GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gag_p17 - gag gene protein p17 (matrix protein)
Pfam: PF00540 (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: CL0074
Length: 140
Sequences: 2236
Seq/Len: 15.97
HH_delta: -0.026 (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
59_I81_V1.266534.239
14_A92_E0.878952.941
11_K14_A0.86462.893
102_K105_E0.844732.827
14_A90_R0.830312.779
57_Q106_E0.801822.683
82_A103_V0.704392.357
60_L103_V0.703862.356
11_K90_R0.683852.289
61_E68_P0.645622.161
60_L82_A0.611522.047
113_K116_Q0.570781.910
66_L71_S0.561311.878
45_L59_I0.558151.868
45_L65_P0.544871.823
85_Y106_E0.538271.801
80_T83_V0.533141.784
45_L71_S0.524871.757
19_R27_K0.500171.674
72_E75_K0.468741.569
97_K101_D0.467491.564
86_C103_V0.461911.546
137_S140_Y0.457861.532
83_V86_C0.4551.523
57_Q89_Q0.450981.509
19_R48_G0.450681.508
72_E104_E0.438881.469
7_L25_K0.423511.417
106_E112_Q0.42261.414
105_E109_K0.416981.395
97_K104_E0.409351.370
61_E110_S0.402151.346
75_K104_E0.402111.346
66_L74_L0.39441.320
50_L81_V0.388591.300
30_L33_L0.38641.293
53_A89_Q0.38521.289
115_Q125_A0.384651.287
51_E54_E0.3841.285
108_N111_K0.383191.282
34_V38_R0.37011.239
41_E74_L0.366081.225
86_C91_I0.362551.213
127_D136_V0.360371.206
7_L11_K0.358631.200
104_E108_N0.356971.195
6_V33_L0.355211.189
48_G71_S0.337141.128
53_A57_Q0.337051.128
29_R33_L0.336831.127
112_Q135_Q0.336441.126
43_F66_L0.330061.105
116_Q125_A0.326611.093
2_A5_S0.320161.071
54_E61_E0.318291.065
78_F85_Y0.315331.055
42_R75_K0.308821.033
29_R34_V0.306361.025
3_R6_V0.304231.018
46_N72_E0.303791.017
14_A94_K0.303471.016
10_G29_R0.303061.014
89_Q94_K0.30191.010
60_L107_Q0.296570.992
19_R29_R0.293870.983
42_R45_L0.293410.982
136_V140_Y0.292620.979
64_Q78_F0.290930.974
51_E73_E0.290060.971
85_Y103_V0.289340.968
116_Q126_A0.282810.946
71_S85_Y0.279690.936
21_R72_E0.274580.919
61_E89_Q0.273280.915
45_L60_L0.265620.889
61_E64_Q0.265620.889
54_E72_E0.265370.888
58_Q135_Q0.263240.881
36_A39_E0.263010.880
30_L34_V0.262980.880
127_D135_Q0.262790.879
111_K135_Q0.26250.878
106_E111_K0.256860.860
54_E90_R0.256290.858
13_D51_E0.254750.853
61_E111_K0.25180.843
68_P75_K0.250240.837
29_R90_R0.24280.813
37_S40_L0.241260.807
36_A40_L0.239290.801
92_E108_N0.239270.801
102_K126_A0.239150.800
89_Q92_E0.237490.795
57_Q110_S0.236110.790
65_P74_L0.235970.790
2_A7_L0.233270.781
6_V10_G0.232330.778
45_L63_L0.231750.776
16_E20_L0.23070.772
29_R74_L0.229930.769
94_K108_N0.229930.769
90_R94_K0.228370.764
106_E110_S0.227420.761
135_Q138_Q0.227170.760
1_G5_S0.225520.755
48_G111_K0.225350.754
57_Q61_E0.225270.754
21_R75_K0.224930.753
110_S114_T0.223470.748
71_S74_L0.222410.744
135_Q140_Y0.221270.741
111_K114_T0.220840.739
11_K33_L0.219560.735
83_V91_I0.217780.729
10_G90_R0.217290.727
112_Q115_Q0.215070.720
30_L46_N0.214730.719
63_L80_T0.21430.717
57_Q85_Y0.214240.717
51_E72_E0.210420.704
15_W18_I0.210060.703
17_K25_K0.208340.697
115_Q126_A0.2080.696
54_E89_Q0.207390.694
3_R10_G0.206080.690
2_A6_V0.205080.686
71_S106_E0.203490.681
86_C135_Q0.203450.681
68_P106_E0.202260.677
61_E107_Q0.199230.667
75_K78_F0.198960.666
27_K75_K0.198910.666
105_E126_A0.198630.665
46_N75_K0.197730.662
34_V37_S0.194790.652
58_Q91_I0.194540.651
54_E73_E0.194370.650
43_F80_T0.192570.644
19_R75_K0.191830.642
60_L66_L0.190250.637
59_I85_Y0.18950.634
66_L73_E0.189420.634
64_Q107_Q0.189040.633
61_E112_Q0.187980.629
95_D106_E0.187540.628
61_E66_L0.18660.624
21_R24_G0.186490.624
9_G12_L0.185820.622
101_D105_E0.185760.622
103_V135_Q0.185050.619
42_R110_S0.184320.617
64_Q68_P0.183180.613
27_K34_V0.18280.612
53_A78_F0.182460.611
19_R67_L0.182250.610
20_L23_G0.181640.608
115_Q127_D0.180990.606
33_L80_T0.180130.603
27_K94_K0.179780.602
81_V85_Y0.179210.600
59_I65_P0.178430.597
9_G13_D0.178310.597
9_G90_R0.178020.596
39_E42_R0.177770.595
71_S75_K0.177760.595
61_E71_S0.17710.593
66_L85_Y0.176880.592
1_G4_A0.176830.592
8_S89_Q0.1760.589
46_N58_Q0.175410.587
42_R66_L0.175370.587
108_N112_Q0.174560.584
23_G26_K0.174020.582
19_R33_L0.172940.579
125_A137_S0.172030.576
101_D104_E0.171640.574
5_S127_D0.171430.574
102_K108_N0.170270.570
58_Q66_L0.170240.570
75_K80_T0.169720.568
111_K127_D0.168170.563
49_L59_I0.166660.558
110_S116_Q0.166270.556
35_W40_L0.166220.556
14_A89_Q0.166090.556
62_Q74_L0.166090.556
105_E111_K0.166050.556
115_Q138_Q0.165630.554
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
2golA0.9357100-0.026
1l6nA0.93571000.05
1ed1A0.92141000.062
3fyfA0.411.20.964
3r8nP0.585710.10.965
1xokC0.15100.965
2z79A0.335790.965
2fa8A0.54298.90.965
1bjaA0.26438.40.966
1ov9A0.35718.30.966

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