GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YscJ_FliF_C - Flagellar M-ring protein C-terminal
Pfam: PF08345 (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: 160
Sequences: 874
Seq/Len: 5.46
HH_delta: 0.927 (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
9_N113_D0.672365.169
28_E91_K0.499493.840
16_A106_L0.392683.019
45_E80_K0.362332.785
38_R88_E0.361692.780
39_S86_N0.329562.533
40_E85_T0.301392.317
135_I155_V0.286572.203
43_S82_E0.286482.202
17_D104_K0.271062.084
38_R89_V0.270422.079
24_E95_Q0.265922.044
136_R140_A0.264092.030
129_P133_A0.260071.999
19_D104_K0.25571.966
41_Q84_T0.252931.944
22_K97_E0.247891.906
42_S83_E0.235181.808
26_T93_V0.223651.719
133_A136_R0.208551.603
37_V85_T0.202351.556
140_A145_I0.202041.553
31_D90_N0.20151.549
108_V143_I0.196141.508
145_I153_V0.195761.505
58_P62_S0.189441.456
30_Y38_R0.188171.447
59_G63_N0.187231.439
36_V89_V0.186941.437
37_V40_E0.186461.433
56_G59_G0.182981.407
140_A153_V0.181631.396
141_S152_Q0.181131.392
26_T95_Q0.176181.354
141_S154_T0.171341.317
115_K131_E0.170441.310
21_D99_A0.170121.308
127_R131_E0.168781.297
59_G62_S0.163891.260
4_I158_M0.159761.228
1_L5_V0.158561.219
44_E81_S0.153151.177
40_E83_E0.153131.177
47_S78_Y0.150841.160
72_G76_S0.150671.158
2_E7_P0.149731.151
60_T64_T0.14881.144
105_R149_R0.148761.144
57_V62_S0.145211.116
36_V90_N0.142891.098
60_T63_N0.142581.096
61_D65_P0.142381.095
109_A138_L0.142061.092
144_G149_R0.140631.081
133_A148_D0.140131.077
43_S84_T0.140121.077
28_E93_V0.139531.073
27_E96_T0.137671.058
38_R86_N0.135581.042
58_P63_N0.132871.021
61_D64_T0.132491.018
2_E10_V0.131731.013
107_S141_S0.131621.012
39_S84_T0.131371.010
3_P10_V0.130511.003
139_V153_V0.130421.003
20_F88_E0.13021.001
130_E134_Q0.129530.996
2_E8_G0.128610.989
27_E94_T0.127960.984
46_S79_S0.127650.981
45_E78_Y0.127210.978
13_S95_Q0.123550.950
12_V109_A0.123260.948
59_G64_T0.121220.932
137_D154_T0.120680.928
8_G97_E0.120630.927
25_T98_K0.119930.922
7_P142_A0.119920.922
125_V128_S0.119430.918
128_S131_E0.119340.917
61_D66_P0.119290.917
11_R78_Y0.117280.902
6_G160_F0.117190.901
58_P65_P0.116650.897
105_R152_Q0.116630.897
14_V109_A0.115610.889
81_S103_I0.115380.887
70_N74_G0.115250.886
59_G65_P0.114320.879
17_D105_R0.113080.869
24_E90_N0.112820.867
115_K155_V0.111890.860
137_D140_A0.111850.860
48_T77_S0.111450.857
60_T65_P0.111390.856
68_T106_L0.110770.852
23_V98_K0.110750.851
32_P72_G0.10950.842
112_V135_I0.109460.841
29_T94_T0.109310.840
133_A137_D0.108960.838
53_G70_N0.108890.837
138_L154_T0.107860.829
6_G9_N0.10730.825
49_G59_G0.107270.825
21_D98_K0.107190.824
105_R151_D0.107060.823
18_L104_K0.10690.822
33_D113_D0.10660.819
106_L143_I0.10650.819
39_S88_E0.105970.815
62_S65_P0.105130.808
61_D108_V0.104670.805
