GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PMT_2 - Dolichyl-phosphate-mannose-protein mannosyltransferase
Pfam: PF13231 (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: CL0111
Length: 159
Sequences: 5813
Seq/Len: 36.56
HH_delta: 0.495 (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
38_L84_L1.41743.515
34_L80_F1.2183.021
43_A52_A1.002392.486
45_R91_R0.984482.442
88_A107_L0.93382.316
43_A55_A0.914782.269
75_D115_K0.881312.186
40_Y56_A0.870182.158
105_G109_G0.860192.133
36_L56_A0.818762.031
45_R94_K0.8182.029
84_L107_L0.80682.001
5_L114_T0.796771.976
35_T83_L0.735721.825
81_F114_T0.688971.709
38_L80_F0.685851.701
88_A100_W0.674651.673
42_I90_Y0.661041.640
36_L60_A0.647211.605
35_T80_F0.643091.595
41_L87_Y0.642221.593
111_A118_F0.634791.574
40_Y52_A0.626691.554
81_F107_L0.621561.542
37_L41_L0.619441.536
92_Y101_W0.60981.512
59_L65_F0.603751.497
13_F23_A0.603051.496
32_S69_S0.597951.483
39_I59_L0.597931.483
48_G51_A0.587421.457
11_A15_K0.57411.424
38_L83_L0.572391.420
13_F27_F0.568271.409
44_R49_R0.568151.409
39_I55_A0.549781.364
87_Y91_R0.535881.329
88_A103_L0.53491.327
31_F77_L0.533731.324
35_T59_L0.525411.303
78_L115_K0.519911.289
42_I83_L0.516321.281
78_L118_F0.514141.275
14_F24_L0.511821.269
109_G113_L0.51161.269
31_F80_F0.508931.262
43_A46_L0.501981.245
6_Y74_P0.495641.229
44_R52_A0.493231.223
52_A56_A0.491831.220
85_A108_L0.491761.220
20_S23_A0.491431.219
36_L59_L0.490781.217
3_P116_Y0.485481.204
81_F110_L0.484141.201
42_I87_Y0.483551.199
41_L44_R0.474791.178
52_A55_A0.455961.131
30_L34_L0.45261.123
91_R94_K0.445711.105
41_L45_R0.445421.105
110_L114_T0.432541.073
40_Y44_R0.426911.059
17_F23_A0.426311.057
39_I43_A0.425471.055
39_I56_A0.418811.039
47_F51_A0.41311.025
74_P115_K0.407291.010
14_F19_D0.405071.005
32_S36_L0.405051.005
89_F104_A0.402960.999
82_F121_L0.40290.999
6_Y10_L0.401880.997
21_V25_R0.399430.991
80_F84_L0.395860.982
91_R95_S0.388630.964
13_F17_F0.387290.961
12_L15_K0.382490.949
43_A47_F0.381270.946
44_R48_G0.379210.941
32_S65_F0.378420.939
92_Y104_A0.376250.933
85_A111_A0.372780.925
6_Y77_L0.369550.917
7_F74_P0.369460.916
97_K100_W0.368020.913
46_L90_Y0.367320.911
7_F73_R0.364290.904
22_W26_L0.359640.892
40_Y49_R0.359420.891
5_L110_L0.355980.883
38_L88_A0.355310.881
10_L72_A0.354460.879
107_L110_L0.354060.878
91_R100_W0.351020.871
85_A125_L0.349710.867
35_T38_L0.3440.853
73_R115_K0.343880.853
35_T65_F0.337320.837
57_L61_L0.336520.835
116_Y119_L0.335880.833
89_F129_L0.334180.829
50_R54_I0.332590.825
102_I105_G0.328030.814
90_Y94_K0.325510.807
51_A55_A0.317960.789
38_L41_L0.316860.786
12_L16_L0.316170.784
111_A115_K0.313460.777
85_A104_A0.31030.770
23_A26_L0.308280.765
108_L122_I0.307170.762
84_L88_A0.305210.757
68_Y73_R0.304020.754
38_L87_Y0.303470.753
119_L123_P0.29890.741
48_G52_A0.297430.738
81_F111_A0.293730.729
84_L87_Y0.292450.725
120_L123_P0.291910.724
88_A104_A0.289530.718
98_W102_I0.289490.718
29_I33_L0.288980.717
28_N77_L0.288260.715
64_M68_Y0.282920.702
35_T79_L0.282070.700
32_S59_L0.28030.695
29_I70_A0.279860.694
28_N76_M0.27850.691
35_T39_I0.276750.686
7_F115_K0.276420.686
45_R90_Y0.275690.684
93_I128_Y0.27540.683
9_L31_F0.275040.682
28_N72_A0.270480.671
45_R95_S0.267710.664
75_D78_L0.267120.663
11_A14_F0.26580.659
100_W103_L0.263840.654
95_S99_R0.263620.654
29_I32_S0.261360.648
41_L91_R0.261060.647
62_S65_F0.260360.646
77_L114_T0.260050.645
83_L87_Y0.25850.641
113_L116_Y0.253790.629
99_R103_L0.253760.629
24_L72_A0.253660.629
28_N69_S0.25340.628
32_S60_A0.252740.627
68_Y71_S0.252640.627
50_R53_L0.252380.626
95_S100_W0.252160.625
3_P74_P0.252040.625
32_S62_S0.250360.621
34_L37_L0.249960.620
39_I83_L0.249370.618
85_A107_L0.249340.618
38_L42_I0.249150.618
66_I69_S0.249050.618
25_R28_N0.24690.612
101_W105_G0.245480.609
45_R87_Y0.245160.608
40_Y53_L0.243840.605
9_L27_F0.243220.603
9_L77_L0.242340.601
75_D79_L0.240530.597
25_R69_S0.239030.593
53_L57_L0.238140.591
75_D116_Y0.229320.569
106_L110_L0.228870.568
69_S76_M0.228850.568
3_P115_K0.228690.567
82_F123_P0.227140.563
76_M79_L0.226160.561
104_A107_L0.225760.560
80_F83_L0.225360.559
43_A51_A0.223060.553
8_L116_Y0.222520.552
6_Y28_N0.221030.548
49_R53_L0.21990.545
48_G94_K0.218160.541
5_L81_F0.217770.540
6_Y114_T0.217050.538
93_I132_S0.216680.537
108_L112_F0.21560.535
103_L107_L0.215320.534
61_L65_F0.214880.533
93_I96_K0.214790.533
103_L106_L0.212780.528
67_F71_S0.212310.527
41_L88_A0.21230.527
27_F31_F0.211930.526
42_I45_R0.211840.525
113_L117_T0.210470.522
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
3rceA0.9937990.495
2l2tA0.27678.90.903
2ks1B0.27044.50.914
3tijA0.34593.80.917
2jwaA0.27673.60.918
4hg6A0.62892.80.922
2l35A0.39622.40.924
2l34A0.20752.30.926
3ne5A0.97481.50.932
2iubA0.66671.40.933

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