GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ANT - Phage antirepressor protein KilAC domain
Pfam: PF03374 (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: 659
Seq/Len: 5.94
HH_delta: 0.853 (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
8_L12_A0.790345.197
5_I8_L0.661364.349
11_K16_D0.495563.258
28_R38_R0.361672.378
4_Q8_L0.353412.324
24_L72_E0.352372.317
80_H86_K0.324932.136
44_W48_K0.314642.069
62_Y65_Y0.257431.693
71_F93_I0.249981.644
63_Q66_I0.249961.644
43_Q47_E0.246291.619
37_G40_K0.237161.559
32_K52_Y0.236281.554
46_R59_N0.235851.551
80_H84_E0.232341.528
71_F91_T0.22741.495
24_L92_R0.222651.464
70_Y100_W0.222341.462
30_A98_L0.215681.418
27_I41_L0.213851.406
50_W100_W0.212251.396
38_R42_F0.208711.372
9_A12_A0.207921.367
9_A13_E0.207781.366
27_I42_F0.207331.363
30_A93_I0.205811.353
48_K104_R0.200091.316
12_A16_D0.194241.277
61_P71_F0.192381.265
26_T92_R0.189651.247
50_W101_I0.188931.242
18_F95_P0.184591.214
42_F46_R0.181851.196
29_E73_V0.176261.159
26_T90_Q0.175291.153
50_W65_Y0.174771.149
69_G96_K0.174681.149
74_K92_R0.173461.141
49_G62_Y0.171331.127
36_I40_K0.165931.091
3_A6_A0.164321.080
27_I38_R0.163831.077
42_F59_N0.158681.043
51_L61_P0.157931.038
6_A9_A0.154541.016
66_I96_K0.153131.007
16_D19_V0.15271.004
4_Q7_E0.150720.991
11_K15_Y0.146940.966
18_F101_I0.145640.958
26_T29_E0.145530.957
48_K105_L0.144040.947
75_E87_T0.140860.926
27_I93_I0.140770.926
79_T85_G0.139620.918
41_L101_I0.139440.917
37_G63_Q0.139370.916
76_T80_H0.139030.914
61_P73_V0.138450.910
30_A101_I0.13710.901
31_A41_L0.136830.900
31_A94_T0.135630.892
29_E60_L0.135420.890
10_P16_D0.135260.889
7_E13_E0.133940.881
76_T88_S0.133350.877
64_K68_A0.132930.874
5_I12_A0.131960.868
28_R42_F0.130830.860
14_F19_V0.130210.856
39_N43_Q0.129620.852
62_Y101_I0.129060.849
23_G75_E0.126020.829
64_K70_Y0.124720.820
7_E12_A0.12430.817
33_L98_L0.124140.816
44_W65_Y0.122690.807
32_K63_Q0.122230.804
4_Q12_A0.12170.800
50_W104_R0.12160.800
5_I16_D0.121270.797
52_Y55_G0.121030.796
51_L71_F0.120450.792
60_L73_V0.120390.792
25_Y30_A0.119880.788
77_T87_T0.119540.786
15_Y18_F0.118790.781
23_G69_G0.118520.779
13_E17_A0.115950.762
55_G58_R0.114980.756
65_Y71_F0.114770.755
14_F18_F0.113330.745
81_S86_K0.113030.743
100_W104_R0.112950.743
14_F98_L0.11110.731
74_K90_Q0.11050.727
62_Y66_I0.110070.724
47_E67_D0.109850.722
50_W71_F0.109660.721
21_S72_E0.109140.718
13_E68_A0.108520.714
44_W88_S0.107710.708
78_Y86_K0.107170.705
6_A84_E0.106470.700
13_E23_G0.106460.700
73_V91_T0.106390.700
37_G93_I0.105480.694
3_A7_E0.105280.692
32_K55_G0.10450.687
30_A41_L0.104260.686
28_R37_G0.104170.685
4_Q107_K0.104090.684
102_A106_A0.103550.681
3_A13_E0.103290.679
9_A100_W0.102650.675
20_D104_R0.102530.674
20_D25_Y0.10170.669
51_L59_N0.100730.662
56_K75_E0.100590.661
32_K74_K0.100440.660
25_Y33_L0.100080.658
6_A64_K0.098630.649
22_D70_Y0.098440.647
34_L105_L0.098010.644
42_F93_I0.097570.642
29_E57_G0.097130.639
43_Q88_S0.096950.637
28_R32_K0.096790.636
80_H104_R0.096750.636
14_F95_P0.096650.635
24_L86_K0.096620.635
95_P99_E0.096390.634
36_I41_L0.096290.633
46_R49_G0.096190.632
17_A102_A0.095440.628
93_I100_W0.094950.624
3_A43_Q0.09460.622
99_E106_A0.093590.615
18_F99_E0.093590.615
52_Y59_N0.093510.615
35_G39_N0.093390.614
34_L102_A0.093260.613
66_I73_V0.092810.610
5_I60_L0.09260.609
81_S84_E0.092560.609
52_Y57_G0.092180.606
81_S85_G0.092040.605
40_K67_D0.091940.605
3_A22_D0.091150.599
55_G66_I0.091030.599
30_A73_V0.090960.598
76_T79_T0.090770.597
35_G43_Q0.090570.596
53_R57_G0.090450.595
19_V99_E0.090410.594
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
1y6uA0.603686.40.853
3hrsA0.648684.90.856
2o0mA0.693784.20.857
1g2hA0.432483.90.858
1ntcA0.432482.70.86
1etoA0.423482.60.86
1umqA0.423482.60.86
3nrvA0.756880.40.863
3fm5A0.765879.90.864
1p4xA0.765877.90.866
If you are interested in a protein containing this domain,
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