GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MetW - Methionine biosynthesis protein MetW
Pfam: PF07021 (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: CL0063
Length: 193
Sequences: 10517
Seq/Len: 54.49
HH_delta: 0.334 (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
22_C41_G1.647073.653
16_R38_D1.403733.113
40_Y76_F1.227882.723
46_P61_Q1.069862.373
18_L76_F1.037262.301
152_E156_R1.036092.298
99_L160_I1.031852.289
21_G84_T1.015122.251
38_D58_S1.010272.241
147_T150_D0.99432.205
42_V62_G0.978422.170
46_P50_A0.963722.137
17_V78_Y0.891911.978
40_Y60_I0.854871.896
92_D157_E0.83261.847
45_D48_N0.831481.844
28_L39_G0.821521.822
71_F76_F0.794691.763
28_L41_G0.788081.748
44_I63_D0.780781.732
12_E15_S0.778581.727
16_R76_F0.778081.726
92_D158_L0.776761.723
90_R93_E0.766211.699
18_L79_V0.763091.692
16_R40_Y0.761211.688
152_E165_R0.754381.673
153_D157_E0.752411.669
96_E158_L0.752031.668
16_R77_D0.747871.659
15_S78_Y0.72951.618
72_P75_S0.71691.590
50_A53_V0.716321.589
51_A54_A0.711351.578
63_D66_E0.699411.551
17_V31_L0.684851.519
81_L84_T0.683261.515
49_V59_V0.682931.515
83_Q86_Q0.67181.490
30_Y33_D0.671071.488
79_V98_M0.652571.447
29_A33_D0.637211.413
43_E49_V0.633491.405
40_Y58_S0.631691.401
52_C59_V0.625091.386
92_D154_L0.623391.383
49_V61_Q0.619451.374
83_Q87_A0.617571.370
20_L98_M0.615751.366
91_P154_L0.613341.360
97_E101_V0.603521.339
77_D100_R0.594061.318
29_A55_R0.5871.302
92_D96_E0.58131.289
19_D22_C0.577721.281
16_R75_S0.551451.223
88_V94_V0.542921.204
42_V60_I0.528151.171
49_V53_V0.524461.163
27_L82_S0.522311.158
41_G59_V0.521311.156
43_E48_N0.515461.143
97_E100_R0.512741.137
153_D156_R0.510831.133
27_L80_I0.502761.115
75_S100_R0.494841.098
21_G81_L0.493221.094
85_L95_L0.488231.083
47_D50_A0.474941.053
99_L103_R0.474841.053
148_I152_E0.474071.051
64_L84_T0.469711.042
154_L158_L0.464821.031
17_V39_G0.455591.010
150_D153_D0.455141.009
73_D100_R0.453931.007
22_C28_L0.45251.004
102_G105_A0.446230.990
27_L31_L0.430560.955
28_L32_K0.42250.937
152_E162_I0.421090.934
83_Q108_S0.418220.928
41_G52_C0.415970.923
40_Y71_F0.412310.914
15_S37_V0.408890.907
81_L105_A0.408250.905
50_A54_A0.405610.900
71_F75_S0.403430.895
43_E59_V0.402810.893
95_L158_L0.39670.880
22_C43_E0.396320.879
98_M105_A0.394880.876
117_N120_Q0.392180.870
149_K152_E0.391810.869
162_I165_R0.39070.867
62_G69_A0.389870.865
31_L80_I0.389570.864
15_S77_D0.388820.862
154_L157_E0.387980.861
20_L64_L0.387780.860
36_Q39_G0.386920.858
19_D27_L0.38660.857
146_C150_D0.386310.857
19_D23_G0.384640.853
32_K56_G0.3840.852
24_D48_N0.377650.838
64_L88_V0.375710.833
155_C160_I0.372690.827
17_V80_I0.371580.824
18_L42_V0.36560.811
148_I167_F0.362820.805
51_A55_R0.361110.801
49_V52_C0.359790.798
125_G128_P0.358360.795
