GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Retrotrans_gag - Retrotransposon gag protein
Pfam: PF03732 (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: CL0523
Length: 96
Sequences: 2032
Seq/Len: 21.17
HH_delta: 0.802 (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
56_L69_R0.670743.316
61_E69_R0.657013.248
67_V90_F0.584972.892
56_L61_E0.524312.592
66_Y93_G0.479012.368
33_K37_R0.388381.920
3_F32_F0.345251.707
69_R72_E0.343461.698
56_L73_L0.313271.549
90_F94_L0.303341.499
70_F90_F0.295951.463
56_L70_F0.288421.426
81_M85_M0.276981.369
83_E86_L0.270311.336
62_S65_E0.267941.324
29_W33_K0.265451.312
3_F29_W0.262251.296
74_A86_L0.260521.288
28_T31_E0.253881.255
11_A14_W0.246831.220
32_F70_F0.246181.217
53_L89_R0.246071.216
58_Q63_V0.243451.203
51_Q55_S0.242791.200
46_K50_R0.241251.193
6_F32_F0.24081.190
13_Q16_R0.240641.190
7_L11_A0.238971.181
36_F41_F0.237411.174
15_Y32_F0.230671.140
49_A52_E0.228541.130
70_F74_A0.22551.115
30_E34_D0.224711.111
14_W29_W0.222871.102
34_D38_K0.221931.097
4_P15_Y0.220181.088
45_R49_A0.215611.066
14_W40_F0.215181.064
20_P24_R0.212251.049
50_R85_M0.211571.046
52_E69_R0.208321.030
48_Q52_E0.206341.020
64_R68_N0.204741.012
32_F36_F0.198310.980
89_R93_G0.197260.975
48_Q51_Q0.196910.973
19_R22_E0.196570.972
41_F44_D0.195220.965
41_F45_R0.194570.962
66_Y70_F0.194570.962
50_R88_E0.19390.958
68_N71_R0.192960.954
83_E87_V0.191650.947
3_F6_F0.191490.947
42_P63_V0.191310.946
49_A76_R0.190040.939
12_R16_R0.188990.934
82_D85_M0.188280.931
86_L91_I0.188140.930
63_V67_V0.188020.929
67_V71_R0.187390.926
19_R23_I0.185220.916
37_R41_F0.184790.913
24_R28_T0.182370.902
42_P45_R0.181530.897
58_Q62_S0.181090.895
18_L22_E0.17840.882
16_R19_R0.178290.881
31_E35_A0.178280.881
56_L66_Y0.177620.878
51_Q92_R0.176430.872
90_F93_G0.173890.860
54_N88_E0.172240.851
49_A53_L0.166760.824
34_D37_R0.165480.818
14_W36_F0.164960.815
54_N89_R0.164680.814
14_W32_F0.163870.810
63_V93_G0.162930.805
71_R75_R0.161330.797
89_R92_R0.16130.797
23_I36_F0.160170.792
3_F36_F0.160090.791
49_A77_A0.157120.777
58_Q66_Y0.157110.777
15_Y19_R0.156550.774
78_P84_E0.156530.774
81_M89_R0.155080.767
14_W28_T0.150930.746
29_W59_G0.150170.742
15_Y81_M0.149860.741
56_L90_F0.149520.739
13_Q72_E0.149180.737
88_E91_I0.147680.730
13_Q46_K0.147010.727
30_E43_P0.146690.725
45_R50_R0.145850.721
72_E87_V0.144640.715
5_S10_P0.143650.710
31_E54_N0.143550.710
53_L70_F0.142980.707
54_N92_R0.141560.700
12_R18_L0.140730.696
22_E31_E0.140690.695
91_I94_L0.140180.693
5_S29_W0.140070.692
6_F14_W0.139560.690
16_R20_P0.139190.688
23_I34_D0.138670.685
62_S83_E0.138040.682
70_F78_P0.137760.681
16_R22_E0.137740.681
52_E79_P0.137530.680
68_N72_E0.137450.679
47_E84_E0.137290.679
16_R21_N0.137160.678
36_F67_V0.13640.674
85_M89_R0.136350.674
46_K84_E0.136170.673
53_L74_A0.136060.673
17_N33_K0.135720.671
30_E35_A0.135520.670
56_L59_G0.13540.669
8_K38_K0.13520.668
88_E94_L0.13490.667
78_P83_E0.13480.666
49_A74_A0.13420.663
18_L35_A0.133220.659
86_L89_R0.132810.657
81_M88_E0.132760.656
4_P8_K0.132480.655
8_K11_A0.131770.651
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
1eoqA0.4479510.802
3g1gA0.479232.20.822
3g21A0.489628.40.827
3tirA125.50.831
2gq0A0.958320.40.838
1d1dA0.906218.20.841
1usuA0.947915.70.845
2ioqA0.958314.80.847
2cgeA0.947913.20.85
3hjcA0.947912.90.851
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