GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNA_pol_Rpb6 - RNA polymerase Rpb6
Pfam: PF01192 (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. )
Length: 57
Sequences: 1327
Seq/Len: 23.28
HH_delta: -0.008 (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
31_L52_K0.788213.022
24_L30_P0.609232.336
34_E43_I0.523022.005
13_L48_I0.450321.726
20_R47_E0.439041.683
20_R23_Q0.416851.598
6_K51_G0.375331.439
4_L8_D0.352941.353
3_L11_Y0.344481.321
2_D49_A0.335261.285
9_N42_S0.332311.274
42_S46_E0.33231.274
2_D5_E0.330031.265
32_V35_D0.328911.261
12_E15_I0.323331.240
34_E37_E0.32271.237
12_E55_I0.308461.183
5_E55_I0.306381.175
42_S45_L0.302231.159
7_V16_L0.288821.107
21_A40_P0.284321.090
32_V43_I0.279671.072
15_I21_A0.279591.072
51_G54_K0.272241.044
19_K26_E0.271611.041
8_D55_I0.271191.040
18_A22_R0.268851.031
17_A45_L0.267581.026
16_L55_I0.2641.012
25_S40_P0.258280.990
37_E42_S0.255930.981
11_Y39_K0.246360.944
37_E46_E0.246210.944
43_I50_E0.241890.927
10_R45_L0.240470.922
31_L53_I0.238420.914
21_A25_S0.237570.911
10_R39_K0.236940.908
3_L8_D0.234310.898
3_L42_S0.232840.893
6_K16_L0.231680.888
15_I19_K0.231040.886
3_L45_L0.226540.868
12_E18_A0.22520.863
18_A21_A0.225180.863
8_D34_E0.22490.862
13_L45_L0.223170.856
24_L40_P0.222040.851
26_E41_V0.218310.837
10_R27_G0.207350.795
27_G44_A0.207270.795
27_G30_P0.203940.782
49_A52_K0.203930.782
9_N12_E0.202990.778
9_N41_V0.202770.777
23_Q30_P0.202720.777
11_Y31_L0.199970.767
21_A44_A0.19860.761
22_R25_S0.197580.757
9_N14_V0.196080.752
30_P33_E0.195990.751
4_L51_G0.19470.746
44_A53_I0.194030.744
16_L28_A0.193640.742
14_V22_R0.192940.740
40_P44_A0.192550.738
10_R18_A0.192090.736
3_L49_A0.190960.732
26_E50_E0.190690.731
45_L49_A0.190240.729
17_A48_I0.189670.727
8_D14_V0.18750.719
9_N22_R0.185460.711
25_S41_V0.185280.710
19_K23_Q0.183630.704
9_N39_K0.182930.701
46_E50_E0.181850.697
14_V18_A0.179510.688
10_R15_I0.179480.688
19_K53_I0.178340.684
15_I40_P0.177340.680
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
4igcE199.5-0.008
3lu0E0.982599.5-0.007
4kn7E0.982599.5-0.007
2a6hE199.40.038
4aybK199.10.193
1qklA199.10.196
1twfF199.10.204
3h0gF199.10.21
1k8wA115.60.839
1r3eA112.70.845

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