GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNA_pol_A_bac - RNA polymerase Rpb3RpoA insert domain
Pfam: PF01000 (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: 112
Sequences: 1946
Seq/Len: 17.38
HH_delta: 0.127 (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
69_I98_L0.955143.831
38_K83_I0.85133.415
57_K95_E0.805543.231
54_F100_I0.79293.181
59_K93_K0.771073.093
13_E95_E0.63092.531
84_Y87_T0.627842.518
53_T97_E0.60882.442
58_V62_G0.598032.399
11_P97_E0.510352.047
63_E84_Y0.491341.971
52_V73_P0.489421.963
57_K93_K0.48381.941
58_V68_D0.468451.879
25_V32_I0.428221.718
36_L39_I0.411691.651
88_L92_Q0.405621.627
10_L36_L0.40031.606
61_P90_E0.39621.589
55_S97_E0.393051.577
55_S70_K0.379171.521
80_N83_I0.376331.510
55_S95_E0.350951.408
66_A83_I0.336981.352
54_F98_L0.329261.321
24_G100_I0.305671.226
86_A94_L0.305571.226
13_E16_A0.297181.192
30_L33_I0.284991.143
51_S99_Y0.283551.137
58_V88_L0.276941.111
47_C74_S0.275951.107
39_I67_G0.275731.106
41_I100_I0.275681.106
47_C77_E0.267121.071
50_C102_K0.266331.068
32_I85_I0.264171.060
65_T84_Y0.263071.055
23_P109_A0.25821.036
10_L33_I0.255791.026
58_V64_V0.255721.026
56_L96_M0.253151.015
63_E87_T0.248850.998
47_C50_C0.244390.980
39_I50_C0.239190.959
66_A81_P0.236860.950
34_L37_K0.233580.937
35_N85_I0.230710.925
55_S74_S0.227930.914
53_T99_Y0.226840.910
103_G107_V0.223710.897
40_V79_V0.222770.894
86_A89_S0.222510.893
39_I66_A0.22110.887
57_K70_K0.218820.878
17_H21_L0.216320.868
41_I78_I0.214960.862
53_T69_I0.213220.855
39_I71_L0.21260.853
22_I85_I0.209320.840
25_V77_E0.208880.838
29_V33_I0.207820.834
39_I83_I0.207690.833
46_G51_S0.206740.829
48_D75_G0.206450.828
54_F71_L0.206040.826
66_A80_N0.200830.806
31_E95_E0.197580.793
36_L98_L0.195110.783
10_L86_A0.19330.775
11_P95_E0.193110.775
56_L85_I0.191680.769
12_D29_V0.190710.765
79_V110_K0.189010.758
56_L64_V0.18660.749
69_I85_I0.185310.743
62_G88_L0.184540.740
71_L74_S0.184360.740
26_S33_I0.183140.735
60_G89_S0.182160.731
50_C101_E0.181080.726
67_G81_P0.180960.726
40_V73_P0.180390.724
41_I98_L0.179670.721
23_P102_K0.179420.720
26_S92_Q0.178910.718
40_V108_H0.178580.716
83_I99_Y0.178430.716
59_K91_G0.17830.715
39_I85_I0.1740.698
51_S97_E0.173840.697
13_E57_K0.171520.688
16_A20_G0.17140.688
61_P84_Y0.171210.687
52_V110_K0.1710.686
23_P92_Q0.170870.685
34_L103_G0.170840.685
19_F33_I0.170070.682
65_T82_D0.169630.680
51_S101_E0.169580.680
45_E79_V0.168610.676
14_G24_G0.166470.668
34_L49_D0.165460.664
64_V96_M0.164940.662
97_E109_A0.163590.656
71_L91_G0.161320.647
91_G96_M0.161120.646
27_E77_E0.160910.645
15_V29_V0.16080.645
56_L69_I0.159460.640
45_E106_Y0.159070.638
37_K106_Y0.158270.635
46_G49_D0.156770.629
15_V22_I0.156440.628
56_L109_A0.156370.627
16_A40_V0.155680.624
27_E35_N0.1550.622
47_C75_G0.154490.620
69_I78_I0.153140.614
56_L88_L0.152580.612
25_V37_K0.150370.603
21_L31_E0.14950.600
12_D16_A0.149240.599
28_D77_E0.149090.598
52_V75_G0.148760.597
45_E48_D0.148730.597
12_D108_H0.148490.596
13_E70_K0.148150.594
20_G48_D0.147950.593
88_L91_G0.146770.589
10_L15_V0.14640.587
35_N106_Y0.146050.586
21_L102_K0.145860.585
19_F87_T0.14440.579
47_C73_P0.144290.579
31_E90_E0.144190.578
15_V34_L0.143870.577
23_P26_S0.143550.576
101_E107_V0.14330.575
53_T76_I0.143070.574
20_G30_L0.142720.572
28_D31_E0.142310.571
104_R107_V0.142240.571
78_I99_Y0.142070.570
25_V28_D0.141750.569
64_V94_L0.141620.568
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
2pa8D0.99111000.127
1twfC0.96431000.14
3h0gC0.98211000.142
1bdfA0.964399.90.15
2a6hA0.982199.90.161
3lu0A0.964399.90.192
4kn7A0.964399.90.192
4igcA0.964399.90.247
2zjrS0.946416.20.922
3vu1A0.839314.50.923

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