Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD2726c_(dapF)_3038941_3039810
DateWed Aug 7 12:50:38 BST 2019
Unique Job IDd68ffc5e037a3359
SequenceMIFAKGHGTQ ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:44.466 Y:56.446 Z:51.540
Model (left) based on template c3fveA_
Top template information
PDB header:isomerase
Chain: A: PDB Molecule:diaminopimelate epimerase;
PDBTitle: crystal structure of diaminopimelate epimerase mycobacterium2 tuberculosis dapf
Confidence and coverage
Confidence:100.0% Coverage: 98%
282 residues ( 98% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
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Sequence analysis 

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Detailed template information [Hide] 

 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3fveA_



100.0 96
PDB header:isomerase
Chain: A: PDB Molecule:diaminopimelate epimerase;
PDBTitle: crystal structure of diaminopimelate epimerase mycobacterium2 tuberculosis dapf
2c5m47A_



100.0 53
PDB header:isomerase
Chain: A: PDB Molecule:diaminopimelate epimerase;
PDBTitle: crystal strcuture of dapf from corynebacterium glutamicum in complex2 with d,l-diaminopimelate
3c2gkjA_



100.0 28
PDB header:isomerase
Chain: A: PDB Molecule:diaminopimelate epimerase;
PDBTitle: crystal structure of diaminopimelate epimerase in complex2 with an irreversible inhibitor dl-azidap
4c5ha4A_



100.0 31
PDB header:isomerase
Chain: A: PDB Molecule:diaminopimelate epimerase;
PDBTitle: structure of a diaminopimelate epimerase from acinetobacter baumannii
5c2otnB_



100.0 31
PDB header:isomerase
Chain: B: PDB Molecule:diaminopimelate epimerase;
PDBTitle: crystal structure of the catalytically active form of diaminopimelate2 epimerase from bacillus anthracis
6c3ekmE_



100.0 35
PDB header:isomerase
Chain: E: PDB Molecule:diaminopimelate epimerase, chloroplastic;
PDBTitle: crystal structure of diaminopimelate epimerase form2 arabidopsis thaliana in complex with irreversible inhibitor3 dl-azidap
7d2gkea1



100.0 32
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:Diaminopimelate epimerase
8c4juuA_



100.0 20
PDB header:isomerase
Chain: A: PDB Molecule:epimerase;
PDBTitle: crystal structure of a putative hydroxyproline epimerase from2 xanthomonas campestris (target efi-506516) with bound phosphate and3 unknown ligand
9c3ednB_



100.0 17
PDB header:biosynthetic protein
Chain: B: PDB Molecule:phenazine biosynthesis protein, phzf family;
PDBTitle: crystal structure of the bacillus anthracis phenazine2 biosynthesis protein, phzf family
10c1qy9B_



100.0 17
PDB header:unknown function
Chain: B: PDB Molecule:hypothetical protein ydde;
PDBTitle: crystal structure of e. coli se-met protein ydde
11d1s7ja_



100.0 15
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PhzC/PhzF-like
12c1ym5A_



100.0 13
PDB header:oxidoreductase
Chain: A: PDB Molecule:hypothetical 32.6 kda protein in dap2-slt2
PDBTitle: crystal structure of yhi9, the yeast member of the2 phenazine biosynthesis phzf enzyme superfamily.
13c4dunA_



100.0 14
PDB header:biosynthetic protein
Chain: A: PDB Molecule:putative phenazine biosynthesis phzc/phzf protein;
PDBTitle: 1.76a x-ray crystal structure of a putative phenazine biosynthesis2 phzc/phzf protein from clostridium difficile (strain 630)
14c2azpA_



100.0 21
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pa1268;
PDBTitle: crystal structure of pa1268 solved by sulfur sad
15c1u1wA_



100.0 15
PDB header:isomerase, lyase
Chain: A: PDB Molecule:phenazine biosynthesis protein phzf;
PDBTitle: structure and function of phenazine-biosynthesis protein phzf from2 pseudomonas fluorescens 2-79
16c1u0kA_



100.0 16
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:gene product pa4716;
PDBTitle: the structure of a predicted epimerase pa4716 from pseudomonas2 aeruginosa
17c4jd7D_



