GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Flagellin_N - Bacterial flagellin N-terminal helical region
Pfam: PF00669 (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: 139
Sequences: 2687
Seq/Len: 19.33
HH_delta: -0.002 (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
109_A113_Q0.874073.267
88_A112_L0.871143.256
81_I119_L0.835223.121
87_R111_E0.755672.824
127_Q132_Y0.723822.705
33_K40_D0.640322.393
114_Q117_D0.628412.349
87_R91_L0.618292.311
55_S90_E0.583052.179
84_I119_L0.555752.077
23_K27_Q0.545012.037
34_I43_A0.538982.014
59_Q62_R0.529681.980
101_S104_D0.522311.952
118_Q121_Q0.519491.941
91_L111_E0.513961.921
88_A115_L0.492551.841
26_E36_S0.467921.749
127_Q130_G0.466871.745
84_I115_L0.464731.737
77_A126_T0.462481.728
87_R90_E0.44421.660
109_A112_L0.435321.627
102_D106_Q0.432481.616
103_E106_Q0.425311.589
106_Q110_A0.421891.577
108_I112_L0.41181.539
95_A108_I0.404231.511
98_G105_R0.397971.487
84_I122_I0.391861.464
80_S83_D0.381981.428
40_D43_A0.38151.426
34_I39_D0.374361.399
81_I84_I0.371311.388
113_Q116_L0.369031.379
86_Q89_R0.367811.375
48_L51_R0.36751.373
77_A122_I0.366911.371
120_N124_N0.362071.353
89_R93_V0.351221.313
94_Q108_I0.350451.310
116_L120_N0.349621.307
59_Q90_E0.346431.295
104_D107_A0.344061.286
16_K20_N0.339641.269
12_N16_K0.332681.243
34_I47_A0.330761.236
17_L21_L0.329991.233
121_Q125_N0.32821.227
132_Y135_S0.321861.203
49_S104_D0.321711.202
84_I118_Q0.321311.201
7_Y11_L0.321031.200
11_L15_N0.318971.192
107_A110_A0.318861.192
62_R66_D0.31391.173
91_L108_I0.31141.164
13_N30_T0.310591.161
92_A96_A0.310131.159
100_N104_D0.30351.134
79_S83_D0.302021.129
82_S86_Q0.299121.118
58_E61_Q0.290451.085
80_S122_I0.288061.077
83_D86_Q0.284931.065
113_Q117_D0.281031.050
17_L20_N0.279481.044
57_L61_Q0.278311.040
78_L81_I0.277071.035
95_A105_R0.273731.023
59_Q63_N0.272891.020
68_K72_S0.268351.003
97_N100_N0.264220.987
93_V96_A0.264080.987
5_S9_N0.26390.986
21_L25_Q0.261540.977
81_I122_I0.258890.968
26_E35_N0.252460.944
42_A46_R0.249630.933
45_S129_N0.249030.931
124_N135_S0.247990.927
6_I25_Q0.242140.905
26_E30_T0.241110.901
33_K43_A0.240680.899
123_A134_F0.238240.890
88_A116_L0.235560.880
6_I22_N0.234580.877
24_L27_Q0.233710.873
9_N12_N0.232160.868
3_T51_R0.23150.865
61_Q65_D0.231060.864
77_A81_I0.229720.859
53_Q57_L0.229260.857
30_T35_N0.228890.855
95_A109_A0.227880.852
77_A134_F0.22740.850
115_L118_Q0.226690.847
91_L94_Q0.223460.835
64_I68_K0.219980.822
23_K26_E0.217420.813
120_N123_A0.217320.812
7_Y10_A0.215940.807
2_S32_K0.215370.805
16_K19_S0.211040.789
100_N105_R0.211020.789
55_S59_Q0.210930.788
45_S50_L0.210030.785
100_N107_A0.208560.779
101_S130_G0.208310.779
54_I121_Q0.207580.776
55_S86_Q0.207210.774
127_Q131_R0.205840.769
64_I67_A0.204970.766
74_A133_L0.204850.766
2_S5_S0.203820.762
6_I10_A0.202170.756
101_S107_A0.200710.750
35_N39_D0.20040.749
69_S128_F0.198920.743
100_N108_I0.195930.732
21_L24_L0.19320.722
87_R115_L0.192750.720
111_E115_L0.192650.720
32_K89_R0.192370.719
124_N132_Y0.188630.705
41_P44_A0.188430.704
34_I40_D0.187880.702
50_L54_I0.186950.699
19_S22_N0.186930.699
81_I85_L0.186880.698
86_Q93_V0.184930.691
45_S93_V0.183610.686
86_Q97_N0.183330.685
22_N25_Q0.183180.685
74_A77_A0.182540.682
12_N15_N0.18220.681
81_I123_A0.18190.680
96_A99_T0.181560.679
117_D124_N0.181380.678
120_N134_F0.181140.677
88_A92_A0.17980.672
95_A98_G0.178660.668
73_T128_F0.177750.664
19_S23_K0.177240.662
44_A48_L0.177240.662
13_N26_E0.177060.662
50_L129_N0.176620.660
51_R55_S0.176430.659
88_A119_L0.174970.654
71_L75_E0.17490.654
85_L88_A0.173630.649
132_Y136_G0.173530.649
91_L115_L0.173420.648
101_S106_Q0.173210.647
116_L123_A0.172110.643
5_S8_N0.171790.642
91_L97_N0.169130.632
133_L136_G0.169010.632
109_A116_L0.168050.628
87_R114_Q0.166080.621
110_A114_Q0.164750.616
53_Q56_R0.164470.615
27_Q33_K0.164340.614
27_Q36_S0.164310.614
86_Q90_E0.16360.611
21_L95_A0.163070.609
115_L119_L0.162070.606
29_S58_E0.161720.604
62_R65_D0.161620.604
113_Q131_R0.160820.601
11_L14_L0.160560.600
55_S58_E0.158950.594
45_S107_A0.158820.594
61_Q64_I0.158420.592
18_Q135_S0.158280.592
51_R65_D0.157910.590
28_L31_G0.157420.588
48_L65_D0.157170.587
4_N8_N0.156970.587
63_N71_L0.156750.586
66_D69_S0.156680.586
84_I88_A0.156390.584
58_E102_D0.155250.580
110_A113_Q0.154090.576
6_I11_L0.153940.575
4_N7_Y0.15340.573
68_K133_L0.152960.572
110_A124_N0.152780.571
52_S130_G0.151790.567
106_Q124_N0.151530.566
1_I4_N0.150180.561
73_T77_A0.150170.561
12_N50_L0.149960.560
112_L116_L0.14940.558
38_S59_Q0.145790.545
76_T80_S0.145310.543
15_N18_Q0.145290.543
37_P46_R0.145060.542
6_I14_L0.145060.542
102_D110_A0.144790.541
69_S72_S0.144520.540
37_P44_A0.144080.538
3_T11_L0.14380.537
41_P46_R0.143570.537
92_A95_A0.143540.536
4_N30_T0.14290.534
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
1ucuA1100-0.002
3k8wA0.884999.90.061
3pwxA0.755499.90.222
2d4xA0.74199.80.248
3v47C0.733899.80.295
1io1A0.647599.70.368
3k1iC0.74196.10.797
3k1hA0.618751.10.886
4af1A0.726624.40.904
3fyqA0.4964150.913

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