GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF285 - Mycoplasma protein of unknown function DUF285
Pfam: PF03382 (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: CL0022
Length: 120
Sequences: 1591
Seq/Len: 13.26
HH_delta: 0.769 (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
28_M50_V0.83942.503
53_M75_V0.781082.329
60_C85_C0.704352.100
49_N74_N0.663241.978
85_C110_C0.622891.857
35_C60_C0.611951.825
45_W70_W0.609361.817
24_N49_N0.60421.802
70_W95_W0.597671.782
3_L25_V0.596791.780
60_C110_C0.596141.778
35_C85_C0.593721.770
74_N99_S0.587031.751
78_M100_V0.583251.739
24_N74_N0.551921.646
49_N99_S0.548581.636
100_V103_M0.504161.503
36_T61_S0.49631.480
20_W45_W0.480021.431
61_S86_S0.478511.427
6_M10_C0.47761.424
10_C13_L0.475341.417
47_T72_T0.456951.363
41_D91_D0.456171.360
62_S87_S0.447551.335
24_N99_S0.445661.329
31_M56_M0.437981.306
73_S98_S0.42941.280
97_T103_M0.427251.274
22_T28_M0.425591.269
40_Q90_Q0.423151.262
75_V78_M0.420241.253
37_S62_S0.420111.253
10_C35_C0.419581.251
84_G109_N0.414031.235
81_M106_M0.410891.225
23_S48_S0.410481.224
39_N89_N0.406591.212
63_L88_L0.401991.199
39_N65_Q0.401351.197
29_S52_N0.400851.195
38_L63_L0.399891.192
22_T47_T0.397051.184
6_M31_M0.395971.181
10_C60_C0.395861.180
50_V53_M0.393921.175
26_T51_T0.393471.173
47_T53_M0.393441.173
56_M81_M0.389621.162
65_Q90_Q0.389011.160
48_S73_S0.385881.151
110_C113_L0.384571.147
54_S77_N0.374951.118
4_S27_D0.37191.109
76_T101_T0.363011.082
40_Q65_Q0.361311.077
3_L6_M0.36041.075
19_N44_N0.358541.069
45_W95_W0.35691.064
43_S68_S0.35671.064
3_L31_M0.355331.060
11_T36_T0.353651.055
42_L67_L0.349271.042
62_S112_N0.347861.037
35_C110_C0.344151.026
44_N69_N0.336521.004
68_S93_S0.328220.979
34_G59_G0.325820.972
30_Y55_G0.322390.961
35_C38_L0.321080.957
38_L88_L0.320320.955
9_N34_G0.319540.953
69_N94_N0.318770.951
25_V28_M0.313510.935
59_G84_G0.312260.931
48_S98_S0.307850.918
42_L92_L0.306920.915
53_M78_M0.306270.913
18_S43_S0.304980.909
10_C85_C0.304730.909
85_C88_L0.302110.901
17_I20_W0.30160.899
67_L92_L0.300690.897
44_N94_N0.29950.893
78_M81_M0.299380.893
13_L16_D0.298440.890
28_M56_M0.297970.889
15_I18_S0.295440.881
10_C15_I0.294240.877
87_S112_N0.292670.873
33_Y58_A0.289550.863
58_A83_S0.288990.862
12_N37_S0.288940.862
53_M81_M0.288790.861
86_S111_S0.287080.856
30_Y33_Y0.286430.854
78_M106_M0.283180.844
65_Q89_N0.280310.836
51_T76_T0.277660.828
15_I40_Q0.277030.826
105_S108_A0.275410.821
72_T97_T0.274930.820
15_I20_W0.272540.813
66_D90_Q0.271640.810
83_S108_A0.270110.805
103_M106_M0.269750.804
60_C63_L0.268940.802
37_S87_S0.268470.801
36_T86_S0.267240.797
54_S79_S0.266810.796
72_T78_M0.266550.795
17_I42_L0.263320.785
36_T111_S0.263130.785
40_Q43_S0.257970.769
79_S102_N0.255870.763
4_S29_S0.252720.754
23_S73_S0.251990.751
80_N105_S0.248910.742
78_M97_T0.246570.735
47_T97_T0.245950.733
19_N94_N0.245930.733
88_L113_L0.243760.727
14_N64_N0.242830.724
20_W95_W0.241690.721
80_N83_S0.241640.721
63_L113_L0.240660.718
22_T72_T0.239110.713
13_L63_L0.235680.703
13_L18_S0.235050.701
41_D66_D0.234460.699
5_S8_A0.233930.698
56_M106_M0.233650.697
96_N100_V0.233620.697
6_M15_I0.229520.684
21_D71_D0.229150.683
97_T100_V0.223360.666
8_A33_Y0.223280.666
46_D96_N0.222660.664
50_V75_V0.220680.658
19_N69_N0.219480.654
38_L65_Q0.219140.653
55_G80_N0.218690.652
5_S30_Y0.218680.652
64_N89_N0.216690.646
61_S111_S0.216150.645
63_L90_Q0.215940.644
38_L60_C0.214790.641
64_N90_Q0.213760.637
29_S54_S0.213360.636
10_C110_C0.211890.632
90_Q95_W0.210720.628
16_D41_D0.208450.622
13_L38_L0.207410.618
33_Y83_S0.206990.617
67_L90_Q0.206460.616
16_D66_D0.20490.611
66_D91_D0.204480.610
26_T76_T0.202980.605
64_N114_N0.202260.603
23_S98_S0.201460.601
9_N84_G0.200990.599
10_C14_N0.199210.594
20_W70_W0.199150.594
108_A112_N0.198760.593
59_G109_N0.198330.591
65_Q68_S0.196430.586
31_M81_M0.196270.585
102_N105_S0.193540.577
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
4fs7A0.858397.90.769
4h09A0.833397.70.782
4gt6A0.883397.50.793
4h09A0.92597.50.793
4fs7A0.67597.30.798
4gt6A0.866797.20.806
3sb4A0.87596.80.818
3sb4A0.796.30.83
4fdwA0.995.20.845
2lz0A0.791778.40.888
If you are interested in a protein containing this domain,
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