100.0 17
PDB header:isomerase
Chain: D: PDB Molecule:proline racemase;
PDBTitle: crystal structure of pput_1285, a putative hydroxyproline epimerase2 from pseudomonas putida f1 (target efi-506500), open form, space3 group p212121, bound sulfate
18c6r77B_



100.0 17
PDB header:lyase
Chain: B: PDB Molecule:proline racemase;
PDBTitle: crystal structure of trans-3-hydroxy-l-proline dehydratase in complex2 with substrate - closed conformation
19d1tm0a_



100.0 13
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:Proline racemase
20c6hjgB_



100.0 19
PDB header:isomerase
Chain: B: PDB Molecule:proline racemase a;
PDBTitle: trypanosoma cruzi proline racemase in complex with inhibitor oxopa
21c1w62B_



not modelled 100.0 16
PDB header:racemase
Chain: B: PDB Molecule:proline racemase a;
PDBTitle: proline racemase in complex with one molecule of pyrrole-2-carboxylic2 acid (hemi form)
22c6j7cA_



not modelled 100.0 14
PDB header:isomerase
Chain: A: PDB Molecule:proline racemase;
PDBTitle: crystal structure of proline racemase-like protein from thermococcus2 litoralis in complex with proline
23c4lb0B_



not modelled 100.0 18
PDB header:isomerase
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a hydroxyproline epimerase from agrobacterium2 vitis, target efi-506420, with bound trans-4-oh-l-proline
24d2gkea2



not modelled 100.0 23
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:Diaminopimelate epimerase
25c4k7gD_



not modelled 100.0 15
PDB header:isomerase
Chain: D: PDB Molecule:3-hydroxyproline dehydratse;
PDBTitle: crystal structure of a 3-hydroxyproline dehydratse from agrobacterium2 vitis, target efi-506470, with bound pyrrole 2-carboxylate, ordered3 active site
26d1qy9a1



not modelled 99.8 18
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PhzC/PhzF-like
27d1xuba1



not modelled 99.7 12
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PhzC/PhzF-like
28d1xuba2



not modelled 99.6 17
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PhzC/PhzF-like
29d1qy9a2



not modelled 99.6 16
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PhzC/PhzF-like
30d1u0ka2



not modelled 99.5 17
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PhzC/PhzF-like
31d1u0ka1



not modelled 99.4 13
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PhzC/PhzF-like
32c6p3hB_



not modelled 98.4 21
PDB header:isomerase
Chain: B: PDB Molecule:(4e)-oxalomesaconate delta-isomerase;
PDBTitle: crystal structure of ligu(k66m) bound to substrate
33c6otvA_



not modelled 98.3 17
PDB header:isomerase
Chain: A: PDB Molecule:putative isomerase ybhh;
PDBTitle: crystal structure of putative isomerase ec2056
34c3g7kD_



not modelled 97.9 15
PDB header:isomerase
Chain: D: PDB Molecule:3-methylitaconate isomerase;
PDBTitle: crystal structure of methylitaconate-delta-isomerase
35c2pw0A_



not modelled 97.1 19
PDB header:unknown function
Chain: A: PDB Molecule:prpf methylaconitate isomerase;
PDBTitle: crystal structure of trans-aconitate bound to methylaconitate2 isomerase prpf from shewanella oneidensis
36d1sr8a_



not modelled 56.4 39
Fold:CbiD-like
Superfamily:CbiD-like
Family:CbiD-like
37d2h9fa2



not modelled 55.6 23
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PA0793-like
38c3axtA_



not modelled 31.9 24
PDB header:transferase
Chain: A: PDB Molecule:probable n(2),n(2)-dimethylguanosine trna methyltransferase
PDBTitle: complex structure of trna methyltransferase trm1 from aquifex aeolicus2 with s-adenosyl-l-methionine
39d2h9fa1



not modelled 25.8 13
Fold:Diaminopimelate epimerase-like
Superfamily:Diaminopimelate epimerase-like
Family:PA0793-like
40d2dula1



not modelled 23.2 33
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:TRM1-like
41c5jvoA_



