GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lactamase_B - Metallo-beta-lactamase superfamily
Pfam: PF00753 (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: CL0381
Length: 194
Sequences: 19600
Seq/Len: 101.03
HH_delta: 0.185 (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
16_G45_D2.437474.543
49_L60_L1.986083.701
123_G132_I1.899753.541
12_E17_A1.736273.236
18_I46_A1.723513.212
20_I50_T1.527922.848
134_Y139_K1.336762.491
20_I142_F1.219082.272
171_N174_E1.208152.252
135_L138_G1.08132.015
17_A45_D1.063231.982
16_G46_A1.048461.954
132_I139_K0.987381.840
10_L17_A0.97981.826
48_I133_I0.957821.785
120_I131_L0.954021.778
139_K188_E0.92271.720
18_I48_I0.898451.674
16_G43_D0.86821.618
112_I117_I0.857671.598
62_E66_A0.85231.588
110_L117_I0.852061.588
17_A44_I0.823681.535
107_E181_R0.80221.495
17_A43_D0.801951.495
110_L119_F0.801171.493
119_F136_P0.785281.464
132_I141_L0.768451.432
9_Y193_G0.746091.390
22_T60_L0.740241.380
9_Y191_I0.737011.374
106_D109_D0.714071.331
118_L135_L0.712131.327
105_E108_D0.711341.326
40_S43_D0.710491.324
174_E177_E0.707351.318
177_E180_R0.70681.317
173_E177_E0.702991.310
61_P65_E0.697991.301
47_V60_L0.696051.297
51_H145_D0.690851.288
180_R183_E0.686421.279
172_W175_S0.683771.274
56_H145_D0.682441.272
154_N157_P0.680281.268
17_A42_E0.680031.267
19_L44_I0.679721.267
120_I133_I0.676181.260
110_L113_G0.674731.258
48_I131_L0.671961.252
9_Y142_F0.670611.250
140_V191_I0.642941.198
11_I20_I0.642781.198
46_A73_Y0.63521.184
61_P64_L0.635151.184
26_P30_K0.633281.180
46_A72_I0.630171.174
75_S78_A0.626181.167
176_I180_R0.624751.164
177_E181_R0.61421.145
46_A71_I0.611541.140
111_E114_G0.603081.124
53_H56_H0.603021.124
13_G16_G0.601761.122
8_S23_G0.593791.107
130_S144_G0.591951.103
10_L19_L0.582951.086
180_R184_A0.580511.082
62_E65_E0.579521.080
22_T47_V0.577731.077
111_E116_R0.568031.059
76_A79_A0.552931.031
68_P71_I0.552771.030
70_V74_S0.552521.030
78_A82_I0.540061.007
79_A83_R0.536371.000
114_G117_I0.534760.997
38_G41_G0.532540.993
168_Y171_N0.532160.992
74_S78_A0.530540.989
71_I74_S0.52930.986
127_G130_S0.52470.978
140_V189_V0.520480.970
181_R184_A0.519160.968
109_D112_I0.519010.967
27_D30_K0.517680.965
11_I18_I0.514320.959
10_L44_I0.512290.955
12_E42_E0.512270.955
38_G66_A0.510940.952
73_Y77_D0.507990.947
141_L185_L0.505570.942
172_W176_I0.503330.938
126_H129_D0.501570.935
17_A39_I0.500450.933
113_G117_I0.497230.927
175_S178_A0.496070.925
109_D116_R0.494530.922
67_G70_V0.494140.921
20_I48_I0.493070.919
171_N175_S0.492080.917
13_G115_D0.490580.914
112_I115_D0.489260.912
49_L57_I0.487290.908
21_D56_H0.485150.904
76_A80_K0.483910.902
125_G128_S0.483320.901
107_E111_E0.48050.896
74_S122_P0.480340.895
59_G62_E0.478820.892
78_A81_A0.478660.892
77_D80_K0.4770.889
50_T142_F0.475860.887
179_L183_E0.47380.883
115_D118_L0.46890.874
27_D31_E0.466030.869
105_E113_G0.465290.867
51_H55_D0.465260.867
25_D59_G0.462250.862
124_P127_G0.460160.858
79_A82_I0.456140.850
105_E111_E0.45580.849
100_P104_D0.455420.849
50_T144_G0.453740.846
12_E39_I0.452240.843
182_L187_P0.448420.836
