GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VirB3 - Type IV secretory pathway VirB3-like protein
Pfam: PF05101 (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: 89
Sequences: 442
Seq/Len: 4.97
HH_delta: 0.897 (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
30_N54_H0.311722.813
82_N86_Y0.181641.639
9_L14_T0.177431.601
56_I71_Y0.175771.586
22_V30_N0.167891.515
31_L39_L0.165511.494
60_T63_D0.163671.477
58_R62_K0.159441.439
84_R87_G0.156961.417
7_S13_L0.151351.366
80_S85_F0.149941.353
12_G17_A0.148921.344
19_I22_V0.144181.301
68_F72_L0.142531.286
17_A23_P0.14231.284
56_I85_F0.138281.248
49_I84_R0.137741.243
19_I27_F0.130991.182
8_P14_T0.13031.176
23_P86_Y0.128511.160
16_P66_Q0.126661.143
48_L52_I0.126511.142
22_V54_H0.126481.142
71_Y87_G0.125511.133
66_Q88_A0.123671.116
18_M53_L0.123461.114
33_L40_I0.122161.103
82_N87_G0.120991.092
29_L47_L0.120991.092
48_L51_I0.12011.084
7_S10_F0.118481.069
32_G47_L0.117821.063
26_P88_A0.117251.058
48_L55_F0.116481.051
33_L46_Y0.115061.038
12_G87_G0.114851.037
59_L70_I0.11441.033
22_V27_F0.112531.016
19_I28_I0.110891.001
43_S58_R0.11040.996
44_L53_L0.109820.991
53_L70_I0.109720.990
45_W48_L0.109020.984
18_M38_F0.108310.978
48_L81_R0.10790.974
14_T23_P0.107460.970
54_H67_F0.106870.965
25_E29_L0.106760.964
45_W49_I0.106230.959
35_F40_I0.105520.952
13_L16_P0.103640.935
23_P68_F0.10350.934
17_A80_S0.103130.931
8_P65_P0.102720.927
20_L41_I0.102490.925
14_T86_Y0.102440.925
28_I42_R0.102180.922
44_L47_L0.102090.921
28_I32_G0.101620.917
22_V61_C0.100780.910
50_F58_R0.100590.908
23_P67_F0.099950.902
66_Q69_E0.099050.894
12_G65_P0.098960.893
19_I58_R0.09850.889
48_L85_F0.098390.888
27_F40_I0.09730.878
33_L52_I0.097270.878
83_R88_A0.096980.875
9_L87_G0.09660.872
12_G73_R0.096580.872
34_A50_F0.095910.866
24_R73_R0.095530.862
29_L45_W0.095290.860
15_R86_Y0.094980.857
12_G34_A0.094670.854
15_R83_R0.094450.852
20_L28_I0.094320.851
49_I52_I0.094040.849
34_A38_F0.093840.847
12_G63_D0.093740.846
82_N88_A0.093680.846
11_K88_A0.093390.843
52_I72_L0.092760.837
10_F22_V0.092280.833
81_R84_R0.092220.832
47_L81_R0.091690.828
35_F44_L0.091520.826
7_S17_A0.091440.825
15_R87_G0.091280.824
36_L40_I0.091150.823
69_E83_R0.090520.817
8_P41_I0.090410.816
11_K37_L0.09020.814
53_L57_A0.089790.810
52_I56_I0.089780.810
15_R70_I0.089490.808
25_E36_L0.089110.804
30_N57_A0.088850.802
20_L36_L0.088820.802
24_R31_L0.088740.801
47_L50_F0.088490.799
69_E72_L0.088480.799
27_F36_L0.088440.798
12_G20_L0.088250.797
31_L37_L0.08820.796
79_R82_N0.088170.796
34_A70_I0.088150.796
12_G23_P0.088040.795
37_L57_A0.087890.793
12_G62_K0.087860.793
45_W72_L0.087810.793
13_L68_F0.087490.790
13_L80_S0.086550.781
26_P63_D0.086390.780
10_F13_L0.086210.778
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:
PDB Cov Prob HH_delta
4djkA0.87648.30.897
2aq4A0.33714.90.906
2kv9B0.28092.90.915
1vq8O0.33712.50.918
3giaA0.85392.30.92
3arcX0.43822.20.92
3ne5A0.741620.922
1ipaA0.35961.50.927
3rq4A0.43821.50.927
3mdmA0.33711.40.929
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0262 seconds.