GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Isochorismatase - Isochorismatase family
Pfam: PF00857 (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. )
Length: 174
Sequences: 5806
Seq/Len: 33.37
HH_delta: 0.055 (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
104_D108_R1.439693.096
96_S132_D1.434023.084
114_T139_R1.41053.033
47_R91_E1.318412.835
104_D138_Y1.253482.696
32_L143_V1.220262.624
36_A41_V1.133762.438
117_L130_A1.126932.424
29_I118_C1.095692.356
162_L167_A1.047552.253
8_M29_I1.023552.201
114_T141_I1.009132.170
2_A112_I0.955842.056
11_D74_G0.94482.032
144_E169_V0.939482.020
97_A129_T0.924671.989
104_D136_R0.911941.961
115_V133_A0.900571.937
127_L131_R0.886191.906
122_T155_H0.850021.828
152_P156_E0.843351.814
28_N31_R0.839631.806
21_N24_A0.822371.769
28_N146_A0.818591.760
90_I106_I0.792161.704
36_A116_I0.790741.701
122_T147_C0.76941.655
10_N73_P0.763591.642
44_I106_I0.734551.580
133_A140_V0.713021.533
35_A39_A0.703241.512
160_E163_R0.702391.511
123_D149_S0.701421.508
37_R87_D0.694271.493
102_D106_I0.688771.481
116_I143_V0.667321.435
5_V33_L0.666621.434
98_F133_A0.66461.429
4_L117_L0.655391.409
117_L129_T0.655261.409
134_F167_A0.637431.371
144_E159_L0.635151.366
30_N34_D0.632461.360
108_R138_Y0.618821.331
46_T97_A0.618071.329
73_P76_E0.612151.317
6_I125_C0.607471.306
105_E109_K0.607381.306
5_V118_C0.602891.297
30_N80_E0.600771.292
3_L36_A0.591251.272
127_L161_E0.590831.271
127_L158_A0.588881.266
144_E171_T0.57611.239
122_T159_L0.570111.226
156_E160_E0.564821.215
28_N145_D0.564291.214
126_V142_V0.562621.210
88_P106_I0.560321.205
13_I78_V0.557651.199
42_P110_R0.547211.177
106_I110_R0.545121.172
142_V147_C0.540651.163
141_I170_I0.538811.159
130_A167_A0.529871.140
10_N79_P0.525031.129
5_V29_I0.523021.125
25_I29_I0.511981.101
49_I75_A0.505331.087
149_S155_H0.491951.058
143_V146_A0.485751.045
151_S154_A0.481411.035
153_E156_E0.479141.030
7_D92_K0.477171.026
33_L45_H0.47341.018
30_N83_P0.473231.018
102_D105_E0.462220.994
2_A44_I0.45810.985
32_L146_A0.456340.981
118_C146_A0.454840.978
5_V8_M0.454440.977
130_A162_L0.451920.972
27_P80_E0.446270.960
159_L169_V0.445990.959
147_C155_H0.44380.954
128_A131_R0.439540.945
113_D139_R0.436170.938
70_P91_E0.435370.936
26_I30_N0.431930.929
49_I91_E0.430810.927
10_N76_E0.424870.914
49_I70_P0.423140.910
122_T149_S0.422390.908
31_R34_D0.41250.887
25_I148_A0.411350.885
158_A162_L0.408570.879
4_L103_L0.407170.876
34_D38_A0.406210.874
106_I109_K0.405070.871
141_I168_E0.401290.863
76_E82_A0.400820.862
132_D136_R0.398540.857
116_I141_I0.395910.851
94_R137_G0.394650.849
107_L138_Y0.393640.847
32_L118_C0.393090.845
45_H83_P0.391120.841
31_R35_A0.388580.836
8_M120_V0.388150.835
84_Q87_D0.382640.823
143_V170_I0.381970.821
8_M78_V0.381490.820
77_L89_V0.379520.816
155_H159_L0.376650.810
27_P31_R0.375950.809
