GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF977 - Bacterial protein of unknown function (DUF977)
Pfam: PF06163 (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: CL0123
Length: 127
Sequences: 1240
Seq/Len: 9.76
HH_delta: 0.53 (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
32_L43_V0.521862.880
41_N45_R0.424732.344
16_R19_E0.40242.221
86_L89_K0.394732.178
41_N101_R0.387352.138
20_L35_K0.38052.100
88_W108_E0.379472.094
15_A19_E0.374272.065
17_I32_L0.360771.991
16_R20_L0.341941.887
47_L58_R0.316241.745
76_K80_K0.296971.639
13_L46_Y0.291781.610
85_D88_W0.290351.602
14_K53_R0.283421.564
19_E23_E0.279921.545
87_I109_C0.268341.481
91_P112_S0.26411.457
38_A43_V0.258781.428
38_A41_N0.25831.425
21_V56_L0.253271.398
20_L27_I0.248941.374
101_R104_I0.248691.372
20_L23_E0.246371.360
20_L24_H0.244341.348
21_V39_S0.242451.338
97_R109_C0.237391.310
12_E16_R0.233871.291
71_R74_W0.232551.283
18_V21_V0.230721.273
30_K40_R0.229311.265
87_I108_E0.229051.264
44_K59_H0.227551.256
32_L47_L0.222221.226
68_E80_K0.218791.207
81_L88_W0.21511.187
84_P103_N0.212211.171
49_E52_A0.211911.169
29_I47_L0.211041.165
12_E26_R0.210011.159
73_D78_R0.208071.148
77_A80_K0.202871.119
87_I104_I0.201271.111
24_H31_Q0.19141.056
51_V58_R0.191131.055
83_D86_L0.190961.054
84_P108_E0.183821.014
42_T46_Y0.183491.013
48_R58_R0.182961.010
18_V55_D0.178590.986
82_V90_L0.178210.983
108_E111_K0.177290.978
75_D78_R0.176970.977
14_K36_T0.176530.974
42_T45_R0.175630.969
16_R35_K0.17240.951
71_R75_D0.171550.947
27_I61_R0.170180.939
48_R56_L0.169560.936
48_R52_A0.168380.929
27_I32_L0.168010.927
80_K90_L0.1680.927
95_I100_R0.165260.912
68_E72_K0.16440.907
76_K79_K0.164350.907
30_K47_L0.163560.903
92_D95_I0.16040.885
12_E15_A0.159470.880
64_V71_R0.159340.879
28_T31_Q0.158660.876
11_E64_V0.157010.866
24_H35_K0.155150.856
58_R100_R0.154710.854
14_K45_R0.153510.847
24_H34_A0.153280.846
91_P94_E0.153060.845
51_V56_L0.151660.837
96_R101_R0.149090.823
29_I41_N0.147270.813
15_A70_A0.147070.812
31_Q35_K0.14660.809
33_V40_R0.146470.808
13_L99_D0.146130.806
48_R107_R0.145080.801
22_R55_D0.144310.796
43_V48_R0.144230.796
29_I40_R0.144010.795
11_E17_I0.1440.795
83_D104_I0.143580.792
22_R65_F0.142050.784
77_A89_K0.141970.783
50_L58_R0.141950.783
84_P96_R0.141820.783
50_L99_D0.140510.775
17_I72_K0.140470.775
29_I43_V0.138850.766
49_E53_R0.137450.758
83_D100_R0.137390.758
18_V50_L0.13520.746
82_V102_Q0.134960.745
89_K93_G0.133380.736
47_L51_V0.133310.736
11_E14_K0.132860.733
69_Q76_K0.132580.732
40_R45_R0.13250.731
27_I33_V0.132090.729
63_G81_L0.131950.728
47_L59_H0.13130.725
21_V34_A0.131070.723
85_D106_C0.129880.717
45_R61_R0.129440.714
71_R91_P0.129420.714
39_S45_R0.128530.709
53_R56_L0.128150.707
45_R101_R0.127560.704
74_W78_R0.127410.703
27_I68_E0.126330.697
14_K18_V0.125870.695
33_V45_R0.125850.694
23_E73_D0.124930.689
80_K94_E0.12360.682
86_L91_P0.12290.678
46_Y60_G0.122530.676
49_E77_A0.122480.676
83_D106_C0.122280.675
26_R33_V0.12220.674
33_V41_N0.121710.672
50_L55_D0.120980.668
94_E110_R0.120530.665
66_P75_D0.120010.662
33_V43_V0.119990.662
68_E74_W0.119360.659
22_R89_K0.119340.659
70_A74_W0.119260.658
77_A95_I0.118450.654
48_R51_V0.11810.652
46_Y99_D0.117970.651
29_I58_R0.117840.650
33_V38_A0.117710.650
75_D79_K0.117590.649
69_Q72_K0.117580.649
21_V50_L0.117490.648
70_A73_D0.117190.647
38_A42_T0.117180.647
67_S71_R0.115970.640
14_K49_E0.115510.637
58_R99_D0.115320.636
71_R76_K0.114630.633
58_R97_R0.114420.631
25_G60_G0.114290.631
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
1stzA199.60.53
2jt1A0.5512990.657
1xn7A0.5906990.661
4a0zA0.960698.90.667
2w48A0.93798.80.687
2b0lA0.653598.80.688
2k02A0.614298.70.689
3f8mA0.929198.70.694
2di3A0.984398.70.698
3c7jA0.984398.70.699
If you are interested in a protein containing this domain,
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