29_A32_K0.357820.794
91_P146_C0.357580.793
93_E96_E0.356520.791
19_D28_L0.35480.787
95_L99_L0.350490.777
22_C52_C0.349650.775
85_L107_V0.349460.775
26_E29_A0.345810.767
131_K134_P0.342970.761
149_K153_D0.341130.757
16_R37_V0.340510.755
151_F155_C0.33930.753
22_C49_V0.337090.748
85_L88_V0.335630.744
27_L86_Q0.332520.738
93_E97_E0.328540.729
84_T88_V0.327060.725
71_F100_R0.326770.725
16_R74_Q0.326550.724
19_D39_G0.32420.719
65_D89_R0.320070.710
19_D41_G0.318840.707
85_L94_V0.316980.703
82_S87_A0.31630.702
20_L79_V0.316150.701
99_L102_G0.314360.697
47_D51_A0.312650.693
148_I165_R0.312270.693
124_R128_P0.311030.690
17_V37_V0.310870.689
155_C162_I0.305760.678
103_R160_I0.3050.676
105_A160_I0.303870.674
65_D90_R0.302320.671
84_T87_A0.301180.668
78_Y106_I0.300270.666
87_A142_N0.299380.664
109_F151_F0.29890.663
19_D80_I0.297810.661
109_F146_C0.297670.660
156_R161_R0.296340.657
25_G52_C0.294220.653
73_D97_E0.293290.650
85_L151_F0.292230.648
107_V155_C0.292010.648
95_L98_M0.29090.645
86_Q146_C0.290070.643
118_R121_L0.289120.641
19_D25_G0.288960.641
20_L42_V0.288320.639
23_G45_D0.286520.635
95_L155_C0.285520.633
117_N121_L0.284720.631
48_N86_Q0.282330.626
86_Q142_N0.281470.624
156_R163_E0.280480.622
16_R100_R0.280180.621
79_V102_G0.279940.621
127_M130_T0.279660.620
27_L30_Y0.278210.617
99_L158_L0.277920.616
26_E30_Y0.276870.614
111_N114_H0.276870.614
48_N87_A0.276710.614
120_Q124_R0.275220.610
18_L101_V0.275210.610
19_D82_S0.274330.608
80_I83_Q0.274120.608
87_A146_C0.273960.608
19_D87_A0.273020.606
78_Y104_R0.271950.603
156_R162_I0.269790.598
102_G106_I0.269660.598
32_K57_V0.267580.593
28_L57_V0.267170.593
62_G66_E0.26540.589
150_D154_L0.264950.588
43_E83_Q0.264660.587
83_Q109_F0.263670.585
68_L97_E0.263570.585
95_L154_L0.263470.584
79_V99_L0.262780.583
118_R122_L0.262430.582
137_W140_T0.262260.582
21_G88_V0.261570.580
22_C42_V0.261540.580
116_R120_Q0.260620.578
29_A57_V0.260210.577
146_C154_L0.259150.575
119_L122_L0.257260.571
115_W119_L0.257180.570
53_V58_S0.256260.568
14_G37_V0.255960.568
25_G41_G0.255330.566
62_G71_F0.255250.566
24_D51_A0.254910.565
127_M131_K0.25150.558
79_V103_R0.251060.557
155_C158_L0.250370.555
28_L80_I0.250290.555
94_V98_M0.249850.554
112_F116_R0.248680.552
105_A109_F0.24740.549
21_G87_A0.246980.548
68_L73_D0.245710.545
65_D91_P0.245160.544
25_G59_V0.244860.543
81_L91_P0.244220.542
146_C151_F0.24370.541
46_P53_V0.243320.540
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
3dliA0.911999.80.334
3l8dA0.922399.80.348
2p7iA0.968999.80.349
4htfA0.968999.80.357
3g5lA0.979399.80.361
4gekA0.932699.80.363
3vc1A0.927599.80.364
3cc8A0.963799.80.366
3ujcA0.922399.80.37
3busA0.937899.80.371

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