GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YtkA - YtkA-like
Pfam: PF13115 (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: CL0488
Length: 86
Sequences: 865
Seq/Len: 10.06
HH_delta: 0.735 (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
46_M77_M0.498883.386
25_T68_V0.331182.247
38_A69_Y0.309222.098
44_I81_W0.303612.060
27_T68_V0.282541.917
37_D63_E0.24191.642
17_P75_F0.216181.467
10_E27_T0.211161.433
76_S81_W0.202491.374
24_I83_I0.201131.365
36_T69_Y0.198181.345
36_T63_E0.192321.305
35_V38_A0.187571.273
22_N81_W0.187491.272
64_T70_E0.182671.240
44_I75_F0.180751.227
8_T29_D0.170171.155
45_W84_T0.169381.149
23_T70_E0.16881.146
21_E26_V0.167571.137
66_P70_E0.167261.135
9_V85_V0.161241.094
34_P66_P0.15831.074
16_P20_G0.157841.071
33_K63_E0.155541.056
24_I59_V0.155241.054
26_V38_A0.153311.040
7_Y35_V0.153071.039
43_E84_T0.15251.035
12_V25_T0.150561.022
64_T68_V0.148621.009
47_P82_Q0.148121.005
34_P67_G0.147931.004
56_T61_L0.147641.002
45_W56_T0.147621.002
45_W61_L0.146580.995
17_P42_F0.146280.993
6_G29_D0.143680.975
56_T59_V0.143510.974
39_D72_E0.143130.971
74_T77_M0.141630.961
13_S24_I0.140420.953
42_F85_V0.139950.950
56_T84_T0.139610.947
44_I83_I0.13860.941
58_K61_L0.138030.937
43_E58_K0.137280.932
75_F81_W0.137130.931
73_V81_W0.136290.925
28_V31_G0.135810.922
10_E23_T0.135720.921
41_Q63_E0.134680.914
11_L39_D0.134290.911
46_M78_A0.133610.907
63_E66_P0.133470.906
16_P19_V0.130740.887
42_F45_W0.130580.886
37_D40_V0.130420.885
42_F83_I0.130090.883
10_E28_V0.128540.872
9_V26_V0.128130.870
18_K21_E0.127910.868
29_D33_K0.127740.867
61_L67_G0.127710.867
75_F83_I0.126790.860
77_M81_W0.125880.854
33_K64_T0.125220.850
68_V82_Q0.123590.839
46_M56_T0.123180.836
10_E16_P0.123040.835
58_K84_T0.12150.825
63_E69_Y0.121330.823
31_G36_T0.120840.820
32_G58_K0.120840.820
23_T72_E0.120560.818
40_V85_V0.119310.810
23_T85_V0.119130.808
38_A63_E0.117870.800
7_Y56_T0.11780.799
46_M57_S0.11780.799
10_E41_Q0.117610.798
44_I48_D0.115990.787
17_P84_T0.115110.781
47_P56_T0.114850.779
16_P36_T0.114620.778
17_P38_A0.114520.777
31_G34_P0.114360.776
70_E75_F0.113710.772
23_T40_V0.113390.769
57_S69_Y0.113390.769
17_P20_G0.11290.766
61_L69_Y0.112770.765
65_G69_Y0.112580.764
9_V38_A0.111520.757
6_G11_L0.110910.753
30_Q69_Y0.110890.753
48_D66_P0.110870.752
42_F64_T0.110710.751
30_Q82_Q0.110480.750
44_I57_S0.109990.746
44_I80_T0.109070.740
40_V77_M0.108260.735
38_A58_K0.10780.732
8_T12_V0.107740.731
47_P71_A0.107660.731
19_V36_T0.107130.727
31_G39_D0.105820.718
6_G41_Q0.105530.716
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
3tkvA0.953590.70.735
1wlhA0.930289.90.74
3tkvA0.790789.20.743
2p9rA0.883789.10.744
2pn5A0.941988.40.747
1qfhA0.930287.20.751
2hr0A0.930281.90.767
1cwvA0.930281.80.767
2j3sA0.930281.60.768
3cu7A0.918681.30.769
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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