not modelled 20.9 21
PDB header:dna binding protein
Chain: A: PDB Molecule:arginine repressor;
PDBTitle: crystal structure of the arginine repressor from the pathogenic2 bacterium corynebacterium pseudotuberculosis
42c5hr4J_



not modelled 20.6 17
PDB header:hydrolase/dna
Chain: J: PDB Molecule:mmei;
PDBTitle: structure of type iil restriction-modification enzyme mmei in complex2 with dna has implications for engineering of new specificities
43d1vema1



not modelled 19.5 11
Fold:Prealbumin-like
Superfamily:Starch-binding domain-like
Family:Starch-binding domain
44d2ih2a1



not modelled 19.2 18
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:DNA methylase TaqI, N-terminal domain
45c4o1hA_



not modelled 19.0 27
PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator glnr;
PDBTitle: crystal structure of the regulatory domain of ameglnr
46d1q7sa_



not modelled 18.7 16
Fold:Peptidyl-tRNA hydrolase II
Superfamily:Peptidyl-tRNA hydrolase II
Family:Peptidyl-tRNA hydrolase II
47d2ar0a1



not modelled 18.7 9
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:N-6 DNA Methylase-like
48c5ybbA_



not modelled 18.5 17
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:type i restriction-modification system methyltransferase
PDBTitle: structural basis underlying complex assembly andconformational2 transition of the type i r-m system
49c1vzhB_



not modelled 16.7 22
PDB header:oxidoreductase
Chain: B: PDB Molecule:desulfoferrodoxin;
PDBTitle: structure of superoxide reductase bound to ferrocyanide and active2 site expansion upon x-ray induced photoreduction
50c3khkA_



not modelled 15.1 11
PDB header:dna binding protein
Chain: A: PDB Molecule:type i restriction-modification system methylation subunit;
PDBTitle: crystal structure of type-i restriction-modification system2 methylation subunit (mm_0429) from methanosarchina mazei.
51c2waqG_



not modelled 14.6 25
PDB header:transcription
Chain: G: PDB Molecule:dna-directed rna polymerase rpo8 subunit;
PDBTitle: the complete structure of the archaeal 13-subunit dna-directed rna2 polymerase
52d2ayxa2



not modelled 14.2 21
Fold:Flavodoxin-like
Superfamily:CheY-like
Family:RcsC linker domain-like
53c2l3bA_



not modelled 14.1 27
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved protein found in conjugate transposon;
PDBTitle: solution nmr structure of the bt_0084 lipoprotein from bacteroides2 thetaiotaomicron, northeast structural genomics consortium target3 btr376
54d1jwya1



not modelled 14.0 28
Fold:SH3-like barrel
Superfamily:Myosin S1 fragment, N-terminal domain
Family:Myosin S1 fragment, N-terminal domain
55c3lkdB_



not modelled 13.9 25
PDB header:transferase
Chain: B: PDB Molecule:type i restriction-modification system methyltransferase
PDBTitle: crystal structure of the type i restriction-modification system2 methyltransferase subunit from streptococcus thermophilus, northeast3 structural genomics consortium target sur80
56c3ufbA_



not modelled 13.9 22
PDB header:transferase
Chain: A: PDB Molecule:type i restriction-modification system methyltransferase
PDBTitle: crystal structure of a modification subunit of a putative type i2 restriction enzyme from vibrio vulnificus yj016
57c2l7qA_



not modelled 13.3 27
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved protein found in conjugate transposon;
PDBTitle: solution nmr structure of conjugate transposon protein bvu_1572(27-2 141) from bacteroides vulgatus, northeast structural genomics3 consortium target bvr155
58c3p9nA_



not modelled 13.0 14
PDB header:transferase
Chain: A: PDB Molecule:possible methyltransferase (methylase);
PDBTitle: rv2966c of m. tuberculosis is a rsmd-like methyltransferase
59c3j3bU_



not modelled 12.7 7
PDB header:ribosome
Chain: U: PDB Molecule:60s ribosomal protein l22;
PDBTitle: structure of the human 60s ribosomal proteins
60c4qxlA_



