GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Plasmid_Txe - Plasmid encoded toxin Txe
Pfam: PF06769 (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: CL0136
Length: 80
Sequences: 5764
Seq/Len: 72.05
HH_delta: 0.091 (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
8_D75_S1.422862.984
1_F27_I1.026722.153
5_A73_I1.004762.107
19_L60_H0.897931.883
67_D72_T0.888231.863
53_S61_R0.881181.848
1_F5_A0.85371.790
29_E36_T0.82771.736
22_K57_N0.817151.714
55_R61_R0.814741.709
1_F6_W0.791321.660
48_L51_Y0.787391.651
67_D70_T0.731271.534
51_Y74_L0.727151.525
57_N60_H0.692691.453
65_E72_T0.689431.446
24_N28_K0.667161.399
9_Y24_N0.659321.383
26_L54_R0.652151.368
6_W10_K0.648581.360
9_Y20_L0.612921.285
51_Y65_E0.607831.275
51_Y63_V0.599341.257
42_E53_S0.596711.251
56_I62_L0.580931.218
19_L57_N0.57361.203
65_E74_L0.571271.198
23_I56_I0.569991.195
35_F66_V0.56641.188
20_L24_N0.562661.180
13_K17_K0.554941.164
26_L29_E0.552911.160
27_I62_L0.544411.142
33_N36_T0.536281.125
2_T5_A0.529721.111
12_W19_L0.512761.075
16_D19_L0.510321.070
6_W9_Y0.508131.066
27_I73_I0.49831.045
30_I71_I0.497281.043
52_W64_Y0.495191.039
3_E6_W0.489771.027
44_L63_V0.47661.000
29_E32_R0.467310.980
53_S63_V0.465770.977
43_P52_W0.463350.972
12_W60_H0.457890.960
13_K20_L0.45170.947
54_R64_Y0.429690.901
1_F9_Y0.428910.900
2_T8_D0.427910.897
23_I60_H0.415520.871
38_I53_S0.409890.860
2_T72_T0.407760.855
54_R62_L0.397510.834
42_E55_R0.391750.822
9_Y23_I0.388670.815
28_K31_K0.385360.808
22_K56_I0.383860.805
37_G54_R0.38110.799
60_H76_C0.37960.796
10_K13_K0.378380.794
3_E7_E0.377980.793
43_P49_S0.373210.783
7_E11_Y0.371280.779
9_Y13_K0.370560.777
30_I64_Y0.361460.758
13_K24_N0.353550.741
4_Q7_E0.352020.738
4_Q75_S0.350610.735
37_G64_Y0.342310.718
53_S59_K0.339690.712
46_G51_Y0.325750.683
17_K21_K0.325260.682
62_L76_C0.324960.682
66_V70_T0.323220.678
64_Y71_I0.317610.666
16_D60_H0.311170.653
22_K26_L0.307430.645
12_W76_C0.306370.643
43_P50_G0.301720.633
21_K25_K0.301510.632
19_L23_I0.300270.630
2_T74_L0.300170.630
34_P71_I0.299720.629
38_I54_R0.293110.615
25_K29_E0.292250.613
36_T64_Y0.286770.601
8_D11_Y0.286510.601
26_L64_Y0.284670.597
30_I36_T0.283560.595
30_I73_I0.279960.587
44_L55_R0.276630.580
29_E38_I0.275410.578
25_K28_K0.274030.575
24_N27_I0.271720.570
61_R75_S0.271140.569
17_K20_L0.269220.565
5_A9_Y0.268220.563
35_F68_D0.266270.558
52_W66_V0.263730.553
53_S57_N0.262610.551
5_A8_D0.262580.551
35_F43_P0.258860.543
53_S60_H0.257710.540
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
2a6sA199.20.091
3oeiC199.20.1
1z8mA0.9875990.194
2otrA0.987598.90.214
1wmiA0.9598.70.27
3g5oB0.912598.70.271
4fxiA0.912598.60.307
3bpqB0.92598.60.312
3kxeA0.92598.50.327
2kheA0.912598.50.329

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