41_Q109_A0.104340.802
48_T73_G0.103680.797
23_V96_T0.103420.795
146_D151_D0.102990.792
28_E41_Q0.102890.791
144_G151_D0.101540.781
70_N130_E0.101420.780
147_P152_Q0.100870.775
48_T79_S0.100720.774
40_E81_S0.100540.773
41_Q86_N0.100480.772
31_D34_S0.100420.772
99_A102_K0.100340.771
14_V106_L0.100230.770
30_Y84_T0.099960.768
129_P134_Q0.099840.768
105_R131_E0.099610.766
40_E113_D0.09960.766
1_L95_Q0.099320.764
17_D109_A0.098920.760
84_T155_V0.098180.755
10_V127_R0.097780.752
130_E133_A0.097720.751
37_V87_Y0.097570.750
57_V64_T0.097530.750
9_N82_E0.097430.749
75_N79_S0.09710.746
47_S87_Y0.096710.743
38_R84_T0.096040.738
99_A139_V0.095940.738
90_N101_G0.095920.737
9_N114_G0.095840.737
106_L110_V0.095710.736
32_P90_N0.095670.735
50_T125_V0.095670.735
49_G54_A0.095450.734
1_L72_G0.095050.731
114_G126_P0.094670.728
49_G76_S0.094620.727
7_P148_D0.093760.721
13_S101_G0.093660.720
72_G77_S0.093350.718
39_S45_E0.093330.717
31_D36_V0.09330.717
126_P143_I0.093120.716
81_S114_G0.092380.710
54_A130_E0.092040.708
59_G66_P0.091370.702
32_P71_G0.090970.699
146_D149_R0.090950.699
74_G126_P0.090850.698
25_T62_S0.090350.695
139_V142_A0.090330.694
54_A71_G0.090240.694
16_A20_F0.090130.693
111_V144_G0.089710.690
112_V155_V0.089650.689
27_E136_R0.089630.689
109_A142_A0.089420.687
132_L136_R0.089260.686
25_T92_T0.089240.686
126_P157_N0.089220.686
13_S26_T0.088950.684
32_P37_V0.088830.683
38_R82_E0.088670.682
57_V61_D0.08830.679
114_G127_R0.087980.676
56_G62_S0.087670.674
50_T71_G0.087520.673
71_G76_S0.087420.672
64_T141_S0.087210.670
56_G107_S0.08720.670
16_A28_E0.087040.669
53_G133_A0.08690.668
29_T155_V0.086520.665
57_V68_T0.086520.665
27_E92_T0.086450.665
2_E85_T0.086160.662
131_E134_Q0.086120.662
16_A101_G0.086040.661
11_R111_V0.085950.661
46_S103_I0.085540.658
34_S37_V0.08540.656
101_G109_A0.085120.654
18_L23_V0.084960.653
16_A103_I0.084950.653
17_D146_D0.084890.653
2_E104_K0.084820.652
7_P74_G0.084540.650
2_E135_I0.084260.648
42_S133_A0.084010.646
83_E125_V0.08390.645
144_G150_G0.083850.645
26_T97_E0.083820.644
34_S68_T0.083810.644
143_I147_P0.083530.642
32_P88_E0.083280.640
88_E138_L0.083120.639
30_Y89_V0.083110.639
1_L110_V0.082920.637
18_L21_D0.082790.636
71_G75_N0.082760.636
64_T90_N0.082290.633
11_R139_V0.082180.632
23_V46_S0.082160.632
53_G115_K0.082120.631
4_I142_A0.082070.631
35_G89_V0.081630.628
87_Y106_L0.081520.627
67_Y126_P0.08110.623
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
2pliA0.4313390.927
2rk5A0.368812.50.941
2p4pA0.375120.942
2plsA0.37511.80.942
3llbA0.37511.40.942
3laeA0.3758.30.945
2ha9A0.48757.50.946
2oaiA0.43137.30.947
2p3hA0.38756.80.947
2nqwA0.41256.80.947
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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