not modelled 12.2 20
PDB header:motor protein
Chain: A: PDB Molecule:flagellar protein flhe;
PDBTitle: crystal structure of flhe
61c5hfjF_



not modelled 12.1 31
PDB header:dna binding protein
Chain: F: PDB Molecule:adenine specific dna methyltransferase (dpna);
PDBTitle: crystal structure of m1.hpyavi-sam complex
62c3j39U_



not modelled 12.1 7
PDB header:ribosome
Chain: U: PDB Molecule:60s ribosomal protein l22;
PDBTitle: structure of the d. melanogaster 60s ribosomal proteins
63c1aqjB_



not modelled 12.0 21
PDB header:methyltransferase
Chain: B: PDB Molecule:adenine-n6-dna-methyltransferase taqi;
PDBTitle: structure of adenine-n6-dna-methyltransferase taqi
64c4lbaB_



not modelled 11.5 20
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:conjugative transposon lipoprotein;
PDBTitle: crystal structure of a conjugative transposon lipoprotein2 (bacegg_03088) from bacteroides eggerthii dsm 20697 at 1.70 a3 resolution
65d2okca1



not modelled 11.3 22
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:N-6 DNA Methylase-like
66c4zyeA_



not modelled 10.8 22
PDB header:transferase
Chain: A: PDB Molecule:methylated-dna--protein-cysteine methyltransferase;
PDBTitle: crystal structure of sulfolobus solfataricus o6-methylguanine2 methyltransferase
67c6h2uA_



not modelled 10.8 29
PDB header:transferase
Chain: A: PDB Molecule:methyltransferase-like protein 5;
PDBTitle: crystal structure of human mettl5-trmt112 complex, the 18s rrna2 m6a1832 methyltransferase at 1.6a resolution
68d2f8la1



not modelled 10.6 17
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:N-6 DNA Methylase-like
69c4qh0D_



not modelled 10.3 9
PDB header:hydrolase
Chain: D: PDB Molecule:dna-entry nuclease (competence-specific nuclease);
PDBTitle: crystal structure of nuca from streptococcus agalactiae with magnesium2 ion bound
70c1xtyD_



not modelled 10.1 14
PDB header:hydrolase
Chain: D: PDB Molecule:peptidyl-trna hydrolase;
PDBTitle: crystal structure of sulfolobus solfataricus peptidyl-trna hydrolase
71c3ldgA_



not modelled 9.9 14
PDB header:transferase
Chain: A: PDB Molecule:putative uncharacterized protein smu.472;
PDBTitle: crystal structure of smu.472, a putative methyltransferase complexed2 with sah
72d1dkua1



not modelled 9.8 17
Fold:PRTase-like
Superfamily:PRTase-like
Family:Phosphoribosylpyrophosphate synthetase-like
73d1rlka_



not modelled 9.7 15
Fold:Peptidyl-tRNA hydrolase II
Superfamily:Peptidyl-tRNA hydrolase II
Family:Peptidyl-tRNA hydrolase II
74c2zv3E_



not modelled 9.6 10
PDB header:hydrolase
Chain: E: PDB Molecule:peptidyl-trna hydrolase;
PDBTitle: crystal structure of project mj0051 from methanocaldococcus2 jannaschii dsm 2661
75c2vwtA_



not modelled 9.5 21
PDB header:lyase
Chain: A: PDB Molecule:yfau, 2-keto-3-deoxy sugar aldolase;
PDBTitle: crystal structure of yfau, a metal ion dependent class ii2 aldolase from escherichia coli k12 - mg-pyruvate product3 complex
76c1g38A_



not modelled 9.5 21
PDB header:transferase/dna
Chain: A: PDB Molecule:modification methylase taqi;
PDBTitle: adenine-specific methyltransferase m. taq i/dna complex
77d1ne2a_



not modelled 9.5 21
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:Ta1320-like
78c2g7hA_



not modelled 9.3 17
PDB header:transferase
Chain: A: PDB Molecule:methylated-dna--protein-cysteine
PDBTitle: structure of an o6-methylguanine dna methyltransferase from2 methanococcus jannaschii (mj1529)
79c4tv6A_



