GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SseB - SseB protein N-terminal domain
Pfam: PF07179 (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: 124
Sequences: 560
Seq/Len: 4.52
HH_delta: 0.829 (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
27_E86_V0.157921.715
73_E110_T0.157221.708
22_A26_A0.156241.697
67_V106_I0.152691.658
91_D94_E0.149141.620
67_V121_I0.146361.590
28_V67_V0.14321.555
64_Y103_G0.139921.520
73_E76_K0.135861.476
75_E79_P0.130141.413
106_I114_F0.128471.395
55_T63_R0.126121.370
114_F120_E0.122861.334
24_L93_L0.121721.322
70_S107_N0.121251.317
51_I87_V0.12091.313
36_D93_L0.118621.288
88_P91_D0.115871.258
103_G114_F0.113281.230
14_E26_A0.111621.212
23_L89_F0.111071.206
16_E19_F0.110411.199
19_F107_N0.110391.199
16_E26_A0.109221.186
71_W75_E0.107891.172
74_L77_W0.107661.169
114_F121_I0.106061.152
67_V104_I0.104721.137
96_L116_L0.104331.133
21_E25_K0.102691.115
18_A50_E0.102191.110
76_K110_T0.101231.099
69_T117_P0.101191.099
53_F65_L0.100991.097
86_V96_L0.100681.094
51_I55_T0.100471.091
79_P96_L0.100151.088
49_S62_E0.100061.087
30_V96_L0.099721.083
102_D106_I0.098781.073
14_E61_G0.098541.070
37_D75_E0.097131.055
35_D51_I0.096481.048
35_D60_D0.096311.046
51_I93_L0.09611.044
69_T79_P0.095891.041
117_P121_I0.095761.040
26_A71_W0.095631.039
105_V115_V0.095021.032
86_V90_E0.093551.016
31_P74_L0.093151.012
101_G118_R0.093061.011
31_P105_V0.092511.005
20_L114_F0.092391.003
103_G120_E0.091670.996
31_P107_N0.091570.995
78_Y107_N0.091110.990
13_E26_A0.090680.985
70_S80_D0.090330.981
72_E75_E0.08980.975
30_V94_E0.089370.971
68_F77_W0.089260.969
74_L84_I0.089230.969
72_E100_E0.088940.966
31_P57_E0.088440.961
57_E63_R0.088370.960
69_T114_F0.088130.957
88_P99_N0.087820.954
84_I89_F0.08760.951
89_F104_I0.087280.948
69_T86_V0.087250.948
15_D18_A0.085940.933
19_F105_V0.085760.931
26_A34_V0.085210.925
35_D117_P0.085180.925
89_F92_L0.085050.924
53_F61_G0.084950.923
30_V34_V0.08480.921
57_E105_V0.084690.920
118_R122_E0.084540.918
20_L120_E0.084370.916
54_L76_K0.084070.913
106_I115_V0.083110.903
75_E122_E0.082520.896
81_E107_N0.082220.893
60_D102_D0.081940.890
32_V37_D0.08160.886
14_E106_I0.081370.884
27_E78_Y0.081090.881
22_A25_K0.080850.878
18_A64_Y0.080790.877
28_V55_T0.080620.876
24_L122_E0.080430.874
73_E103_G0.080380.873
31_P65_L0.079530.864
63_R111_P0.07950.863
53_F99_N0.079340.862
26_A64_Y0.079190.860
66_P104_I0.078940.857
30_V99_N0.078860.857
55_T70_S0.078840.856
117_P122_E0.078820.856
21_E53_F0.07860.854
20_L121_I0.078550.853
21_E110_T0.077940.847
14_E50_E0.077850.846
25_K104_I0.077820.845
60_D88_P0.07780.845
31_P78_Y0.077750.844
87_V99_N0.077640.843
19_F57_E0.077470.841
27_E85_I0.077450.841
32_V89_F0.077260.839
24_L104_I0.077250.839
67_V103_G0.077130.838
16_E115_V0.07660.832
33_D52_Q0.076570.832
105_V109_G0.076140.827
59_P90_E0.075760.823
57_E93_L0.075510.820
24_L120_E0.07540.819
19_F78_Y0.075380.819
93_L107_N0.075350.818
54_L116_L0.075110.816
95_M100_E0.075070.815
54_L99_N0.074840.813
25_K117_P0.074440.809
87_V92_L0.07440.808
54_L122_E0.074270.807
19_F67_V0.074250.806
72_E111_P0.074070.804
119_E122_E0.073160.795
36_D57_E0.073140.794
92_L104_I0.072930.792
57_E81_E0.072850.791
28_V37_D0.072650.789
19_F23_L0.072570.788
73_E78_Y0.072530.788
18_A21_E0.072450.787
60_D100_E0.072170.784
23_L28_V0.072120.783
28_V62_E0.072060.783
107_N110_T0.072040.782
70_S105_V0.072030.782
30_V51_I0.072010.782
59_P67_V0.071670.778
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
4ev1A0.798486.30.829
3g0tA0.919435.40.88
3ihjA0.911334.80.88
3dydA0.911331.70.882
3tcmA0.959730.50.883
3rq1A0.9113270.886
3jtxA0.9113250.888
3ffhA0.911323.80.889
3ezsA0.911323.40.889
3kaxA0.911323.20.89
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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