47_R89_V0.375290.807
130_A142_V0.371530.799
126_V147_C0.370490.797
3_L118_C0.369930.796
42_P112_I0.369080.794
6_I117_L0.367090.789
47_R77_L0.367020.789
97_A103_L0.365810.787
71_G76_E0.362320.779
72_S75_A0.361940.778
37_R86_G0.361840.778
96_S135_D0.354050.761
142_V159_L0.349090.751
120_V148_A0.347860.748
95_Y129_T0.346320.745
48_D121_A0.343060.738
26_I78_V0.34280.737
10_N78_V0.339930.731
153_E157_A0.338810.729
94_R100_G0.337460.726
37_R84_Q0.337410.726
117_L126_V0.335680.722
34_D84_Q0.335330.721
13_I22_A0.335080.721
24_A27_P0.333210.717
115_V140_V0.329270.708
139_R168_E0.328820.707
7_D125_C0.328320.706
121_A124_V0.327730.705
123_D150_Y0.327460.704
88_P110_R0.326450.702
51_D70_P0.32610.701
32_L36_A0.323660.696
105_E108_R0.323440.696
29_I146_A0.322160.693
69_I72_S0.321870.692
2_A107_L0.317760.683
32_L116_I0.317440.683
130_A140_V0.317040.682
6_I97_A0.316780.681
3_L33_L0.316710.681
12_F125_C0.316140.680
131_R165_R0.313860.675
25_I120_V0.311740.670
12_F95_Y0.307590.662
3_L43_V0.30640.659
27_P30_N0.305960.658
35_A38_A0.304190.654
48_D123_D0.30240.650
103_L107_L0.301910.649
117_L140_V0.301310.648
115_V138_Y0.300250.646
18_A23_E0.299230.644
45_H77_L0.298680.642
71_G75_A0.296630.638
3_L32_L0.296150.637
132_D135_D0.294190.633
123_D161_E0.293040.630
68_C75_A0.292590.629
157_A160_E0.291750.627
107_L115_V0.291730.627
116_I145_D0.290770.625
142_V167_A0.289140.622
128_A166_G0.28710.617
2_A110_R0.286590.616
33_L43_V0.284650.612
83_P87_D0.283960.611
11_D68_C0.283860.610
98_F104_D0.283360.609
83_P89_V0.283130.609
150_Y154_A0.28310.609
48_D67_H0.281720.606
160_E164_K0.280490.603
30_N81_L0.279530.601
20_P24_A0.279480.601
77_L83_P0.279370.601
158_A161_E0.276180.594
122_T158_A0.27570.593
124_V150_Y0.275120.592
45_H87_D0.275110.592
99_F136_R0.272910.587
119_G126_V0.27220.585
78_V81_L0.271720.584
94_R99_F0.270250.581
45_H86_G0.269260.579
144_E155_H0.269160.579
100_G105_E0.269120.579
13_I26_I0.268780.578
95_Y124_V0.268370.577
154_A157_A0.268020.576
83_P86_G0.267940.576
73_P79_P0.267030.574
34_D82_A0.265150.570
30_N82_A0.264080.568
147_C159_L0.260890.561
28_N143_V0.259210.557
20_P148_A0.258950.557
12_F121_A0.258150.555
98_F136_R0.257850.555
33_L37_R0.257260.553
26_I80_E0.255940.550
50_H67_H0.25570.550
21_N148_A0.253080.544
2_A115_V0.252790.544
123_D154_A0.251030.540
145_D171_T0.250740.539
163_R169_V0.250440.539
48_D68_C0.249610.537
92_K125_C0.24920.536
118_C143_V0.248590.535
51_D69_I0.248380.534
23_E80_E0.247880.533
79_P82_A0.244690.526
131_R135_D0.243630.524
145_D170_I0.24230.521
37_R45_H0.242270.521
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
3irvA11000.055
3hb7A0.97131000.058
1nf9A0.99431000.062
2fq1A11000.065
3ot4A11000.069
3hu5A11000.069
3eefA0.95981000.073
1nbaA11000.074
3kl2A11000.079
3lqyA0.94251000.081

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