not modelled 9.2 18
PDB header:lyase
Chain: A: PDB Molecule:2-dehydro-3-deoxyglucarate aldolase;
PDBTitle: crystal structure of citrate synthase variant sbng e151q
80c6b3oB_



not modelled 9.0 31
PDB header:viral protein
Chain: B: PDB Molecule:spike glycoprotein;
PDBTitle: tectonic conformational changes of a coronavirus spike glycoprotein2 promote membrane fusion
81c3hvzB_



not modelled 8.8 7
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the tgs domain of the clolep_03100 protein from2 clostridium leptum, northeast structural genomics consortium target3 qlr13a
82c5fgwA_



not modelled 8.6 24
PDB header:metal binding, dna binding protein
Chain: A: PDB Molecule:extracellular streptodornase d;
PDBTitle: structure of sda1 nuclease with bound zinc ion
83c3owvA_



not modelled 8.6 14
PDB header:hydrolase
Chain: A: PDB Molecule:dna-entry nuclease;
PDBTitle: structural insights into catalytic and substrate binding mechanisms of2 the strategic enda nuclease from streptococcus pneumoniae
84d1wy7a1



not modelled 8.4 21
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:Ta1320-like
85c5e72A_



not modelled 8.3 13
PDB header:transferase
Chain: A: PDB Molecule:n2, n2-dimethylguanosine trna methyltransferase;
PDBTitle: crystal structure of the archaeal trna m2g/m22g10 methyltransferase2 (atrm11) in complex with s-adenosyl-l-methionine (sam) from3 thermococcus kodakarensis
86d1xo8a_



not modelled 8.3 14
Fold:Immunoglobulin-like beta-sandwich
Superfamily:LEA14-like
Family:LEA14-like
87c5egpB_



not modelled 8.3 25
PDB header:transferase
Chain: B: PDB Molecule:ubie/coq5 family methyltransferase, putative;
PDBTitle: crystal structure of the s-methyltransferase tmta
88d1mgta1



not modelled 7.8 11
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Methylated DNA-protein cysteine methyltransferase, C-terminal domain
Family:Methylated DNA-protein cysteine methyltransferase, C-terminal domain
89d1bf2a2



not modelled 7.7 10
Fold:Glycosyl hydrolase domain
Superfamily:Glycosyl hydrolase domain
Family:alpha-Amylases, C-terminal beta-sheet domain
90d2esra1



not modelled 7.5 20
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:YhhF-like
91d1ws6a1



not modelled 7.5 27
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:YhhF-like
92c3qz6A_



not modelled 7.4 23
PDB header:lyase
Chain: A: PDB Molecule:hpch/hpai aldolase;
PDBTitle: the crystal structure of hpch/hpai aldolase from desulfitobacterium2 hafniense dcb-2
93d2p92a1



not modelled 7.4 16
Fold:eIF1-like
Superfamily:TM1457-like
Family:TM1457-like
94c3cioA_



not modelled 7.4 27
PDB header:signaling protein, transferase
Chain: A: PDB Molecule:tyrosine-protein kinase etk;
PDBTitle: the kinase domain of escherichia coli tyrosine kinase etk
95c2xh3B_



not modelled 7.3 14
PDB header:hydrolase
Chain: B: PDB Molecule:spd1 nuclease;
PDBTitle: extracellular nuclease
96c4he5A_



not modelled 7.1 8
PDB header:unknown function
Chain: A: PDB Molecule:peptidase family u32;
PDBTitle: crystal structure of the selenomethionine variant of the c-terminal2 domain of geobacillus thermoleovorans putative u32 peptidase
97c2d3kA_



not modelled 7.1 19
PDB header:hydrolase
Chain: A: PDB Molecule:peptidyl-trna hydrolase;
PDBTitle: structural study on project id ph1539 from pyrococcus2 horikoshii ot3
98c2p35A_



not modelled 7.0 19
PDB header:transferase
Chain: A: PDB Molecule:trans-aconitate 2-methyltransferase;
PDBTitle: crystal structure of trans-aconitate methyltransferase from2 agrobacterium tumefaciens
99d2fpoa1



not modelled 7.0 13
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:YhhF-like

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