GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Nitroreductase - Nitroreductase family
Pfam: PF00881 (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: CL0529
Length: 165
Sequences: 7447
Seq/Len: 45.13
HH_delta: 0.042 (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_P19_D1.969573.972
22_E129_L1.778073.586
17_D21_E1.293822.609
23_I126_A1.284452.590
41_F118_A1.246942.515
3_N127_T1.212762.446
17_D45_N1.1922.404
19_D129_L1.191082.402
123_L133_S1.175712.371
131_L165_Y1.125682.270
13_E165_Y1.11942.258
25_E28_R0.954911.926
52_R148_L0.951681.919
19_D131_L0.934111.884
49_G52_R0.9261.867
146_K157_P0.917071.849
27_A122_L0.891231.797
119_A159_A0.889891.795
26_A125_A0.852961.720
126_A163_V0.847871.710
47_Q51_Y0.843431.701
113_I116_G0.791941.597
123_L135_P0.782771.579
119_A161_I0.779641.572
19_D22_E0.761421.536
23_I122_L0.760391.533
123_L161_I0.742751.498
117_I120_Q0.717261.447
19_D165_Y0.708161.428
47_Q50_R0.707321.426
135_P159_A0.698251.408
131_L163_V0.696541.405
127_T132_G0.69481.401
6_S134_C0.676311.364
90_I122_L0.667121.345
40_R155_E0.6421.295
41_F90_I0.637491.286
51_Y84_K0.636991.285
91_I157_P0.630291.271
140_D143_K0.621.250
42_Y155_E0.619311.249
30_A121_N0.606071.222
51_Y55_D0.601741.214
16_P165_Y0.594191.198
21_E25_E0.589011.188
53_L145_L0.584621.179
54_A84_K0.584341.178
10_F162_A0.582251.174
48_E52_R0.578611.167
49_G148_L0.575931.161
23_I163_V0.571951.153
92_I119_A0.570961.151
2_R25_E0.569611.149
120_Q124_L0.566711.143
91_I160_L0.561551.132
2_R29_W0.558191.126
45_N88_V0.556121.122
115_A158_L0.555361.120
126_A133_S0.554141.118
43_V88_V0.553131.116
48_E51_Y0.552081.113
56_A148_L0.551421.112
52_R55_D0.54571.101
23_I131_L0.54531.100
15_V131_L0.536451.082
88_V163_V0.52821.065
110_W137_G0.516441.042
133_S161_I0.511311.031
24_L27_A0.509411.027
125_A129_L0.506451.021
125_A128_A0.501021.010
44_V91_I0.499111.007
143_K147_E0.498611.006
46_D49_G0.497061.002
11_D165_Y0.496721.002
53_L58_H0.491660.992
134_C162_A0.489120.986
139_F160_L0.488510.985
18_E21_E0.484450.977
109_R156_E0.476580.961
20_L88_V0.47620.960
26_A129_L0.473360.955
121_N124_L0.473170.954
32_S37_Q0.467310.942
90_I163_V0.464590.937
116_G135_P0.461670.931
136_M162_A0.458750.925
92_I161_I0.457660.923
108_Y156_E0.457410.922
1_I124_L0.456560.921
92_I122_L0.455190.918
146_K156_E0.451020.910
119_A135_P0.448510.905
24_L43_V0.446350.900
152_P155_E0.446060.900
22_E25_E0.446010.899
44_V49_G0.444530.896
41_F92_I0.443150.894
14_P45_N0.442880.893
112_L158_L0.436720.881
32_S39_W0.436630.881
11_D14_P0.429770.867
113_I137_G0.427740.863
122_L161_I0.427460.862
133_S163_V0.42430.856
89_L160_L0.424080.855
92_I115_A0.420050.847
22_E26_A0.417380.842
55_D58_H0.416810.841
33_S110_W0.413250.833
2_R26_A0.41250.832
13_E16_P0.408120.823
8_R134_C0.4050.817
15_V87_P0.398870.804
81_K84_K0.395620.798
1_I121_N0.395170.797
120_Q123_L0.393380.793
15_V19_D0.393350.793
117_I121_N0.392440.791
25_E29_W0.387510.781
32_S38_P0.386990.780
43_V90_I0.386050.779
52_R56_A0.38270.772
23_I129_L0.382080.771
78_G81_K0.380890.768
79_N82_A0.372430.751
18_E22_E0.370080.746
39_W118_A0.368330.743
1_I120_Q0.365060.736
56_A143_K0.359250.725
124_L128_A0.357770.722
151_L155_E0.357060.720
113_I135_P0.350670.707
33_S137_G0.349220.704
122_L163_V0.347390.701
146_K153_D0.345280.696
10_F13_E0.344640.695
7_I10_F0.341770.689
82_A85_G0.338250.682
145_L148_L0.333750.673
112_L116_G0.330810.667
77_A80_Q0.328960.663
14_P165_Y0.32730.660
15_V165_Y0.3270.659
108_Y112_L0.326760.659
20_L24_L0.32550.656
113_I158_L0.322010.649
80_Q83_I0.321930.649
87_P90_I0.321740.649
117_I135_P0.321260.648
49_G149_L0.320930.647
20_L43_V0.311030.627
22_E125_A0.310690.627
10_F134_C0.310030.625
80_Q84_K0.308040.621
109_R112_L0.306730.619
79_N85_G0.306640.618
53_L56_A0.304680.614
109_R113_I0.304020.613
110_W113_I0.303870.613
112_L156_E0.302530.610
91_I149_L0.299920.605
32_S114_D0.299390.604
7_I132_G0.299350.604
32_S35_N0.298480.602
142_D146_K0.296480.598
116_G120_Q0.294950.595
114_D137_G0.290260.585
27_A118_A0.289660.584
20_L90_I0.287790.580
39_W115_A0.287650.580
106_R109_R0.286340.577
146_K151_L0.285730.576
153_D156_E0.28510.575
50_R89_L0.284880.575
56_A145_L0.283480.572
4_R31_P0.281480.568
9_D85_G0.278110.561
27_A41_F0.275870.556
102_K107_S0.275690.556
49_G53_L0.273630.552
44_V149_L0.273380.551
24_L90_I0.271250.547
127_T131_L0.271160.547
31_P117_I0.270030.545
83_I162_A0.269460.543
30_A117_I0.266870.538
87_P165_Y0.265280.535
103_Y106_R0.264960.534
51_Y54_A0.264560.534
139_F157_P0.263830.532
147_E150_G0.261260.527
19_D23_I0.261040.526
46_D50_R0.25850.521
139_F143_K0.258230.521
12_P47_Q0.256990.518
30_A37_Q0.256680.518
7_I11_D0.255690.516
45_N48_E0.254110.512
81_K85_G0.253630.511
134_C137_G0.252950.510
55_D148_L0.250990.506
34_G103_Y0.250120.504
33_S138_G0.248270.501
109_R141_D0.247610.499
23_I125_A0.247330.499
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
4eo3A0.86671000.042
3ge5A0.848599.90.095
3n2sA0.872799.90.097
3ge6A0.878899.90.098
3g14A0.884899.90.1
3gbhA0.878899.90.101
3hoiA0.963699.90.101
2freA0.884899.90.101
3eofA0.872799.90.101
3hj9A0.957699.90.102

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