GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VirJ - Bacterial virulence protein (VirJ)
Pfam: PF06057 (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: CL0028
Length: 192
Sequences: 52628
Seq/Len: 274.1
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
71_V99_Q4.390724.684
148_E169_P2.554272.725
166_I184_R2.540352.710
38_L53_D2.540312.710
86_Y100_V2.398512.559
143_Q188_A2.284462.437
72_L82_L2.088082.228
148_E167_A1.987732.121
4_L31_P1.910652.038
104_S150_E1.907172.035
21_I182_A1.88272.009
28_Q186_L1.813311.935
69_R98_A1.792931.913
55_A85_I1.792221.912
8_F54_L1.785771.905
168_L184_R1.710711.825
71_V98_A1.706681.821
102_L105_P1.695271.809
137_L140_A1.660221.771
55_A89_L1.639911.750
103_L181_L1.626351.735
55_A59_R1.600211.707
71_V189_L1.594641.701
10_G76_S1.575121.680
79_A105_P1.566851.672
73_I103_L1.543211.646
143_Q166_I1.527081.629
83_P102_L1.487871.587
4_L33_V1.478531.577
184_R187_D1.467391.566
159_R163_V1.46411.562
85_I89_L1.456781.554
84_F88_R1.448671.546
82_L100_V1.436431.532
180_A184_R1.417931.513
84_F87_N1.39371.487
146_Y167_A1.37361.465
101_V185_I1.369311.461
155_C167_A1.361741.453
58_I70_V1.359691.451
100_V142_V1.358821.450
75_Y104_S1.35661.447
51_A84_F1.354531.445
71_V101_V1.351271.442
146_Y165_V1.331531.421
24_A182_A1.283561.369
24_A28_Q1.280111.366
89_L96_R1.278271.364
59_R96_R1.277291.363
7_F73_I1.274481.360
102_L144_C1.260651.345
5_A30_V1.252661.336
101_V143_Q1.209041.290
183_K187_D1.204351.285
33_V57_I1.194191.274
55_A88_R1.191641.271
90_P95_A1.188441.268
143_Q164_E1.187261.267
8_F37_S1.174041.253
22_A34_G1.164931.243
99_Q141_P1.154071.231
52_A88_R1.149811.227
133_E136_K1.137871.214
15_R36_D1.133971.210
164_E184_R1.133291.209
29_G186_L1.124231.199
99_Q143_Q1.118321.193
54_L85_I1.110651.185
5_A73_I1.106661.181
89_L95_A1.097211.171
8_F82_L1.077711.150
73_I101_V1.067271.139
7_F32_V1.066521.138
13_G17_L1.062521.134
7_F18_D1.059231.130
145_I168_L1.051621.122
76_S172_H1.042171.112
24_A186_L1.041241.111
58_I97_V1.032861.102
30_V71_V1.028961.098
8_F35_V1.02641.095
59_R89_L1.026281.095
24_A27_K1.017461.085
56_R59_R1.013851.082
146_Y155_C1.011321.079
9_S37_S1.004231.071
11_D77_F1.000081.067
37_S77_F0.995511.062
67_R70_V0.994981.062
149_D170_G0.971841.037
70_V97_V0.971581.037
180_A183_K0.964261.029
8_F72_L0.960681.025
37_S81_V0.955761.020
74_G82_L0.951561.015
181_L185_I0.949631.013
66_G69_R0.946751.010
26_A32_V0.945311.009
74_G78_G0.932520.995
144_C163_V0.909140.970
15_R42_W0.900250.960
4_L70_V0.896290.956
145_I166_I0.895880.956
35_V54_L0.892860.953
99_Q188_A0.882740.942
179_D183_K0.882730.942
9_S40_Y0.881140.940
90_P96_R0.863150.921
101_V189_L0.85860.916
55_A96_R0.858060.915
168_L180_A0.846110.903
46_T49_Q0.845490.902
72_L97_V0.843320.900
22_A32_V0.842130.898
12_G76_S0.841840.898
35_V57_I0.839340.895
80_D106_S0.831210.887
84_F133_E0.830940.887
87_N133_E0.830160.886
57_I60_H0.828440.884
56_R60_H0.826420.882
4_L67_R0.809430.864
6_V70_V0.801070.855
7_F34_G0.800830.854
148_E170_G0.798290.852
52_A55_A0.79620.849
104_S147_G0.791170.844
104_S146_Y0.789220.842
36_D41_F0.785920.838
148_E155_C0.781370.834
145_I181_L0.780060.832
11_D14_W0.776840.829
75_Y103_L0.774320.826
19_K23_E0.774160.826
