GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pox_A22 - Poxvirus A22 protein
Pfam: PF04848 (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: CL0219
Length: 143
Sequences: 1518
Seq/Len: 10.62
HH_delta: 0.195 (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
55_V77_F0.803733.897
2_I19_E0.653763.170
98_E101_K0.646523.135
90_K96_Y0.566752.748
27_V30_I0.549512.664
87_V139_Y0.521972.531
107_F137_L0.503632.442
113_E124_K0.494522.398
25_I137_L0.493442.393
72_F75_G0.48632.358
93_G97_R0.435262.110
16_C133_F0.430582.088
19_E26_R0.423822.055
71_H74_H0.408821.982
67_V71_H0.389431.888
41_Y45_K0.364251.766
44_L79_I0.359791.745
44_L76_Y0.34131.655
19_E28_I0.339471.646
49_K80_K0.323921.571
108_K123_S0.317531.540
3_I140_L0.312411.515
15_Y31_S0.311671.511
105_E109_N0.310861.507
104_V130_A0.299331.451
56_L135_Q0.295171.431
2_I28_I0.294761.429
102_R106_V0.294291.427
20_F25_I0.289651.404
21_E24_K0.284441.379
100_K103_S0.266771.294
93_G100_K0.26391.280
30_I129_L0.252381.224
103_S107_F0.252131.223
44_L75_G0.248911.207
93_G98_E0.248491.205
106_V110_W0.247491.200
12_N34_D0.243481.181
41_Y81_N0.242611.176
87_V138_A0.24171.172
48_L80_K0.238141.155
4_L55_V0.238131.155
40_E72_F0.237971.154
92_K97_R0.237871.153
127_D130_A0.237461.151
5_S8_I0.236841.148
54_T139_Y0.23411.135
41_Y78_Y0.230691.119
124_K130_A0.229551.113
29_D50_Y0.229511.113
27_V133_F0.228811.109
39_W43_I0.227731.104
12_N128_D0.22691.100
91_M97_R0.226141.097
105_E108_K0.22341.083
32_K129_L0.218541.060
10_I63_R0.218111.058
41_Y79_I0.217831.056
42_R46_D0.216511.050
6_I73_I0.214571.040
5_S136_A0.214351.039
45_K79_I0.21381.037
97_R103_S0.212911.032
17_I50_Y0.209081.014
10_I35_W0.208981.013
18_I133_F0.206551.002
38_D45_K0.206161.000
25_I140_L0.205430.996
28_I50_Y0.205160.995
16_C132_A0.202930.984
55_V82_T0.201440.977
62_P89_P0.200690.973
97_R100_K0.200620.973
10_I68_K0.196560.953
103_S134_C0.196380.952
15_Y29_D0.196240.952
18_I136_A0.192890.935
12_N32_K0.192440.933
11_K127_D0.192140.932
67_V75_G0.18730.908
35_W39_W0.18610.902
94_W97_R0.183820.891
4_L17_I0.182920.887
54_T83_K0.179180.869
56_L139_Y0.178370.865
9_G12_N0.177970.863
17_I28_I0.176720.857
112_K121_P0.17670.857
4_L48_L0.17550.851
56_L87_V0.17550.851
89_P130_A0.173640.842
21_E121_P0.172730.838
92_K103_S0.172610.837
54_T87_V0.170460.827
11_K15_Y0.168650.818
8_I136_A0.167490.812
92_K102_R0.167260.811
63_R96_Y0.166790.809
62_P66_N0.166010.805
74_H86_C0.165980.805
35_W43_I0.164170.796
25_I29_D0.163020.790
123_S126_K0.162960.790
53_D83_K0.161950.785
7_D58_E0.159730.774
91_M110_W0.159650.774
64_N67_V0.1590.771
3_I18_I0.158010.766
103_S106_V0.157460.763
6_I47_L0.156840.760
47_L67_V0.156810.760
43_I46_D0.154070.747
3_I53_D0.153690.745
47_L140_L0.153160.743
101_K105_E0.152820.741
41_Y44_L0.151590.735
93_G96_Y0.14890.722
54_T85_I0.147910.717
57_I74_H0.147110.713
113_E126_K0.145110.704
40_E75_G0.145020.703
59_R63_R0.144690.702
15_Y30_I0.143620.696
75_G79_I0.143290.695
47_L76_Y0.142740.692
73_I76_Y0.142410.691
2_I26_R0.142310.690
62_P65_P0.142150.689
59_R90_K0.141750.687
59_R66_N0.141610.687
16_C111_I0.14080.683
37_R78_Y0.140160.680
36_S45_K0.140050.679
14_A39_W0.139790.678
11_K35_W0.139150.675
105_E123_S0.13870.673
37_R68_K0.137990.669
48_L79_I0.137920.669
2_I50_Y0.13790.669
24_K112_K0.137530.667
20_F140_L0.137480.667
94_W98_E0.136640.663
69_I75_G0.136460.662
61_P128_D0.136390.661
15_Y33_V0.13630.661
65_P69_I0.136150.660
113_E121_P0.135720.658
37_R41_Y0.135590.657
39_W76_Y0.135510.657
58_E131_D0.134120.650
63_R93_G0.13410.650
80_K121_P0.134080.650
62_P90_K0.133930.649
29_D42_R0.133330.646
28_I31_S0.132940.645
35_W46_D0.132890.644
62_P69_I0.132870.644
59_R89_P0.132710.643
4_L16_C0.132630.643
111_I137_L0.132590.643
21_E26_R0.132410.642
44_L72_F0.131620.638
57_I84_V0.131430.637
69_I97_R0.131240.636
14_A132_A0.130220.631
48_L122_K0.129920.630
43_I63_R0.129870.630
20_F54_T0.129670.629
6_I55_V0.129630.629
10_I90_K0.129570.628
62_P86_C0.128750.624
11_K62_P0.128490.623
107_F134_C0.127890.620
33_V40_E0.127460.618
95_S134_C0.126930.615
104_V123_S0.126590.614
24_K122_K0.126530.614
60_Q63_R0.126110.611
26_R42_R0.125910.611
6_I9_G0.125820.610
61_P88_S0.125790.610
101_K104_V0.125760.610
7_D100_K0.125460.608
66_N69_I0.125090.607
40_E43_I0.124460.603
40_E44_L0.124390.603
101_K127_D0.124260.603
43_I73_I0.12420.602
128_D135_Q0.123970.601
80_K83_K0.123760.600
33_V43_I0.123620.599
14_A95_S0.123620.599
104_V113_E0.123460.599
77_F84_V0.123440.599
16_C136_A0.123010.596
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
4ep4A0.94411000.195
1hjrA0.93711000.222
1kcfA199.60.539
1vhxA0.846298.80.691
1iv0A0.636497.60.793
1nu0A0.874196.90.82
3c6aA0.972960.84
3cpeA0.916195.40.848
4bijA0.783295.30.849
3bzcA0.909192.40.867

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