GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bactofilin - Polymer-forming cytoskeletal
Pfam: PF04519 (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: 101
Sequences: 1401
Seq/Len: 13.87
HH_delta: 0.766 (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
28_E46_K0.656462.966
12_E28_E0.58642.650
24_D40_G0.570142.576
72_I76_A0.524632.371
95_I99_V0.501172.265
14_D30_N0.488772.209
46_K61_D0.448352.026
26_R44_E0.438131.980
51_A54_V0.429141.939
63_N81_D0.421981.907
76_A93_A0.418861.893
17_S33_A0.392571.774
48_D63_N0.370681.675
50_K65_E0.353941.599
61_D79_E0.352771.594
81_D98_N0.343311.551
10_K26_R0.342271.547
36_K53_D0.341531.543
18_D34_E0.33481.513
57_S73_Y0.332361.502
32_K50_K0.330871.495
25_G58_G0.33061.494
30_N48_D0.330221.492
52_D68_G0.309291.398
54_V66_A0.302061.365
25_G43_G0.299321.353
11_I27_V0.297371.344
44_E59_S0.288051.302
66_A70_V0.284251.284
72_I93_A0.28051.267
57_S75_T0.276861.251
65_E83_T0.274711.241
74_G90_E0.270231.221
16_S32_K0.26441.195
34_E52_D0.255871.156
68_G85_G0.255331.154
79_E96_N0.254591.150
39_I43_G0.249581.128
22_R38_K0.238781.079
81_D97_G0.237051.071
84_A99_V0.236821.070
17_S21_V0.232551.051
63_N80_G0.229671.038
30_N47_G0.227821.029
70_V82_I0.22171.002
37_V51_A0.221411.000
60_V64_V0.220030.994
42_N59_S0.219490.992
24_D42_N0.218060.985
53_D68_G0.216650.979
45_V60_V0.216080.976
7_K42_N0.21490.971
72_I89_V0.214650.970
39_I56_I0.211050.954
73_Y90_E0.207030.935
41_G74_G0.205720.930
88_E91_G0.204950.926
20_D36_K0.202710.916
33_A37_V0.202440.915
89_V99_V0.196830.889
40_G57_S0.196640.889
86_K91_G0.194750.880
31_I45_V0.190590.861
53_D69_K0.188510.852
69_K86_K0.188410.851
56_I78_V0.186810.844
22_R40_G0.18610.841
13_G80_G0.18480.835
5_I10_K0.184760.835
49_I60_V0.184690.835
29_G51_A0.180490.816
54_V70_V0.18040.815
69_K91_G0.179570.811
41_G75_T0.179520.811
89_V95_I0.179230.810
10_K28_E0.1760.795
69_K88_E0.175090.791
89_V93_A0.170870.772
13_G58_G0.167480.757
60_V97_G0.167170.755
26_R46_K0.166330.752
5_I62_G0.165740.749
85_G88_E0.164830.745
74_G91_G0.164390.743
36_K55_I0.164050.741
43_G76_A0.163870.740
24_D90_E0.163240.738
34_E83_T0.162640.735
88_E95_I0.161580.730
64_V78_V0.161460.730
18_D21_V0.161290.729
12_E21_V0.160310.724
12_E16_S0.15950.721
27_V31_I0.159430.720
75_T92_G0.158920.718
8_G18_D0.158360.716
59_S77_R0.158180.715
66_A85_G0.158010.714
15_I27_V0.156660.708
11_I47_G0.155790.704
7_K74_G0.15410.696
4_I12_E0.154050.696
9_T15_I0.152990.691
9_T17_S0.151330.684
32_K37_V0.151190.683
40_G73_Y0.14890.673
16_S65_E0.148310.670
41_G91_G0.148270.670
15_I37_V0.147650.667
10_K18_D0.146650.663
6_G24_D0.146120.660
5_I9_T0.144750.654
4_I10_K0.144750.654
43_G47_G0.144050.651
77_R94_S0.143320.648
7_K10_K0.141590.640
43_G93_A0.140870.637
36_K96_N0.140630.635
37_V54_V0.138440.626
38_K69_K0.137850.623
54_V64_V0.137430.621
87_L98_N0.136510.617
15_I21_V0.136050.615
36_K57_S0.135950.614
5_I83_T0.135430.612
78_V82_I0.135290.611
21_V30_N0.135170.611
69_K89_V0.135170.611
14_D27_V0.134540.608
8_G36_K0.134330.607
8_G53_D0.134190.606
44_E61_D0.134060.606
34_E50_K0.133890.605
8_G77_R0.133590.604
29_G45_V0.133130.602
9_T13_G0.13230.598
81_D87_L0.132040.597
48_D52_D0.13170.595
24_D59_S0.131160.593
5_I17_S0.131040.592
56_I60_V0.130010.587
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
2pigA192.50.766
2pigA0.970390.40.779
2ggoA187.90.789
3c8vA0.970385.60.796
3pmoA185.10.797
3r5dA0.920882.80.802
4eqyA182.30.804
3hsqA0.980276.90.813
3fs8A176.80.813
3eh0A175.10.816
If you are interested in a protein containing this domain,
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