184_R188_A0.773670.825
75_Y173_H0.77230.824
177_D180_A0.771350.823
61_Y67_R0.770950.823
57_I61_Y0.769450.821
33_V61_Y0.764670.816
9_S35_V0.762850.814
74_G79_A0.758930.810
6_V33_V0.756250.807
5_A71_V0.754840.805
52_A56_R0.754570.805
23_E27_K0.754030.804
53_D56_R0.750940.801
166_I180_A0.750910.801
4_L61_Y0.750130.800
58_I85_I0.747580.798
87_N136_K0.74620.796
132_P135_A0.736520.786
100_V140_A0.728540.777
79_A102_L0.728250.777
85_I97_V0.725630.774
130_V133_E0.723680.772
24_A179_D0.721380.770
22_A26_A0.720850.769
141_P162_G0.719360.767
6_V58_I0.717260.765
156_P160_Q0.713980.762
5_A32_V0.712030.760
20_Q23_E0.711790.759
51_A88_R0.711790.759
30_V189_L0.700560.747
183_K186_L0.696460.743
70_V98_A0.684190.730
157_S160_Q0.684090.730
51_A81_V0.68370.729
15_R34_G0.680070.726
103_L185_I0.679170.725
76_S173_H0.678420.724
146_Y153_S0.678420.724
145_I184_R0.675630.721
7_F22_A0.67450.720
77_F81_V0.673740.719
156_P159_R0.673110.718
83_P107_T0.670890.716
80_D83_P0.666640.711
103_L145_I0.66560.710
51_A55_A0.664160.709
138_P161_P0.662030.706
25_L185_I0.658210.702
18_D75_Y0.652420.696
178_Y182_A0.650750.694
30_V186_L0.650010.693
150_E153_S0.649080.692
144_C165_V0.647260.691
85_I96_R0.641990.685
182_A186_L0.641060.684
159_R165_V0.640150.683
75_Y175_D0.636390.679
37_S40_Y0.635780.678
16_D19_K0.631940.674
147_G174_F0.63050.673
6_V72_L0.630350.673
166_I187_D0.624640.666
114_H117_G0.615640.657
160_Q163_V0.615570.657
48_E88_R0.613220.654
102_L142_V0.612990.654
99_Q189_L0.611530.652
55_A58_I0.60860.649
182_A185_I0.608350.649
116_S120_G0.603960.644
32_V35_V0.600690.641
50_T77_F0.599920.640
101_V145_I0.597610.638
31_P35_V0.596290.636
155_C165_V0.594930.635
18_D22_A0.594090.634
5_A189_L0.593140.633
72_L85_I0.5930.633
129_P133_E0.590730.630
101_V188_A0.58980.629
134_I137_L0.588520.628
29_G32_V0.584280.623
163_V166_I0.5840.623
164_E188_A0.583120.622
6_V57_I0.582860.622
4_L30_V0.57990.619
23_E26_A0.579010.618
155_C159_R0.574670.613
73_I185_I0.574130.613
86_Y140_A0.57070.609
164_E167_A0.570020.608
77_F80_D0.568790.607
98_A101_V0.56820.606
120_G123_G0.568050.606
90_P97_V0.567570.606
31_P34_G0.565190.603
8_F81_V0.563060.601
143_Q184_R0.561890.599
80_D84_F0.560690.598
78_G82_L0.559340.597
82_L86_Y0.557380.595
54_L81_V0.556990.594
40_Y43_S0.554430.592
53_D57_I0.554020.591
18_D21_I0.550560.587
12_G77_F0.5490.586
90_P138_P0.548710.585
70_V96_R0.548510.585
164_E187_D0.547150.584
76_S104_S0.545490.582
19_K34_G0.544550.581
25_L32_V0.536250.572
167_A170_G0.536110.572
13_G75_Y0.535720.572
17_L175_D0.535640.571
21_I25_L0.535280.571
128_Y131_I0.531490.567
9_S14_W0.527360.563
104_S174_F0.523850.559
68_K96_R0.521090.556
82_L102_L0.520410.555
36_D43_S0.520370.555
48_E52_A0.520120.555
105_P144_C0.516050.551
50_T53_D0.515650.550
103_L174_F0.514870.549
147_G150_E0.514480.549
51_A54_L0.514140.549
10_G13_G0.513720.548
25_L73_I0.513390.548
20_Q24_A0.512190.546
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
2wtmA0.97499.90.152
3pfbA0.97499.90.164
3hjuA0.97499.90.167
3om8A0.942799.90.17
4fblA0.958399.90.175
1k8qA0.97499.90.175
1b6gA0.947999.90.176
3pe6A0.97499.90.178
1zoiA0.947999.90.18
3i28A0.953199.90.182

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