GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNA_pol_Rpb1_3 - RNA polymerase Rpb1 domain 3
Pfam: PF04983 (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: 158
Sequences: 2221
Seq/Len: 14.06
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
59_L68_K0.673993.656
52_V71_F0.608443.300
59_L66_T0.531682.884
53_L56_P0.522312.833
4_S11_I0.397792.158
57_A66_T0.389672.114
33_S36_E0.377072.045
38_Q42_M0.363021.969
130_A133_Q0.359341.949
122_I134_F0.350571.902
38_Q78_E0.339131.840
77_N80_N0.338081.834
144_R148_R0.316681.718
28_E57_A0.313341.700
121_Q125_E0.307531.668
130_A137_A0.303281.645
69_Q74_I0.302041.638
37_A74_I0.291461.581
4_S7_N0.290091.574
37_A71_F0.289251.569
26_T76_P0.285381.548
34_R74_I0.280051.519
75_L145_Y0.274091.487
52_V58_I0.27251.478
114_S117_S0.26851.456
41_L71_F0.263081.427
28_E70_T0.259821.409
57_A68_K0.253971.378
122_I126_Y0.253861.377
9_K116_G0.247271.341
30_T59_L0.246261.336
18_M139_K0.244491.326
29_D53_L0.242571.316
127_G130_A0.242351.315
21_G142_G0.240441.304
97_N114_S0.235981.280
127_G131_T0.235051.275
52_V56_P0.23041.250
28_E68_K0.227241.233
33_S62_K0.221961.204
84_F122_I0.221931.204
12_I135_L0.219791.192
57_A69_Q0.218651.186
74_I141_L0.212271.151
36_E148_R0.207921.128
85_S93_V0.207211.124
3_L123_Y0.206651.121
133_Q137_A0.203891.106
119_I135_L0.202131.096
31_F58_I0.198451.076
31_F52_V0.197751.073
123_Y131_T0.197431.071
25_L145_Y0.196761.067
24_Y149_S0.196731.067
21_G149_S0.196191.064
1_N152_S0.194711.056
129_E133_Q0.191131.037
93_V100_L0.190881.035
96_N99_E0.189911.030
43_N51_I0.189711.029
56_P68_K0.189381.027
60_K74_I0.189331.027
82_E96_N0.187931.019
130_A134_F0.18551.006
100_L114_S0.184851.003
34_R63_E0.18451.001
40_A70_T0.184321.000
19_V115_L0.184130.999
2_I116_G0.183390.995
37_A58_I0.182030.987
134_F138_I0.18010.977
31_F40_A0.178880.970
5_P21_G0.177290.962
56_P69_Q0.176930.960
12_I18_M0.175880.954
38_Q75_L0.175560.952
122_I131_T0.175190.950
123_Y127_G0.175060.950
37_A73_R0.173890.943
83_G126_Y0.172170.934
6_A158_M0.171460.930
41_L73_R0.169360.919
2_I12_I0.169030.917
35_D38_Q0.161730.877
35_D78_E0.161270.875
118_L146_L0.161180.874
54_L72_S0.159730.866
44_G148_R0.158410.859
94_V125_E0.158190.858
41_L145_Y0.158120.858
136_D152_S0.1570.852
18_M143_F0.156410.848
96_N100_L0.155880.846
34_R38_Q0.155760.845
95_I118_L0.155630.844
3_L136_D0.155250.842
25_L116_G0.154240.837
83_G130_A0.154220.837
2_I123_Y0.154080.836
41_L54_L0.153730.834
141_L145_Y0.153190.831
84_F94_V0.152450.827
44_G51_I0.152170.825
80_N85_S0.152110.825
97_N117_S0.151940.824
65_W68_K0.151560.822
25_L141_L0.151140.820
85_S118_L0.150920.819
137_A140_R0.150150.814
75_L78_E0.149190.809
25_L60_K0.148190.804
30_T66_T0.147090.798
13_G67_G0.147070.798
155_I158_M0.146960.797
2_I10_P0.146870.797
146_L151_F0.146830.796
140_R151_F0.146550.795
11_I118_L0.146470.795
77_N95_I0.145590.790
5_P26_T0.144260.783
34_R78_E0.144060.781
14_P18_M0.143730.780
8_G14_P0.14360.779
26_T64_L0.142090.771
29_D56_P0.14180.769
32_L36_E0.141640.768
22_A138_I0.14150.768
79_I134_F0.141190.766
154_G157_D0.140920.764
133_Q158_M0.139970.759
76_P98_G0.139860.759
18_M142_G0.137610.746
124_R135_L0.136380.740
8_G15_T0.136140.738
96_N138_I0.136030.738
116_G120_H0.135750.736
80_N83_G0.135260.734
53_L57_A0.134930.732
22_A134_F0.134920.732
20_L36_E0.13470.731
1_N23_Y0.134470.729
14_P23_Y0.133960.727
8_G139_K0.132970.721
79_I121_Q0.132160.717
8_G142_G0.132030.716
36_E136_D0.132020.716
34_R75_L0.132010.716
2_I131_T0.131850.715
75_L79_I0.131680.714
33_S60_K0.130410.707
9_K120_H0.130040.705
62_K65_W0.130.705
6_A19_V0.129790.704
12_I23_Y0.129720.704
25_L41_L0.129410.702
22_A115_L0.12940.702
67_G100_L0.129140.701
31_F57_A0.12870.698
23_Y136_D0.128620.698
84_F126_Y0.128520.697
65_W93_V0.127820.693
64_L67_G0.127340.691
20_L123_Y0.127120.690
8_G11_I0.127060.689
9_K27_S0.126710.687
52_V55_H0.126640.687
40_A72_S0.126590.687
7_N16_Q0.126440.686
18_M140_R0.126240.685
68_K98_G0.126160.684
33_S40_A0.126130.684
51_I63_E0.126030.684
34_R141_L0.126010.684
1_N153_V0.12590.683
139_K143_F0.125710.682
58_I61_P0.125650.682
4_S134_F0.125580.681
19_V139_K0.125320.680
53_L65_W0.124710.676
79_I158_M0.124650.676
152_S158_M0.124510.675
5_P72_S0.124490.675
14_P142_G0.124490.675
81_P85_S0.124440.675
95_I114_S0.12410.673
65_W75_L0.123670.671
9_K12_I0.122930.667
84_F121_Q0.12270.666
6_A14_P0.122690.666
72_S76_P0.122660.665
123_Y128_P0.121870.661
29_D57_A0.121850.661
13_G116_G0.120720.655
148_R156_D0.120720.655
139_K142_G0.12010.651
22_A76_P0.119990.651
144_R147_T0.119980.651
12_I132_V0.119820.650
78_E97_N0.118890.645
26_T62_K0.118810.644
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
3h0gA0.9811000.067
4aybA0.9811000.071
1twfA0.9811000.079
1hqmD0.90511000.289
3lu0D0.86081000.295
4kn7D0.86081000.295
2a6hD0.90511000.299
4igcD0.94399.90.405
3k8gA0.677224.10.936
3qasB0.487316.70.94

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