GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
KilA-N - KilA-N domain
Pfam: PF04383 (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. )
Length: 111
Sequences: 513
Seq/Len: 4.62
HH_delta: 0.704 (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
88_H98_A0.511293.759
32_K35_S0.388262.855
36_N39_R0.350842.580
40_N43_T0.299612.203
87_I106_N0.246361.811
11_R15_D0.229731.689
101_V105_I0.228451.680
104_I108_Y0.225891.661
98_A102_S0.218181.604
20_A81_V0.215571.585
99_L102_S0.213291.568
49_E96_K0.193621.424
23_L90_A0.188441.386
88_H91_M0.18451.357
47_I85_L0.184241.355
48_K51_S0.183571.350
74_G77_Q0.181531.335
12_R28_G0.180681.328
53_E56_I0.174871.286
73_N77_Q0.17271.270
83_P106_N0.168791.241
101_V104_I0.167631.233
70_K73_N0.166111.221
99_L103_K0.165261.215
46_L85_L0.162991.198
24_C89_Y0.162711.196
83_P87_I0.162481.195
42_S49_E0.159911.176
91_M102_S0.158461.165
46_L99_L0.158071.162
55_N58_K0.155221.141
46_L98_A0.147971.088
51_S58_K0.147841.087
33_R36_N0.147411.084
46_L102_S0.14641.076
69_I75_R0.144851.065
9_I12_R0.144441.062
96_K100_K0.144151.060
51_S55_N0.143671.056
41_K45_E0.142731.049
34_P76_I0.141191.038
19_N82_H0.141091.037
34_P89_Y0.141031.037
46_L88_H0.140381.032
37_W43_T0.138641.019
7_E17_Y0.137851.014
66_S72_K0.135360.995
91_M98_A0.135220.994
72_K77_Q0.134820.991
70_K74_G0.134690.990
92_W96_K0.133660.983
24_C32_K0.131580.967
18_I21_T0.130660.961
54_Y58_K0.130510.960
74_G89_Y0.130340.958
23_L101_V0.12970.954
84_E103_K0.128920.948
44_K47_I0.128710.946
9_I14_E0.128170.942
32_K36_N0.127820.940
24_C34_P0.126460.930
9_I15_D0.125730.924
49_E92_W0.125640.924
69_I72_K0.125150.920
82_H105_I0.123870.911
24_C36_N0.123610.909
35_S40_N0.123430.908
52_E55_N0.122230.899
7_E11_R0.121940.897
35_S44_K0.121570.894
21_T24_C0.121290.892
71_G77_Q0.119490.879
17_Y21_T0.117860.867
81_V86_A0.116940.860
19_N105_I0.116210.854
87_I102_S0.115770.851
37_W80_Y0.115690.851
44_K48_K0.115060.846
68_V73_N0.114920.845
35_S39_R0.114860.845
79_T99_L0.114720.843
95_P98_A0.113950.838
88_H102_S0.113450.834
27_F93_I0.113440.834
97_F101_V0.11280.829
11_R14_E0.110730.814
26_A90_A0.110230.810
39_R44_K0.11020.810
83_P102_S0.109890.808
17_Y82_H0.109730.807
71_G79_T0.109720.807
81_V91_M0.108760.800
50_L55_N0.108560.798
18_I81_V0.108410.797
53_E57_S0.107010.787
8_V19_N0.105150.773
52_E57_S0.105040.772
37_W47_I0.104770.770
24_C91_M0.10430.767
7_E25_K0.102860.756
23_L26_A0.102680.755
23_L93_I0.102330.752
81_V89_Y0.101860.749
100_K107_E0.101790.748
16_G83_P0.101520.746
9_I106_N0.101030.743
49_E95_P0.100680.740
106_N109_H0.100360.738
84_E89_Y0.100070.736
51_S54_Y0.099880.734
40_N65_I0.099850.734
68_V74_G0.099740.733
68_V77_Q0.099670.733
71_G74_G0.098780.726
21_T79_T0.09850.724
19_N22_K0.098120.721
23_L91_M0.097840.719
36_N53_E0.097780.719
46_L91_M0.097320.716
51_S57_S0.097320.716
84_E99_L0.097280.715
48_K55_N0.09710.714
86_A90_A0.097060.714
28_G33_R0.096310.708
51_S56_I0.096080.706
7_E12_R0.095910.705
53_E65_I0.09580.704
105_I108_Y0.095790.704
46_L49_E0.09540.701
92_W97_F0.095370.701
50_L58_K0.094870.698
84_E106_N0.094780.697
25_K44_K0.094550.695
17_Y83_P0.094420.694
8_V11_R0.094330.694
94_S97_F0.094270.693
90_A97_F0.094160.692
65_I71_G0.093860.690
8_V17_Y0.093350.686
32_K93_I0.092550.680
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
1mb1A0.792898.40.704
1bm8A0.711798.10.733
2czyA0.621651.90.898
2do5A0.378434.10.908
2cr7A0.630622.80.915
1i17A0.585614.10.922
2hpsA0.747713.60.923
3lr1A0.414410.70.926
3muqA0.43249.80.927
2gutA0.25238.90.929
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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