GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RsbRD_N - RsbT co-antagonist protein rsbRD N-terminal domain
Pfam: PF14361 (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: 105
Sequences: 549
Seq/Len: 5.23
HH_delta: 0.516 (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
10_R46_D0.192921.939
65_E68_E0.173721.746
70_L91_V0.173641.745
9_H101_R0.173251.741
9_H12_A0.172781.737
17_W94_L0.170491.714
14_L94_L0.16821.691
39_Q73_L0.165911.668
73_L90_F0.157591.584
92_F95_K0.156611.574
70_L74_S0.156151.570
84_P88_A0.152771.536
90_F99_F0.147091.479
90_F95_K0.138971.397
4_E8_E0.138161.389
70_L92_F0.133271.340
16_R100_E0.131411.321
70_L95_K0.130031.307
4_E53_E0.127271.279
44_V90_F0.126481.271
70_L97_P0.125861.265
45_L94_L0.124891.255
80_Q86_E0.12471.253
74_S78_A0.123251.239
17_W99_F0.119581.202
78_A91_V0.119481.201
44_V80_Q0.119191.198
39_Q42_N0.119111.197
63_W97_P0.116841.174
26_P43_P0.115261.159
73_L91_V0.115221.158
2_L7_R0.114081.147
17_W95_K0.113741.143
9_H34_E0.111451.120
71_E96_R0.109161.097
43_P76_I0.107731.083
83_T86_E0.105491.060
33_S36_E0.105191.057
19_E35_K0.105181.057
74_S95_K0.104531.051
74_S87_T0.104411.050
21_V74_S0.103261.038
40_F74_S0.102911.034
8_E65_E0.102291.028
87_T92_F0.101931.025
85_S96_R0.101681.022
16_R101_R0.10111.016
7_R71_E0.10031.008
42_N90_F0.099350.999
20_A97_P0.099270.998
88_A97_P0.099080.996
41_A50_A0.098190.987
15_D46_D0.097980.985
15_D19_E0.097970.985
75_R79_V0.097740.982
6_L50_A0.09590.964
36_E80_Q0.095890.964
87_T95_K0.095410.959
77_R90_F0.095330.958
76_I80_Q0.094680.952
89_S93_A0.09420.947
48_L55_G0.093920.944
39_Q90_F0.093750.942
12_A75_R0.093580.941
12_A15_D0.093060.935
40_F95_K0.092940.934
40_F76_I0.092920.934
23_A54_S0.092080.926
17_W82_F0.091940.924
33_S96_R0.091860.923
61_P66_L0.091570.920
65_E72_E0.091490.920
52_L69_A0.090110.906
9_H43_P0.089830.903
15_D50_A0.08950.900
42_N46_D0.089440.899
91_V95_K0.089350.898
40_F69_A0.089260.897
99_F103_Q0.089120.896
77_R95_K0.088970.894
77_R82_F0.088570.890
7_R53_E0.088540.890
69_A76_I0.088540.890
7_R49_A0.088230.887
30_D103_Q0.088140.886
68_E98_L0.087590.880
21_V41_A0.087440.879
15_D38_R0.087210.877
4_E61_P0.08680.872
86_E101_R0.086280.867
17_W90_F0.086210.867
6_L66_L0.085690.861
82_F90_F0.085640.861
24_S82_F0.08550.859
23_A64_E0.085390.858
87_T90_F0.085250.857
6_L51_A0.084570.850
90_F94_L0.084520.850
83_T94_L0.083930.844
14_L61_P0.083650.841
12_A68_E0.083420.839
42_N73_L0.083170.836
7_R50_A0.0830.834
66_L91_V0.082580.830
81_G88_A0.082530.830
8_E72_E0.082380.828
64_E79_V0.082260.827
84_P99_F0.082090.825
91_V99_F0.082080.825
52_L55_G0.081680.821
17_W44_V0.081070.815
4_E12_A0.080820.812
12_A64_E0.080760.812
29_T37_L0.080720.811
26_P64_E0.080650.811
2_L9_H0.080620.810
49_A103_Q0.080520.809
40_F44_V0.080310.807
82_F86_E0.079620.800
17_W73_L0.078560.790
13_I94_L0.078190.786
32_F42_N0.078060.785
55_G81_G0.077880.783
37_L40_F0.077720.781
44_V76_I0.077570.780
11_E14_L0.077540.779
77_R86_E0.077310.777
34_E38_R0.07720.776
28_R31_R0.077120.775
4_E7_R0.07710.775
82_F94_L0.07710.775
17_W74_S0.077070.775
30_D78_A0.076990.774
14_L18_L0.076720.771
74_S91_V0.076620.770
70_L87_T0.076570.770
50_A53_E0.076480.769
6_L56_L0.076360.768
44_V94_L0.076260.767
40_F92_F0.076210.766
20_A100_E0.076120.765
93_A98_L0.075560.760
55_G70_L0.075110.755
28_R78_A0.074950.753
13_I100_E0.074880.753
6_L25_Y0.074580.750
69_A91_V0.074330.747
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
2bnlA0.923898.10.516
3pmdA0.914396.90.638
1ykuA0.914396.80.643
1or4A0.933391.80.736
2w31A0.942990.90.742
1xg0C0.942984.80.767
2vmlA0.942983.10.771
2vmlB0.952482.80.772
1kn1A0.942979.70.779
2c7lB0.942976.20.785
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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