GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
P-II - Nitrogen regulatory protein P-II
Pfam: PF00543 (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: CL0089
Length: 102
Sequences: 2861
Seq/Len: 28.05
HH_delta: -0.034 (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
61_V93_V1.171653.897
62_V70_I1.024993.410
66_D69_E0.887872.953
2_E91_S0.750492.497
63_P66_D0.722452.403
3_A74_I0.655352.180
13_V78_A0.613362.040
20_A73_A0.605942.016
2_E57_K0.595951.982
72_E76_E0.557481.854
9_K12_E0.549931.829
71_V90_V0.535971.783
26_T30_V0.528041.757
73_A77_A0.524331.744
75_S79_R0.517561.722
26_T37_K0.508121.690
10_L56_V0.484041.610
15_E19_E0.459941.530
62_V67_V0.449741.496
28_S59_E0.443081.474
46_D49_F0.442251.471
69_E73_A0.420491.399
10_L27_V0.417181.388
28_S57_K0.409371.362
68_E72_E0.408831.360
17_L60_I0.408711.360
30_V57_K0.407871.357
5_I13_V0.399961.330
68_E95_D0.387261.288
1_I62_V0.379731.263
22_V70_I0.374521.246
33_R52_F0.370111.231
9_K43_Y0.359881.197
72_E75_S0.359881.197
2_E61_V0.359471.196
69_E72_E0.350731.167
16_A77_A0.350571.166
71_V88_I0.345081.148
2_E59_E0.341421.136
37_K50_V0.339291.129
16_A73_A0.331721.103
40_A47_E0.325881.084
67_V90_V0.322441.073
39_Q51_E0.322351.072
10_L14_I0.317361.056
16_A76_E0.313551.043
4_I89_F0.31011.032
23_P70_I0.309021.028
20_A69_E0.306041.018
16_A20_A0.30081.001
43_Y46_D0.297770.991
42_I49_F0.290450.966
4_I26_T0.284940.948
16_A19_E0.284790.947
14_I18_R0.280480.933
3_A78_A0.279660.930
36_Q55_K0.278420.926
2_E89_F0.276640.920
18_R33_R0.275350.916
67_V71_V0.274070.912
39_Q42_I0.272040.905
39_Q47_E0.268220.892
14_I25_M0.267170.889
13_V16_A0.266030.885
31_R54_P0.261920.871
74_I78_A0.261070.868
7_P54_P0.260860.868
61_V89_F0.259910.865
7_P31_R0.259180.862
1_I70_I0.247570.824
5_I58_I0.247090.822
87_K96_A0.237850.791
34_G84_G0.237320.789
34_G38_G0.235870.785
8_E12_E0.23560.784
62_V68_E0.235280.783
6_R81_G0.227970.758
44_R53_S0.225290.749
69_E76_E0.224810.748
19_E69_E0.224730.748
15_E46_D0.222390.740
68_E76_E0.221380.736
68_E75_S0.220780.734
66_D70_I0.216550.720
71_V75_S0.212380.706
5_I10_L0.210910.702
63_P67_V0.21090.702
7_P29_E0.209930.698
23_P49_F0.209330.696
3_A60_I0.207690.691
79_R82_E0.206740.688
18_R42_I0.205610.684
11_E37_K0.203370.677
29_E56_V0.199810.665
16_A78_A0.199160.663
19_E77_A0.198820.661
41_E46_D0.198770.661
25_M58_I0.197790.658
11_E52_F0.196950.655
8_E52_F0.196470.654
6_R84_G0.195330.650
6_R55_K0.194780.648
32_G84_G0.193710.644
24_G83_P0.193440.643
13_V17_L0.189090.629
33_R54_P0.188550.627
10_L58_I0.188260.626
36_Q87_K0.188060.626
22_V66_D0.18710.622
45_G48_Y0.1870.622
33_R39_Q0.186590.621
15_E49_F0.18590.618
3_A17_L0.18490.615
80_T84_G0.183970.612
1_I90_V0.181970.605
17_L58_I0.18130.603
42_I48_Y0.180520.600
14_I95_D0.178830.595
4_I24_G0.178630.594
42_I46_D0.178380.593
20_A23_P0.178130.593
27_V58_I0.178110.592
81_G88_I0.17780.591
62_V92_P0.177060.589
75_S92_P0.175870.585
15_E56_V0.175710.584
20_A70_I0.175160.583
23_P63_P0.175110.583
12_E77_A0.174630.581
36_Q53_S0.173670.578
60_I75_S0.173240.576
90_V95_D0.173170.576
64_D67_V0.172410.574
42_I82_E0.171770.571
65_E68_E0.170680.568
12_E48_Y0.16930.563
14_I27_V0.168550.561
21_G96_A0.167880.558
14_I23_P0.167220.556
25_M60_I0.167030.556
1_I13_V0.165810.552
21_G58_I0.165790.551
33_R40_A0.165560.551
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
3mhyA199.8-0.034
3ncqA199.8-0.03
3t9zA199.8-0.028
4affA199.8-0.024
3l7pA199.8-0.022
2ns1B199.8-0.003
1hwuA199.80.001
1vfjA199.80.001
2gw8A199.70.005
2j9cA199.70.006

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