0.159620.891
21_V84_L0.159610.891
26_R31_T0.159610.891
17_L21_V0.157340.878
59_E62_A0.155790.869
9_L37_N0.155070.865
75_R81_V0.152510.851
48_Y81_V0.152070.849
24_A60_L0.149780.836
13_G85_G0.144950.809
19_A23_D0.144590.807
46_T49_Y0.144370.806
71_V80_V0.144160.804
7_E34_E0.144140.804
13_G42_D0.144110.804
61_A67_A0.141840.791
32_V35_V0.141720.791
4_V56_A0.140610.785
21_V66_G0.140590.784
17_L20_R0.139840.780
45_T64_L0.139050.776
5_R26_R0.137810.769
43_E86_K0.135570.756
28_R40_S0.135190.754
21_V28_R0.134790.752
10_N17_L0.134260.749
12_T84_L0.134190.749
47_I66_G0.134180.749
4_V59_E0.133960.747
11_G85_G0.133760.746
19_A34_E0.131740.735
18_A22_A0.131060.731
16_G37_N0.130640.729
13_G29_G0.130150.726
20_R54_E0.129730.724
56_A80_V0.12960.723
10_N14_V0.129060.720
36_G83_V0.129010.720
26_R32_V0.128430.717
84_L89_Q0.127470.711
3_D45_T0.127420.711
33_V79_D0.127370.711
24_A86_K0.127120.709
33_V74_D0.1270.709
42_D60_L0.126910.708
33_V53_D0.126430.705
61_A82_V0.126210.704
21_V38_A0.12610.704
8_V63_A0.125230.699
9_L32_V0.124840.697
27_N82_V0.124560.695
50_G88_F0.124120.693
61_A68_E0.123610.690
8_V18_A0.123120.687
71_V86_K0.123020.686
23_D35_V0.121670.679
14_V33_V0.121440.678
45_T75_R0.121160.676
47_I69_I0.120990.675
20_R43_E0.120050.670
6_V24_A0.119680.668
6_V65_G0.119440.666
4_V19_A0.118980.664
30_F75_R0.118830.663
28_R44_T0.118610.662
4_V66_G0.118050.659
60_L63_A0.118010.658
7_E75_R0.11790.658
69_I79_D0.117830.657
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
3c5yA0.844434.80.849
2re1A0.722231.20.853
2f06A0.877829.50.854
2r6zA0.488928.40.855
3s5pA0.811122.40.862
3dm5A0.920.30.865
3iwhA0.555618.10.867
4ix1A0.977817.20.869
2dt9A0.9444170.869
3flhA0.611116.90.869
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