GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RnfC_N - RnfC Barrel sandwich hybrid domain
Pfam: PF13375 (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: CL0105
Length: 101
Sequences: 894
Seq/Len: 8.85
HH_delta: 0.776 (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
78_T97_E0.615822.971
73_V98_N0.611912.952
51_K76_T0.561592.709
32_I72_S0.542.605
50_D56_Q0.529912.556
45_V57_L0.518632.502
76_T97_E0.434582.096
47_K50_D0.429552.072
29_K97_E0.339371.637
74_S99_D0.338421.632
28_K97_E0.335451.618
82_K92_P0.33031.593
57_L68_P0.327351.579
31_V93_A0.321891.553
7_I11_E0.317111.530
57_L60_E0.314671.518
42_A59_A0.309681.494
54_K74_S0.305541.474
59_A94_I0.304721.470
61_A66_S0.293471.416
51_K99_D0.293081.414
91_V94_I0.29281.412
32_I69_I0.290791.403
48_V79_A0.288581.392
30_V73_V0.285691.378
30_V96_I0.28191.360
29_K78_T0.277831.340
43_E60_E0.263341.270
63_G66_S0.252551.218
83_R95_V0.251961.215
30_V72_S0.246541.189
83_R93_A0.241691.166
77_V96_I0.238441.150
27_P30_V0.236831.142
81_E95_V0.235391.135
8_H11_E0.234191.130
74_S100_G0.230671.113
54_K73_V0.222631.074
31_V83_R0.218371.053
44_P58_I0.212991.027
33_P93_A0.211111.018
38_I65_L0.210541.016
32_I58_I0.207311.000
44_P59_A0.206540.996
32_I96_I0.204720.987
34_L59_A0.202590.977
24_A27_P0.200980.969
11_E14_E0.200870.969
62_E82_K0.198740.959
79_A95_V0.197210.951
40_A62_E0.196290.947
59_A69_I0.193470.933
42_A68_P0.193390.933
40_A63_G0.192840.930
81_E93_A0.191070.922
77_V94_I0.190680.920
79_A83_R0.189750.915
58_I96_I0.189730.915
61_A64_F0.188360.909
4_R17_K0.186290.899
59_A80_I0.185120.893
53_K56_Q0.182150.879
53_K76_T0.180910.873
44_P94_I0.18070.872
74_S98_N0.180650.871
31_V95_V0.179610.866
30_V98_N0.179190.864
54_K71_A0.177550.856
29_K83_R0.175810.848
60_E63_G0.174890.844
10_P14_E0.173670.838
8_H13_K0.172790.833
43_E62_E0.172440.832
59_A67_A0.17140.827
33_P36_Q0.171360.827
60_E68_P0.17110.825
5_G11_E0.169970.820
42_A63_G0.169960.820
61_A65_L0.165240.797
29_K79_A0.165040.796
12_H17_K0.160960.776
7_I10_P0.16020.773
5_G9_P0.159620.770
45_V68_P0.159550.770
9_P12_H0.159440.769
35_R91_V0.159250.768
44_P67_A0.158770.766
7_I17_K0.158280.763
34_L44_P0.158220.763
84_P90_K0.157780.761
61_A67_A0.155350.749
42_A61_A0.15280.737
46_V56_Q0.152630.736
7_I13_K0.152520.736
28_K76_T0.152020.733
45_V60_E0.151710.732
39_G50_D0.151370.730
28_K98_N0.150460.726
54_K100_G0.150110.724
40_A66_S0.147360.711
88_G91_V0.146450.706
37_H41_P0.145260.701
53_K99_D0.144480.697
11_E17_K0.142330.687
4_R25_P0.141490.682
29_K95_V0.141320.682
14_E47_K0.140070.676
42_A58_I0.138380.667
34_L80_I0.137560.664
4_R78_T0.137120.661
39_G46_V0.137120.661
36_Q41_P0.135570.654
64_F67_A0.134760.650
47_K64_F0.134360.648
42_A66_S0.133660.645
31_V94_I0.132960.641
31_V81_E0.132120.637
42_A67_A0.131230.633
34_L94_I0.130770.631
32_I70_H0.13070.630
53_K74_S0.130550.630
3_F6_G0.130530.630
58_I91_V0.130350.629
6_G9_P0.130270.628
25_P28_K0.129460.624
73_V90_K0.128470.620
5_G13_K0.128460.620
71_A74_S0.128140.618
14_E18_D0.127840.617
24_A100_G0.127540.615
48_V80_I0.127340.614
49_G69_I0.126390.610
19_K22_E0.125410.605
38_I66_S0.125020.603
46_V77_V0.125010.603
26_L30_V0.1250.603
48_V51_K0.123720.597
79_A82_K0.123530.596
18_D22_E0.123410.595
49_G94_I0.122820.592
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
3u9tA0.930797.10.776
3hblA0.940697.10.776
3va7A0.90196.90.784
3n6rA0.920896.80.789
3dvaI0.762496.60.793
1y8oB0.940696.60.794
1qjoA0.732796.50.797
2k7vA0.693196.40.798
3crkC0.762496.40.8
4hr7B0.891196.40.8
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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