GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FliD_N - Flagellar hook-associated protein 2 N-terminus
Pfam: PF02465 (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: 964
Seq/Len: 9.74
HH_delta: 0.887 (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
5_D8_S0.802694.831
6_T10_V0.581653.500
74_V89_I0.42372.550
8_S12_Q0.40822.457
36_S39_G0.402442.422
7_E11_D0.348372.096
10_V14_M0.346372.084
35_Q39_G0.326471.965
12_Q15_Q0.30311.824
22_D26_Q0.287181.728
25_Q28_K0.283671.707
64_K78_A0.276881.666
29_T33_W0.272991.643
46_S49_Q0.265931.600
17_E20_P0.262141.578
42_N46_S0.248411.495
14_M18_R0.244741.473
70_N73_V0.227371.368
39_G42_N0.222551.339
15_Q19_A0.220361.326
68_S71_E0.216221.301
14_M21_I0.213841.287
19_A22_D0.210511.267
51_A54_D0.205941.239
20_P23_R0.205721.238
31_L35_Q0.204731.232
82_A85_G0.20251.219
22_D25_Q0.20171.214
53_S57_S0.197711.190
11_D15_Q0.194671.172
20_P24_L0.191031.150
82_A87_Y0.189611.141
68_S73_V0.188451.134
13_L17_E0.184511.110
31_L34_K0.179351.079
4_I9_L0.177681.069
66_A76_V0.175171.054
91_V95_A0.173541.044
48_L52_L0.173021.041
28_K32_E0.171711.033
32_E35_Q0.168161.012
9_L23_R0.167081.005
36_S40_S0.162720.979
21_I97_A0.162310.977
16_A19_A0.159730.961
12_Q16_A0.159220.958
14_M20_P0.158530.954
50_S54_D0.15840.953
12_Q19_A0.156820.944
6_T11_D0.156720.943
14_M64_K0.156060.939
59_S93_Q0.155710.937
13_L70_N0.154670.931
57_S60_T0.153170.922
73_V91_V0.153050.921
2_S13_L0.153020.921
26_Q33_W0.151770.913
12_Q17_E0.149110.897
58_S81_G0.148510.894
83_S89_I0.14810.891
51_A55_L0.1470.885
78_A82_A0.146930.884
8_S11_D0.14680.883
79_T92_N0.14680.883
21_I24_L0.146360.881
27_K80_S0.146350.881
39_G43_S0.145580.876
76_V87_Y0.144620.870
15_Q22_D0.143780.865
51_A65_K0.142190.856
64_K84_A0.14160.852
37_A41_L0.140560.846
18_R21_I0.138630.834
26_Q30_S0.137360.827
55_L87_Y0.136710.823
30_S34_K0.136160.819
19_A24_L0.136050.819
56_N87_Y0.135730.817
77_T84_A0.134150.807
47_T50_S0.133940.806
48_L58_S0.133580.804
6_T9_L0.133430.803
11_D67_T0.132990.800
44_K81_G0.131410.791
21_I25_Q0.130580.786
12_Q18_R0.129050.777
43_S55_L0.128420.773
14_M39_G0.127430.767
42_N55_L0.126850.763
52_L90_E0.126370.760
54_D57_S0.126320.760
66_A85_G0.126240.760
6_T14_M0.126030.758
7_E98_Q0.125530.755
91_V94_L0.125250.754
50_S53_S0.125080.753
75_T86_S0.124690.750
43_S86_S0.123860.745
63_S80_S0.123590.744
4_I16_A0.121950.734
8_S33_W0.121790.733
11_D63_S0.121340.730
33_W36_S0.120320.724
28_K66_A0.119030.716
24_L37_A0.118970.716
65_K69_S0.118450.713
21_I89_I0.116570.702
30_S72_S0.116360.700
40_S48_L0.115860.697
41_L56_N0.115830.697
3_G94_L0.115230.693
15_Q34_K0.114590.690
27_K31_L0.114480.689
64_K93_Q0.114050.686
7_E33_W0.113760.685
31_L38_Y0.113590.684
14_M24_L0.113330.682
46_S50_S0.113040.680
53_S56_N0.112190.675
60_T80_S0.1120.674
6_T61_F0.111920.674
11_D44_K0.111710.672
21_I31_L0.111380.670
44_K48_L0.111230.669
25_Q29_T0.11090.667
15_Q25_Q0.110180.663
16_A20_P0.109860.661
26_Q29_T0.109840.661
41_L82_A0.109780.661
33_W70_N0.109660.660
54_D69_S0.109430.659
24_L27_K0.108790.655
12_Q96_Q0.107960.650
66_A89_I0.107550.647
9_L16_A0.107470.647
21_I38_Y0.107330.646
65_K80_S0.107230.645
83_S96_Q0.107190.645
16_A27_K0.107030.644
36_S94_L0.106810.643
12_Q32_E0.106380.640
15_Q26_Q0.10620.639
36_S47_T0.105740.636
45_L87_Y0.105680.636
61_F89_I0.105650.636
24_L31_L0.10560.635
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
2bnxA0.575822.40.887
1r8dA0.535419.20.89
1fzcC0.888918.50.891
2vz4A0.535413.40.897
3e5nA0.343413.10.897
3tqtA0.383812.50.898
3nmdA0.515212.40.898
2fztA0.464610.90.901
3kinB0.39398.40.905
4b7yA0.41418.30.905
If you are interested in a protein containing this domain,
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