GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TrbC - TrbCVIRB2 family
Pfam: PF04956 (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: 99
Sequences: 560
Seq/Len: 5.66
HH_delta: 0.825 (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
40_S44_K0.296752.096
21_L24_L0.28942.045
70_M89_V0.269611.905
43_C47_D0.256641.813
66_G85_G0.241311.705
24_L47_D0.216211.527
40_S47_D0.21391.511
39_T48_W0.207971.469
66_G88_I0.1981.399
68_M78_W0.197451.395
23_L97_S0.191881.356
25_A29_F0.19091.349
39_T43_C0.186981.321
47_D50_T0.185191.308
58_A86_I0.184741.305
26_S29_F0.18361.297
42_L92_A0.183331.295
19_L26_S0.173751.227
20_A24_L0.172021.215
64_V68_M0.169631.198
20_A25_A0.168791.192
53_I86_I0.167611.184
48_W51_G0.165651.170
25_A45_I0.165171.167
69_M79_F0.162781.150
87_I91_G0.162181.146
24_L29_F0.159991.130
18_A24_L0.159611.128
23_L29_F0.158531.120
34_G47_D0.157261.111
72_G90_F0.156761.107
27_P31_Q0.155631.099
61_A82_V0.153261.083
20_A29_F0.153141.082
19_L22_L0.151411.070
34_G40_S0.151151.068
19_L25_A0.150591.064
40_S43_C0.148931.052
62_I82_V0.148861.052
51_G54_G0.147761.044
21_L47_D0.147081.039
21_L29_F0.144451.020
21_L97_S0.144051.018
55_K90_F0.142341.006
59_I90_F0.140770.994
29_F57_I0.140440.992
54_G81_G0.14030.991
42_L77_R0.140150.990
59_I93_P0.139070.982
70_M85_G0.137920.974
69_M76_W0.137550.972
48_W53_I0.136320.963
43_C63_I0.134980.954
43_C56_A0.134210.948
58_A63_I0.133370.942
66_G89_V0.133130.941
41_F53_I0.131760.931
44_K73_R0.131430.929
93_P96_V0.130390.921
80_I88_I0.130370.921
67_I89_V0.129960.918
36_D41_F0.129840.917
31_Q82_V0.129730.916
75_S95_I0.128120.905
67_I73_R0.127970.904
36_D39_T0.127970.904
19_L34_G0.127290.899
58_A90_F0.125730.888
22_L26_S0.124610.880
43_C46_I0.124330.878
88_I92_A0.123130.870
18_A34_G0.122950.869
63_I76_W0.122810.868
54_G90_F0.121670.860
60_I86_I0.121450.858
55_K88_I0.121320.857
66_G90_F0.121220.856
36_D40_S0.120810.853
29_F60_I0.119510.844
19_L29_F0.11640.822
69_M73_R0.114340.808
22_L29_F0.113960.805
23_L47_D0.11350.802
24_L27_P0.113320.801
24_L31_Q0.113230.800
49_L64_V0.112650.796
38_W48_W0.112470.795
45_I50_T0.112120.792
41_F73_R0.111980.791
26_S40_S0.111960.791
53_I84_I0.111940.791
48_W64_V0.111780.790
42_L56_A0.110060.778
39_T64_V0.109520.774
24_L64_V0.108410.766
19_L23_L0.108260.765
72_G79_F0.107910.762
31_Q40_S0.107480.759
20_A26_S0.107030.756
74_Q78_W0.106860.755
71_F87_I0.106440.752
23_L27_P0.106120.750
42_L71_F0.105090.742
22_L84_I0.104620.739
42_L61_A0.104480.738
37_P72_G0.104080.735
39_T54_G0.104050.735
22_L40_S0.103820.733
65_A75_S0.103010.728
18_A33_G0.102980.728
58_A91_G0.102740.726
44_K95_I0.102240.722
26_S44_K0.101110.714
67_I71_F0.100780.712
22_L27_P0.099960.706
26_S34_G0.099960.706
19_L27_P0.099910.706
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
4hygA0.909170.60.825
4i0uA0.727325.20.867
2iubA0.727323.60.869
4ev6A0.727319.70.874
1fftB0.9596150.88
2b2hA0.86877.40.894
4a01A0.7986.80.896
3kcuA0.96975.90.899
3klyA0.96975.30.901
1ifpA0.444440.906
If you are interested in a protein containing this domain,
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