189_V192_P0.447870.835
134_Y141_L0.447850.835
51_H56_H0.447820.835
132_I146_L0.447470.834
143_T190_I0.444950.829
108_D112_I0.444340.828
56_H194_H0.443180.826
13_G18_I0.442920.825
74_S79_A0.44130.822
50_T133_I0.441180.822
108_D115_D0.437320.815
84_P87_R0.4370.814
73_Y78_A0.436210.813
142_F193_G0.435560.812
72_I105_E0.431910.805
19_L22_T0.430610.803
38_G42_E0.429590.801
151_E154_N0.428080.798
18_I113_G0.421580.786
99_P102_I0.419720.782
108_D111_E0.417790.779
77_D129_D0.416850.777
169_G172_W0.416480.776
103_I109_D0.41620.776
170_S175_S0.414950.773
72_I75_S0.412960.770
175_S179_L0.408150.761
132_I182_L0.406270.757
119_F134_Y0.4060.757
6_S22_T0.404090.753
126_H130_S0.403540.752
103_I106_D0.403260.752
107_E110_L0.40290.751
182_L185_L0.400980.747
186_D189_V0.398310.742
18_I45_D0.397150.740
123_G127_G0.396790.740
80_K83_R0.394410.735
8_S19_L0.394280.735
125_G130_S0.393080.733
85_P88_D0.389670.726
109_D113_G0.389250.725
44_I67_G0.388790.725
46_A70_V0.388220.724
134_Y189_V0.387740.723
105_E109_D0.387430.722
170_S174_E0.387230.722
12_E15_D0.386530.720
69_V72_I0.386120.720
123_G178_A0.386030.719
182_L190_I0.384990.718
74_S77_D0.382550.713
69_V73_Y0.381380.711
114_G118_L0.381160.710
178_A181_R0.378330.705
143_T192_P0.378030.705
126_H147_L0.37540.700
130_S146_L0.374160.697
47_V70_V0.372580.694
183_E187_P0.370310.690
22_T49_L0.370270.690
21_D51_H0.370190.690
25_D29_A0.369880.689
125_G178_A0.369560.689
75_S79_A0.36890.688
121_I181_R0.368020.686
123_G130_S0.36760.685
64_L69_V0.366790.684
70_V73_Y0.366680.683
170_S173_E0.365450.681
25_D31_E0.365040.680
74_S82_I0.364160.679
110_L114_G0.364150.679
181_R185_L0.362270.675
152_H155_P0.36190.674
143_T146_L0.36140.674
74_S131_L0.361120.673
21_D50_T0.361050.673
108_D113_G0.358420.668
123_G146_L0.357970.667
47_V63_L0.356340.664
116_R135_L0.356050.664
105_E110_L0.355560.663
101_P105_E0.35260.657
121_I124_P0.352540.657
52_A57_I0.347350.647
28_F32_L0.346310.645
10_L39_I0.343920.641
20_I133_I0.343590.640
135_L140_V0.343360.640
55_D145_D0.342730.639
178_A185_L0.342450.638
60_L71_I0.341730.637
174_E178_A0.340860.635
173_E176_I0.340740.635
54_P58_G0.340240.634
171_N178_A0.339810.633
178_A182_L0.339680.633
53_H124_P0.338490.631
108_D119_F0.338330.631
25_D28_F0.337490.629
64_L70_V0.335150.625
125_G129_D0.335070.624
64_L71_I0.334660.624
9_Y20_I0.333090.621
121_I134_Y0.332230.619
22_T59_G0.331980.619
111_E117_I0.331480.618
184_A187_P0.331480.618
38_G43_D0.331240.617
64_L68_P0.331080.617
6_S23_G0.330590.616
118_L134_Y0.329790.615
148_F153_P0.329270.614
104_D107_E0.328510.612
46_A49_L0.327850.611
187_P190_I0.327590.611
71_I75_S0.327170.610
7_N193_G0.326510.609
68_P75_S0.326240.608
57_I60_L0.326030.608
113_G116_R0.323460.603
109_D118_L0.322620.601
50_T53_H0.322530.601
37_L40_S0.319990.596
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
4eybA0.922799.80.185
3hnnA0.948599.80.204
2zo4A0.963999.80.21
4dikA0.93399.80.215
3iogA0.912499.80.216
4fr7A0.902199.80.217
3vpeA0.984599.80.218
4efzA0.958899.80.22
3m8tA0.953699.80.227
4hl2A0.922799.80.23

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