GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SHS2_FTSA - SHS2 domain inserted in FTSA
Pfam: PF02491 (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: CL0319
Length: 80
Sequences: 897
Seq/Len: 11.21
HH_delta: 0.152 (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
23_E27_D0.457292.854
26_V64_I0.41232.573
7_S76_H0.351962.196
9_N76_H0.321282.005
42_R79_T0.313951.959
23_E64_I0.306791.915
6_R42_R0.284821.777
7_S46_H0.262241.637
12_G29_L0.232921.454
60_I68_G0.228141.424
33_A75_V0.225951.410
21_I74_D0.219021.367
66_M72_E0.218321.362
14_V29_L0.208661.302
13_I70_R0.205941.285
29_L32_Q0.203341.269
56_G80_G0.200371.250
1_S46_H0.19951.245
73_V76_H0.198141.237
21_I54_L0.192161.199
60_I70_R0.189591.183
1_S5_I0.189121.180
12_G79_T0.183491.145
5_I78_V0.183411.145
28_R31_E0.183351.144
11_N72_E0.179781.122
51_E74_D0.179491.120
27_D30_L0.178531.114
29_L33_A0.176331.100
60_I66_M0.17551.095
17_E35_R0.174721.090
44_I53_I0.17211.074
1_S59_G0.16851.052
31_E35_R0.167181.043
2_G57_Q0.165641.034
11_N74_D0.164911.029
48_I62_N0.164731.028
68_G71_L0.162711.015
15_S69_S0.16061.002
37_A40_P0.160341.001
14_V68_G0.160070.999
26_V70_R0.159820.997
11_N21_I0.159310.994
55_D68_G0.158560.990
2_G68_G0.156890.979
5_I34_R0.156320.976
40_P43_E0.155860.973
16_I19_R0.155480.970
45_I80_G0.154740.966
16_I21_I0.152120.949
44_I50_Q0.151170.943
15_S32_Q0.151130.943
50_Q75_V0.150850.941
29_L73_V0.150720.941
37_A48_I0.149730.934
24_S27_D0.148410.926
15_S35_R0.144220.900
16_I76_H0.144030.899
17_E74_D0.142680.890
55_D63_P0.141820.885
32_Q69_S0.139790.872
42_R59_G0.13970.872
3_G40_P0.139560.871
6_R24_S0.139480.870
69_S80_G0.13840.864
29_L52_Y0.137770.860
1_S10_S0.1370.855
8_V64_I0.136820.854
30_L62_N0.136520.852
18_G22_T0.135920.848
2_G78_V0.13590.848
46_H76_H0.135370.845
26_V65_G0.134940.842
3_G41_D0.134360.838
47_V78_V0.133730.835
26_V53_I0.133410.833
43_E54_L0.132750.828
12_G32_Q0.130790.816
30_L35_R0.130750.816
26_V52_Y0.130080.812
1_S8_V0.129010.805
1_S7_S0.128130.800
50_Q74_D0.127970.799
46_H57_Q0.126490.789
13_I72_E0.126190.788
4_H80_G0.126160.787
10_S73_V0.125580.784
7_S75_V0.124810.779
10_S75_V0.123470.771
11_N69_S0.12230.763
14_V28_R0.121510.758
38_L79_T0.121090.756
7_S29_L0.120860.754
13_I32_Q0.120590.753
21_I60_I0.120490.752
30_L69_S0.120230.750
24_S74_D0.119910.748
53_I59_G0.119520.746
25_D55_D0.118730.741
11_N19_R0.118490.739
13_I78_V0.117860.736
54_L61_K0.117520.733
12_G77_V0.117460.733
1_S4_H0.116940.730
36_K44_I0.116630.728
11_N48_I0.116530.727
9_N50_Q0.115910.723
15_S45_I0.115870.723
25_D59_G0.115360.720
22_T26_V0.115360.720
69_S77_V0.114750.716
50_Q54_L0.113990.711
6_R40_P0.113840.710
24_S44_I0.11230.701
24_S61_K0.11220.700
27_D36_K0.111580.696
43_E52_Y0.111210.694
30_L78_V0.111150.694
18_G61_K0.110890.692
29_L75_V0.109950.686
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
4a2aA199.60.152
2d0oA0.77598.80.446
1nbwA0.77598.80.447
2ychA0.787594.90.737
4b4tL0.67.90.889
3kw6A0.4756.60.892
2jobA0.46.40.893
1u5tA0.96256.40.893
3imlA0.93755.80.895
3eofA0.9255.70.896

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