GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_9 - RNA polymerase III subunit RPC82 helix-turn-helix domain
Pfam: PF08221 (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: CL0123
Length: 62
Sequences: 34959
Seq/Len: 563.85
HH_delta: 0.067 (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
21_V36_R2.841542.264
29_T32_E2.354931.876
15_V47_A2.277961.815
52_I59_Y2.176821.734
30_L45_K2.037841.623
34_V41_P2.035851.622
15_V54_H1.981791.579
30_L41_P1.830981.459
15_V50_V1.808141.440
21_V28_L1.742431.388
40_S43_Q1.698351.353
50_V54_H1.697271.352
14_I47_A1.647081.312
14_I39_L1.603561.277
31_R35_R1.59741.273
28_L36_R1.590191.267
45_K49_V1.569771.251
17_K21_V1.564131.246
42_K45_K1.530211.219
25_R28_L1.516741.208
41_P45_K1.507781.201
28_L32_E1.464211.166
27_R60_F1.39791.114
32_E36_R1.389461.107
39_L43_Q1.350541.076
34_V44_V1.343691.070
12_G15_V1.332531.062
21_V25_R1.32371.055
30_L48_L1.311791.045
14_I17_K1.311421.045
25_R36_R1.278181.018
31_R41_P1.274061.015
19_G23_L1.243940.991
49_V53_Q1.221950.973
18_V47_A1.174290.935
18_V33_I1.155310.920
39_L44_V1.152930.918
43_Q46_K1.123750.895
21_V37_T1.113390.887
18_V44_V1.109180.884
11_F15_V1.106820.882
17_K22_L1.095980.873
13_E16_A1.068050.851
52_I57_V1.047960.835
16_A20_E1.045790.833
32_E35_R1.04330.831
19_G56_L1.042370.830
13_E17_K1.039030.828
46_K49_V1.036930.826
31_R45_K1.036690.826
46_K50_V1.028390.819
21_V24_S0.979030.780
17_K20_E0.951910.758
33_I44_V0.948320.755
49_V52_I0.938950.748
17_K37_T0.936480.746
50_V53_Q0.901040.718
43_Q47_A0.861780.687
11_F50_V0.860420.685
30_L44_V0.853920.680
48_L52_I0.841910.671
12_G47_A0.829340.661
21_V33_I0.811670.647
42_K46_K0.794650.633
11_F16_A0.794170.633
48_L57_V0.783610.624
47_A50_V0.780940.622
14_I43_Q0.777060.619
14_I37_T0.775080.617
37_T44_V0.762050.607
51_L56_L0.759630.605
49_V59_Y0.755930.602
31_R34_V0.726140.578
22_L57_V0.725530.578
52_I60_F0.720240.574
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
1hsjA198.10.067
2fxaA198.10.082
3hsrA198.10.084
4em2A198.10.084
3k0lA1980.088
4g9yA1980.09
4fhtA1980.09
4hblA1980.09
3echA1980.09
3s2wA1980.091

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