GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Terminase_4 - Phage terminase small subunit
Pfam: PF05119 (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: 100
Sequences: 559
Seq/Len: 5.59
HH_delta: 0.862 (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
4_E7_R0.45343.276
5_W30_C0.393082.840
22_D87_R0.371492.684
40_E66_L0.268261.938
39_A65_I0.262761.898
71_K75_S0.260191.880
29_Y73_M0.257561.861
42_E46_E0.238881.726
35_R40_E0.237661.717
25_L80_L0.22211.605
25_L83_T0.216171.562
33_Y73_M0.214671.551
27_E37_R0.211511.528
42_E62_A0.198081.431
36_Y66_L0.19441.405
67_N71_K0.189181.367
25_L79_E0.187731.356
5_W10_P0.187381.354
79_E83_T0.181641.312
38_E44_K0.176181.273
28_R36_Y0.175381.267
42_E60_N0.175261.266
11_E21_L0.174091.258
46_E60_N0.170981.235
28_R77_A0.170811.234
18_L26_L0.166771.205
70_M76_L0.160711.161
28_R76_L0.158791.147
4_E29_Y0.153151.106
52_T55_G0.152351.101
9_V26_L0.151111.092
77_A83_T0.150491.087
21_L84_P0.149331.079
43_L46_E0.148991.076
43_L66_L0.148511.073
15_L90_L0.146971.062
29_Y77_A0.145491.051
36_Y73_M0.145231.049
3_K6_K0.144211.042
15_L21_L0.144061.041
43_L47_G0.142591.030
85_A89_K0.142051.026
7_R11_E0.141521.022
84_P88_A0.141251.021
2_K6_K0.140191.013
75_S79_E0.138891.003
52_T58_K0.134630.973
4_E8_I0.134510.972
35_R66_L0.133930.968
81_G87_R0.133320.963
33_Y87_R0.127470.921
31_E36_Y0.126550.914
28_R70_M0.126310.913
24_P29_Y0.126220.912
53_K56_N0.125780.909
8_I26_L0.125420.906
77_A90_L0.124620.900
29_Y80_L0.124040.896
30_C33_Y0.122590.886
79_E88_A0.122520.885
32_A73_M0.122160.883
83_T86_S0.122160.883
11_E20_N0.122140.882
46_E62_A0.122010.882
39_A62_A0.121690.879
12_L32_A0.121340.877
62_A68_K0.119530.864
24_P36_Y0.119070.860
12_L90_L0.118380.855
28_R33_Y0.118360.855
28_R37_R0.116910.845
85_A88_A0.116790.844
12_L16_G0.116330.840
68_K89_K0.114880.830
25_L29_Y0.114470.827
18_L30_C0.114370.826
36_Y40_E0.113780.822
11_E15_L0.113770.822
14_E53_K0.113640.821
68_K71_K0.113580.821
26_L80_L0.113290.819
59_K64_S0.113230.818
50_V57_P0.113190.818
30_C73_M0.112630.814
5_W27_E0.111680.807
49_V65_I0.111480.805
74_R78_S0.109990.795
39_A69_A0.109620.792
79_E85_A0.109550.791
43_L64_S0.109060.788
47_G61_P0.108980.787
80_L84_P0.108850.786
67_N72_Q0.108280.782
18_L22_D0.108240.782
10_P14_E0.108150.781
66_L70_M0.107770.779
79_E84_P0.107090.774
32_A69_A0.106950.773
79_E86_S0.106240.768
36_Y69_A0.106220.767
19_S89_K0.105780.764
25_L76_L0.104520.755
8_I82_L0.103860.750
3_K59_K0.103720.749
2_K45_K0.101380.732
11_E16_G0.101260.732
30_C34_S0.100740.728
17_I90_L0.100640.727
10_P13_K0.100640.727
49_V62_A0.100010.723
7_R24_P0.099970.722
42_E49_V0.099120.716
10_P30_C0.098870.714
5_W23_V0.098040.708
24_P48_F0.097960.708
32_A72_Q0.097280.703
23_V34_S0.097280.703
27_E47_G0.096240.695
4_E19_S0.096030.694
43_L62_A0.095850.693
33_Y37_R0.095760.692
58_K64_S0.095260.688
44_K64_S0.095110.687
48_F62_A0.094750.685
29_Y33_Y0.094030.679
52_T57_P0.093920.679
39_A48_F0.093860.678
4_E33_Y0.093560.676
19_S37_R0.093290.674
11_E54_N0.092940.671
9_V80_L0.092850.671
19_S84_P0.092780.670
44_K50_V0.092360.667
15_L77_A0.092070.665
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
4ahqA0.62520.862
3f8mA0.9731.50.878
4bgoA0.7726.20.883
2ra5A0.9824.70.884
2o35A0.8622.70.885
3neuA0.9922.40.886
2wv0A119.10.889
3by6A118.20.89
2bbzA0.9915.20.894
3fybA0.86150.894
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0302 seconds.