GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FAR1 - FAR1 DNA-binding domain
Pfam: PF03101 (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: CL0274
Length: 91
Sequences: 684
Seq/Len: 7.52
HH_delta: 0.816 (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
3_Y64_A0.390193.157
60_T86_N0.260072.104
3_Y6_Y0.242291.960
41_Y57_S0.235821.908
66_I78_V0.218331.767
13_S36_S0.213211.725
6_Y10_H0.203161.644
31_V68_V0.200891.625
40_K61_G0.195881.585
38_G59_K0.194451.573
3_Y7_A0.189291.532
16_K19_S0.187121.514
15_R59_K0.17351.404
20_R30_R0.169731.373
6_Y12_F0.166471.347
6_Y83_L0.163461.323
37_R60_T0.162121.312
15_R38_G0.160211.296
39_G59_K0.159661.292
12_F89_L0.155341.257
34_V39_G0.155131.255
36_S58_K0.154091.247
43_S47_N0.14731.192
3_Y12_F0.140771.139
64_A68_V0.139411.128
7_A14_V0.138381.120
71_R88_P0.136291.103
15_R40_K0.135111.093
45_K66_I0.134171.086
12_F64_A0.13221.070
70_R88_P0.130931.059
19_S31_V0.128631.041
20_R32_T0.128121.037
21_K33_F0.127091.028
15_R34_V0.126951.027
32_T69_K0.126871.027
43_S46_K0.125131.012
35_C39_G0.124651.009
22_S70_R0.124581.008
64_A89_L0.123731.001
18_S32_T0.121830.986
30_R70_R0.120910.978
19_S25_N0.12070.977
40_K59_K0.120460.975
17_S34_V0.120390.974
4_N14_V0.120150.972
7_A13_S0.120030.971
26_G42_K0.117250.949
47_N72_K0.116930.946
30_R60_T0.115680.936
41_Y58_K0.115220.932
15_R31_V0.115160.932
43_S57_S0.114160.924
21_K83_L0.114080.923
19_S28_I0.113710.920
18_S29_K0.113630.919
12_F39_G0.113410.918
30_R67_N0.11220.908
15_R64_A0.111640.903
54_N58_K0.111390.901
39_G55_R0.11130.901
52_R57_S0.111240.900
7_A12_F0.111160.899
14_V18_S0.110570.895
4_N7_A0.110130.891
34_V38_G0.110020.890
60_T63_K0.109180.883
17_S59_K0.108910.881
83_L89_L0.108530.878
31_V64_A0.107040.866
3_Y15_R0.1070.866
51_R54_N0.106940.865
52_R69_K0.106080.858
65_R80_S0.104690.847
66_I74_G0.103650.839
17_S67_N0.103250.835
38_G80_S0.102640.830
83_L88_P0.102370.828
3_Y31_V0.101980.825
65_R82_V0.100660.814
16_K42_K0.09970.807
16_K65_R0.099360.804
24_K79_T0.099350.804
13_S81_F0.099130.802
18_S67_N0.098790.799
72_K77_R0.097590.790
37_R83_L0.097260.787
17_S33_F0.096560.781
73_D88_P0.096530.781
17_S31_V0.096360.780
59_K80_S0.096330.779
53_R88_P0.096240.779
33_F71_R0.096130.778
8_R76_W0.095210.770
5_S77_R0.095060.769
64_A78_V0.094510.765
68_V78_V0.094490.765
74_G83_L0.094480.764
22_S32_T0.094080.761
16_K70_R0.093890.760
37_R51_R0.093380.756
10_H26_G0.09280.751
22_S30_R0.092470.748
54_N79_T0.092210.746
40_K54_N0.092130.745
18_S73_D0.091980.744
44_K47_N0.091810.743
68_V77_R0.09180.743
33_F76_W0.091630.741
18_S30_R0.091560.741
5_S9_R0.090660.734
8_R13_S0.09060.733
22_S29_K0.090470.732
52_R79_T0.089890.727
10_H77_R0.089760.726
71_R75_K0.089370.723
13_S89_L0.089260.722
5_S8_R0.089250.722
10_H89_L0.089060.721
53_R57_S0.088860.719
22_S37_R0.088590.717
51_R58_K0.0880.712
63_K88_P0.087780.710
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
2rprA0.648487.20.816
2aydA0.747380.20.83
1wj2A0.747379.90.83
1odhA18.40.903
2ihr10.901170.906
2b3tB0.94516.90.906
1gqeA0.90116.70.907
1rq0A0.94516.70.907
1zbtA0.93416.40.907
3d5aX0.94516.30.908
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