GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
phage_tail_N - Prophage tail fibre N-terminal
Pfam: PF08400 (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: CL0287
Length: 134
Sequences: 1738
Seq/Len: 12.97
HH_delta: 0.456 (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
7_G49_Y0.715133.473
44_G48_E0.708343.440
20_C62_L0.576642.800
24_L51_F0.491132.385
108_E116_S0.426812.073
111_A116_S0.399371.939
61_T71_Y0.396841.927
25_K61_T0.372331.808
8_V48_E0.365171.773
59_R71_Y0.36091.753
70_V73_G0.34911.695
17_V20_C0.34671.684
105_R108_E0.325831.582
17_V64_V0.314461.527
61_T69_P0.311081.511
9_L43_T0.306551.489
68_P89_F0.301781.465
8_V85_T0.292861.422
22_I43_T0.290411.410
10_K14_G0.289011.403
24_L58_Y0.286561.392
113_A116_S0.286071.389
19_G40_S0.280031.360
113_A117_A0.278051.350
49_Y84_G0.2771.345
12_G87_N0.276411.342
101_E116_S0.27591.340
41_V51_F0.261351.269
23_T37_T0.258211.254
25_K59_R0.257021.248
106_F116_S0.253771.232
11_D67_R0.253481.231
44_G47_G0.252771.227
92_A95_E0.251791.223
103_L112_Q0.251491.221
21_T40_S0.248111.205
57_V74_D0.244211.186
56_G77_V0.241621.173
43_T47_G0.240721.169
26_A30_S0.240351.167
15_K18_P0.238961.160
105_R113_A0.23851.158
18_P45_E0.234541.139
101_E108_E0.234221.137
19_G45_E0.233421.134
49_Y82_K0.232131.127
4_K50_S0.231661.125
63_K69_P0.231031.122
106_F117_A0.226981.102
11_D15_K0.225461.095
102_V111_A0.222981.083
5_I24_L0.221261.074
10_K87_N0.220351.070
108_E117_A0.219151.064
107_E111_A0.214941.044
111_A118_E0.21391.039
20_C43_T0.212771.033
6_S83_P0.211321.026
108_E115_R0.211051.025
99_R112_Q0.203370.988
40_S108_E0.202060.981
93_P96_D0.201860.980
6_S50_S0.199390.968
57_V76_T0.196870.956
106_F111_A0.196690.955
93_P98_L0.190780.926
10_K16_P0.190290.924
30_S59_R0.190270.924
26_A29_T0.189250.919
27_R74_D0.189120.918
108_E111_A0.187260.909
116_S119_A0.186660.906
104_K110_V0.186130.904
107_E116_S0.183980.893
70_V86_L0.183550.891
100_P113_A0.183010.889
115_R119_A0.178130.865
23_T61_T0.177070.860
84_G88_D0.176750.858
103_L110_V0.176510.857
49_Y87_N0.173120.841
100_P103_L0.172390.837
104_K109_M0.172070.836
104_K108_E0.171750.834
20_C68_P0.170250.827
18_P43_T0.169590.824
38_V58_Y0.168940.820
9_L20_C0.16790.815
48_E86_L0.167080.811
53_V58_Y0.165830.805
4_K79_E0.16570.805
46_A99_R0.163370.793
6_S82_K0.161050.782
40_S65_E0.16080.781
101_E111_A0.160390.779
11_D17_V0.159390.774
102_V113_A0.158760.771
15_K85_T0.158060.768
30_S37_T0.157120.763
39_A99_R0.156270.759
108_E113_A0.155950.757
106_F109_M0.155690.756
49_Y88_D0.155360.754
113_A119_A0.155150.753
27_R59_R0.15430.749
92_A99_R0.152570.741
40_S101_E0.152170.739
74_D82_K0.151580.736
53_V56_G0.151440.735
106_F119_A0.150860.733
104_K111_A0.150760.732
17_V29_T0.149830.728
62_L70_V0.149550.726
102_V116_S0.148390.721
102_V110_V0.147470.716
114_A119_A0.146170.710
21_T65_E0.145970.709
11_D64_V0.145390.706
100_P116_S0.14530.706
4_K18_P0.144910.704
114_A117_A0.144670.703
105_R116_S0.143940.699
105_R109_M0.142850.694
9_L85_T0.142290.691
9_L62_L0.142230.691
65_E96_D0.141860.689
105_R110_V0.141710.688
60_V70_V0.141510.687
29_T37_T0.14080.684
4_K52_D0.140730.683
17_V67_R0.140470.682
93_P111_A0.139610.678
69_P80_D0.138910.675
75_I84_G0.138710.674
110_V113_A0.137650.668
40_S51_F0.136970.665
112_Q115_R0.136150.661
21_T63_K0.135610.659
63_K66_G0.135580.658
101_E104_K0.134420.653
20_C64_V0.133980.651
27_R57_V0.133790.650
7_G11_D0.13370.649
14_G67_R0.133090.646
60_V88_D0.133060.646
103_L113_A0.132110.642
87_N90_L0.131920.641
9_L70_V0.131580.639
102_V119_A0.131230.637
103_L114_A0.131190.637
96_D111_A0.130760.635
12_G52_D0.129790.630
55_P79_E0.129310.628
6_S48_E0.129260.628
75_I78_Y0.128290.623
100_P111_A0.128060.622
14_G87_N0.126710.615
14_G50_S0.126470.614
109_M115_R0.125470.609
24_L53_V0.125320.609
19_G115_R0.125290.608
101_E106_F0.124970.607
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
3mn8A0.70999.20.456
2nsmA0.850799.20.474
1uwyA0.873199.10.496
1h8lA0.6045990.523
4jdzB0.80696.80.742
3e8vA0.611996.80.744
3kcpA0.80696.60.75
3irpX0.820996.20.763
1nkgA0.8731960.766
2boyA0.858295.80.771

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