GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NusG - Transcription termination factor nusG
Pfam: PF02357 (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: CL0439
Length: 92
Sequences: 1759
Seq/Len: 19.12
HH_delta: 0.046 (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
17_A21_E1.042514.773
26_E60_R0.668313.060
33_E47_R0.655473.001
33_E49_E0.531442.433
36_R50_R0.47022.153
16_V76_V0.463342.121
8_T13_E0.45452.081
31_M49_E0.4361.996
35_I45_V0.414711.899
32_R50_R0.413781.895
61_M67_L0.383091.754
23_Q73_T0.360971.653
60_R91_D0.3111.424
15_K18_E0.308551.413
18_E22_R0.296261.356
13_E29_L0.292191.338
12_K75_G0.291941.337
52_L58_F0.285121.305
9_K12_K0.284921.305
16_V57_V0.275791.263
15_K19_R0.271681.244
6_L76_V0.26781.226
7_R77_S0.266271.219
38_R46_K0.262511.202
53_F56_Y0.261871.199
58_F89_V0.260351.192
37_R45_V0.256411.174
34_V50_R0.253941.163
38_R41_R0.253781.162
25_I60_R0.252311.155
43_K46_K0.252121.154
41_R46_K0.247391.133
19_R73_T0.239821.098
19_R23_Q0.238361.091
35_I47_R0.23641.082
7_R78_G0.235181.077
64_E67_L0.233981.071
12_K15_K0.232151.063
13_E55_G0.2311.058
66_E69_K0.230991.058
16_V73_T0.227981.044
53_F58_F0.224881.030
23_Q74_P0.214460.982
20_L76_V0.209970.961
78_G81_R0.209930.961
76_V86_P0.208360.954
5_V80_L0.205320.940
6_L22_R0.203950.934
68_W71_R0.200310.917
37_R43_K0.199450.913
62_D69_K0.194830.892
81_R88_P0.194240.889
14_Q31_M0.19420.889
5_V89_V0.189020.865
23_Q59_V0.187970.861
31_M82_F0.187640.859
14_Q49_E0.187180.857
18_E21_E0.186870.856
21_E27_A0.18270.837
69_K72_S0.181860.833
9_K75_G0.181640.832
8_T12_K0.181520.831
77_S80_L0.180480.826
21_E26_E0.180110.825
23_Q92_E0.177070.811
31_M46_K0.176510.808
14_Q17_A0.176460.808
11_G68_W0.175180.802
36_R42_G0.174870.801
24_G64_E0.174030.797
7_R81_R0.174010.797
19_R72_S0.172920.792
53_F70_I0.171680.786
7_R55_G0.17060.781
28_F31_M0.170530.781
20_L23_Q0.169350.775
70_I83_G0.168060.769
77_S81_R0.167470.767
12_K19_R0.166040.760
74_P82_F0.163170.747
24_G70_I0.162660.745
81_R86_P0.162570.744
34_V48_V0.162560.744
37_R64_E0.162140.742
31_M87_A0.161030.737
8_T14_Q0.160950.737
28_F91_D0.160540.735
17_A29_L0.160420.735
63_M68_W0.160060.733
28_F60_R0.159290.729
20_L73_T0.159110.729
72_S77_S0.158430.725
24_G59_V0.157220.720
61_M76_V0.157190.720
14_Q21_E0.15650.717
28_F33_E0.156320.716
63_M84_G0.155850.714
49_E91_D0.153970.705
8_T55_G0.153910.705
80_L83_G0.153610.703
15_K91_D0.152740.699
31_M53_F0.152670.699
82_F87_A0.151920.696
32_R88_P0.150240.688
29_L57_V0.14920.683
7_R48_V0.149150.683
9_K53_F0.148620.680
58_F87_A0.147970.678
37_R41_R0.146220.669
48_V69_K0.145830.668
22_R51_P0.145470.666
26_E82_F0.14530.665
25_I66_E0.1450.664
18_E43_K0.143670.658
36_R48_V0.142630.653
19_R75_G0.14220.651
28_F53_F0.141940.650
20_L27_A0.139620.639
37_R47_R0.139580.639
26_E66_E0.139190.637
10_P30_P0.138910.636
2_R88_P0.138710.635
53_F75_G0.138590.635
20_L59_V0.138520.634
59_V73_T0.137850.631
12_K29_L0.137850.631
43_K60_R0.137350.629
68_W80_L0.137040.627
49_E74_P0.136920.627
22_R35_I0.136390.624
12_K51_P0.135830.622
24_G84_G0.134840.617
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
2ougA0.967499.80.046
1nz8A0.967499.80.077
2jvvA0.967499.80.08
2lq8A0.945799.70.185
1m1hA0.989199.70.212
3p8bB0.793599.30.395
3lpeA0.7599.20.411
2xhcA0.9239990.455
2xhcA0.934896.90.712
2exuA0.902293.30.781

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