GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GlnD_UR_UTase - GlnD PII-uridylyltransferase
Pfam: PF08335 (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: CL0291
Length: 142
Sequences: 1821
Seq/Len: 12.82
HH_delta: 0.228 (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
114_Y126_E0.771313.946
85_L123_L0.556852.849
59_E76_R0.528862.705
62_A72_A0.507232.595
74_A133_R0.443562.269
127_L131_R0.404642.070
55_I76_R0.399632.044
78_A134_V0.362361.854
116_D119_A0.348961.785
68_S71_E0.347321.777
3_M7_I0.345161.766
36_R90_R0.342271.751
71_E137_I0.339331.736
60_A64_A0.335641.717
81_F85_L0.330871.693
71_E140_R0.316651.620
76_R80_R0.307641.574
78_A130_H0.304011.555
38_I134_V0.302871.549
126_E130_H0.302231.546
10_E138_F0.300061.535
27_D99_R0.297621.522
135_R139_D0.294591.507
62_A69_E0.294441.506
124_M128_Y0.292671.497
4_R8_E0.284531.456
81_F130_H0.270171.382
88_A111_R0.264981.356
2_F6_K0.264581.353
92_V108_L0.244011.248
56_D60_A0.243931.248
55_I80_R0.242921.243
42_A57_A0.242451.240
105_Q124_M0.242311.240
126_E129_R0.237381.214
86_R98_D0.235971.207
78_A133_R0.235251.203
85_L112_L0.234771.201
27_D30_L0.232591.190
84_R88_A0.232111.187
74_A137_I0.232091.187
72_A76_R0.227891.166
81_F114_Y0.22621.157
40_F138_F0.22361.144
49_H66_L0.217971.115
77_E130_H0.217941.115
39_E43_Q0.215391.102
123_L127_L0.208631.067
83_R86_R0.208241.065
108_L111_R0.203471.041
100_L127_L0.201941.033
36_R86_R0.201581.031
49_H54_T0.20031.025
130_H133_R0.200211.024
133_R136_R0.199141.019
69_E73_E0.199111.019
45_L49_H0.198111.013
6_K9_E0.197591.011
90_R98_D0.197541.011
57_A60_A0.196071.003
90_R97_T0.195791.002
109_A119_A0.195731.001
79_Y83_R0.19190.982
68_S72_A0.189260.968
114_Y123_L0.185720.950
81_F126_E0.184220.942
10_E14_H0.181660.929
28_L85_L0.18160.929
8_E135_R0.179460.918
86_R90_R0.178270.912
46_Q57_A0.17820.912
3_M32_P0.17730.907
106_E110_R0.176540.903
89_L100_L0.175780.899
88_A112_L0.175590.898
8_E12_E0.174190.891
115_E119_A0.173850.889
27_D127_L0.172860.884
35_L90_R0.171340.876
41_I67_L0.170070.870
90_R96_Q0.169780.869
88_A108_L0.169640.868
62_A76_R0.169380.866
7_I40_F0.169160.865
76_R110_R0.167430.856
3_M6_K0.167360.856
92_V107_R0.166630.852
104_E107_R0.166320.851
37_D96_Q0.166110.850
70_E74_A0.165930.849
67_L72_A0.165380.846
54_T58_L0.164470.841
62_A73_E0.163630.837
97_T100_L0.16290.833
88_A91_L0.162330.830
35_L96_Q0.161610.827
77_E80_R0.160110.819
12_E15_G0.159940.818
34_G46_Q0.159890.818
5_A9_E0.158710.812
92_V104_E0.158480.811
71_E74_A0.157350.805
40_F134_V0.157210.804
35_L39_E0.156560.801
44_Y141_L0.156490.801
55_I58_L0.156460.800
36_R82_L0.156090.798
10_E13_R0.155210.794
40_F83_R0.154930.793
129_R133_R0.153050.783
55_I70_E0.152940.782
77_E129_R0.152910.782
42_A54_T0.152220.779
32_P92_V0.151650.776
93_S104_E0.151570.775
59_E72_A0.151550.775
77_E133_R0.150920.772
36_R97_T0.150850.772
2_F9_E0.150630.771
56_D62_A0.150210.768
59_E73_E0.149910.767
73_E76_R0.149840.767
128_Y132_R0.14980.766
61_L66_L0.149260.764
2_F5_A0.149140.763
82_L134_V0.148280.759
54_T57_A0.148160.758
4_R7_I0.148020.757
89_L97_T0.147980.757
42_A45_L0.147960.757
7_I30_L0.14790.757
6_K13_R0.147830.756
86_R94_G0.147570.755
45_L141_L0.147510.755
124_M127_L0.147280.753
70_E73_E0.146210.748
105_Q117_K0.145850.746
8_E11_R0.14550.744
93_S97_T0.145270.743
63_A110_R0.144110.737
11_R15_G0.143630.735
64_A98_D0.142550.729
10_E40_F0.142130.727
59_E69_E0.141790.725
36_R96_Q0.141770.725
89_L99_R0.141610.724
41_I141_L0.141520.724
82_L86_R0.141210.722
45_L55_I0.140590.719
12_E135_R0.140420.718
102_F105_Q0.139530.714
13_R105_Q0.139390.713
83_R98_D0.139330.713
105_Q128_Y0.137550.704
88_A109_A0.136590.699
63_A76_R0.13580.695
78_A127_L0.135540.693
4_R12_E0.135440.693
32_P139_D0.135290.692
9_E135_R0.134840.690
45_L57_A0.134730.689
28_L112_L0.134470.688
34_G82_L0.134080.686
9_E140_R0.134010.686
105_Q141_L0.133480.683
73_E77_E0.133420.683
70_E115_E0.132760.679
31_G86_R0.132180.676
89_L131_R0.131970.675
118_D132_R0.13090.670
3_M48_R0.130790.669
63_A70_E0.130560.668
81_F112_L0.130320.667
89_L92_V0.129390.662
95_R100_L0.129060.660
39_E101_P0.128620.658
37_D98_D0.128590.658
38_I75_L0.128570.658
38_I79_Y0.127840.654
81_F123_L0.127110.650
82_L131_R0.126880.649
59_E62_A0.126290.646
132_R136_R0.126190.646
3_M47_L0.125860.644
37_D48_R0.125440.642
73_E126_E0.125380.641
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
1v4aA0.964899.90.228
3k7dA0.83199.80.368
3nxqA0.901419.70.922
3fapB0.528219.10.923
1d5yA0.683115.40.926
4eivA0.640810.90.931
3oouA0.69728.60.933
2vakA0.80998.40.934
3us6A0.85217.60.935
2a4aA0.42257.50.935

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