GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Flavodoxin_NdrI - NrdI Flavodoxin like
Pfam: PF07972 (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: CL0042
Length: 122
Sequences: 4917
Seq/Len: 40.3
HH_delta: 0.188 (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
11_R15_E1.036613.210
79_G93_A0.971883.010
91_L95_K0.946692.932
44_I78_I0.877452.718
1_I18_G0.869012.691
10_T44_I0.833622.582
18_G22_P0.669232.073
6_L59_K0.610881.892
57_V92_A0.587411.819
97_A101_G0.576011.784
42_V76_G0.563591.745
75_R97_A0.561841.740
16_K20_Y0.561761.740
40_P74_L0.56051.736
91_L94_D0.559321.732
4_S58_P0.543131.682
62_I66_E0.480361.488
4_S60_Q0.472621.464
45_T96_I0.467241.447
43_L100_Y0.435761.350
20_Y24_I0.427911.325
10_T80_S0.42381.313
4_S61_V0.416761.291
17_L20_Y0.416231.289
43_L61_V0.412921.279
77_V93_A0.407121.261
12_R16_K0.4021.245
34_D37_V0.401361.243
65_L96_I0.400871.242
88_N91_L0.40061.241
19_L22_P0.381851.183
17_L42_V0.38131.181
4_S45_T0.381241.181
75_R101_G0.369851.145
8_G11_R0.356191.103
65_L95_K0.355971.102
5_S8_G0.353081.094
92_A96_I0.350191.085
95_K98_E0.346281.072
17_L44_I0.343441.064
81_G85_F0.34191.059
3_Y11_R0.336831.043
47_T88_N0.335481.039
5_S10_T0.330041.022
14_V78_I0.323841.003
13_F80_S0.320150.992
20_Y23_A0.318390.986
90_C93_A0.313720.972
47_T79_G0.311850.966
25_R28_I0.308120.954
49_G85_F0.305290.946
4_S46_P0.300960.932
2_Y43_L0.296750.919
1_I42_V0.293050.908
4_S48_Y0.292510.906
29_R34_D0.290010.898
90_C94_D0.287260.890
16_K19_L0.284720.882
80_S85_F0.279590.866
69_D99_K0.27870.863
21_A26_I0.278380.862
45_T61_V0.276750.857
47_T90_C0.275990.855
5_S50_F0.273420.847
9_N88_N0.272670.844
46_P58_P0.272090.843
82_N89_F0.269970.836
57_V65_L0.267710.829
61_V64_F0.265430.822
81_G90_C0.2640.818
18_G28_I0.263990.818
51_G76_G0.262880.814
82_N85_F0.261110.809
19_L24_I0.260520.807
10_T46_P0.258050.799
22_P28_I0.255650.792
71_R74_L0.255330.791
47_T85_F0.25530.791
15_E18_G0.255020.790
94_D98_E0.254350.788
21_A25_R0.252280.781
13_F79_G0.25050.776
43_L96_I0.249990.774
42_V75_R0.245950.762
93_A97_A0.243220.753
45_T92_A0.240320.744
89_F97_A0.239040.740
6_L46_P0.238290.738
22_P25_R0.238190.738
45_T58_P0.238070.737
22_P27_P0.236920.734
46_P82_N0.236640.733
67_N70_N0.234540.726
9_N12_R0.234090.725
66_E70_N0.233590.723
40_P45_T0.232060.719
57_V61_V0.23090.715
37_V40_P0.229960.712
57_V62_I0.229170.710
31_I38_D0.227650.705
2_Y41_F0.226330.701
4_S49_G0.22560.699
37_V72_K0.22450.695
19_L23_A0.224210.694
35_L64_F0.224170.694
13_F44_I0.224010.694
75_R100_Y0.22170.687
46_P60_Q0.221040.685
65_L99_K0.219420.680
13_F82_N0.219410.680
87_D90_C0.219370.679
1_I21_A0.219310.679
45_T49_G0.21890.678
79_G85_F0.218850.678
84_N87_D0.216820.672
47_T93_A0.21650.671
41_F73_L0.215410.667
46_P61_V0.214890.666
21_A24_I0.214750.665
34_D67_N0.214480.664
11_R63_R0.214320.664
44_I75_R0.212820.659
98_E101_G0.210270.651
64_F96_I0.207420.642
63_R67_N0.206980.641
51_G81_G0.206860.641
48_Y81_G0.205480.636
1_I14_V0.205380.636
43_L64_F0.202950.629
81_G89_F0.20220.626
7_T48_Y0.201450.624
73_L100_Y0.201270.623
3_Y15_E0.20010.620
94_D97_A0.200030.620
3_Y26_I0.199820.619
1_I17_L0.199290.617
35_L41_F0.197870.613
35_L38_D0.196770.609
18_G21_A0.196550.609
51_G92_A0.196440.608
77_V97_A0.195560.606
67_N87_D0.195390.605
31_I72_K0.194840.603
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
3n3aC0.942699.80.188
1rljA0.901699.80.212
2xodA0.893499.80.224
2hnaA0.95999.70.248
1bvyF0.950899.70.259
3qe2A0.95999.70.272
3hr4A0.950899.70.272
5nulA0.950899.70.273
2bpoA0.95999.70.278
4dikA0.942699.70.28

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