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The map label for this gene is truD

Identifier: 59712678

GI number: 59712678

Start: 2306701

End: 2307756

Strand: Reverse

Name: truD

Synonym: VF_2071

Alternate gene names: 59712678

Gene position: 2307756-2306701 (Counterclockwise)

Preceding gene: 59712679

Following gene: 59712677

Centisome position: 79.65

GC content: 38.45

Gene sequence:

>1056_bases
ATGTCAGACATCATGTCTAATTTTTCGTGGTTATACGGAAAGCCAGTAGCAACAGGTAAATTAAAACAACTTCCTGAGCA
CTTTATTGTAAAAGAGATCTTAGGTTTTGAGTTCACTGGTAATGGTGAACACTTAATGGTTAAAATCCGTAAAACGGGTG
AAAATACCAAATATGTTGCTAATGAATTGGCAAAATTCTGTGGTGTTAAATCTAAAAATGTTAGTTGGGCTGGGTTGAAA
GATCGCCATGCCGTGACAGAGCAATGGTTAAGTGTTCAAGTTGCTAACAGTGATGAATTAAACTTTGCTAAATTTGAAGC
AACACATCCCGGTGTTGAAATTTTAGAAGTCACTCGTCATAACAAAAAGTTACGTCCTGGTGATTTACAAGGTAATCAGT
TCCAAGTTATTGCAACGGAAGTCACCGATATTGACGATGTGTTAGCGCGTCTAGAAAAAGTAAAATTAGCAGGTGTTCCT
AATTATTTTGGTTCGCAACGTTTCGGACATGAAGGTAATAACGTTAACGAAGCTCGTCGTTGGGGACGAGATAATGTTCG
TACTCGTGATAACAGCAAGCGTAGTTTTTATTTATCAGCAGCTCGTTCTTGGATTTTTAACCACATTGTTTCTCAAAGAA
TAACAGAGGGTTACTTCTCTCAACCTGTTGATGGTGATATTCTACTTGATCGCAATGATCGTATCGTAAATGAGAATGTA
ACGTCTGAAGAGAGCATTCAAAAGATTCAAAATGGTGAATTATCTATTACAGCAGCATTGGCTGGAGATAATCAATTACC
AACAACAGGCACAGCTCTGACATTAGAACAACCTCATTTAGATGCTGAACCTGATTTAATGGCGTTAATTCGTGGTAACC
GTATGCGTCATGAACGTCGTGCGATTGAGCTTCATCCTGAAAACCTAACATGGTCAGCTGAAGGCGATACGCTAACGCTA
AACTTCTCATTAACTTCAGGCAGTTTTGCTACGGTAATCGTACGTGAATTGCTACAAGAAATTGAAGTTGAGCGTACTTA
TAGCTCAAACGATTAA

Upstream 100 bases:

>100_bases
AAGCCACGACTTCTGAGCGTTTGGGTTTTACCGGTAGAAAAGAAGGCATTGCTTGTGAAGCAGTAGTGCTGTTAGTTAAA
GCATCTTAAGAGATAGATTT

Downstream 100 bases:

>100_bases
TATTAATATGGAGACAAGAGTGAAGAAGTTACGCATTTTGCTTAGTAACGATGATGGTGTATTTGCTGAAGGGATAAATA
CGTTAGCTCGTGTATTAGCT

Product: tRNA pseudouridine synthase D

Products: pseudouridine 5'-phosphate; H2O

Alternate protein names: tRNA pseudouridylate synthase D; tRNA-uridine isomerase D

Number of amino acids: Translated: 351; Mature: 350

Protein sequence:

>351_residues
MSDIMSNFSWLYGKPVATGKLKQLPEHFIVKEILGFEFTGNGEHLMVKIRKTGENTKYVANELAKFCGVKSKNVSWAGLK
DRHAVTEQWLSVQVANSDELNFAKFEATHPGVEILEVTRHNKKLRPGDLQGNQFQVIATEVTDIDDVLARLEKVKLAGVP
NYFGSQRFGHEGNNVNEARRWGRDNVRTRDNSKRSFYLSAARSWIFNHIVSQRITEGYFSQPVDGDILLDRNDRIVNENV
TSEESIQKIQNGELSITAALAGDNQLPTTGTALTLEQPHLDAEPDLMALIRGNRMRHERRAIELHPENLTWSAEGDTLTL
NFSLTSGSFATVIVRELLQEIEVERTYSSND

Sequences:

>Translated_351_residues
MSDIMSNFSWLYGKPVATGKLKQLPEHFIVKEILGFEFTGNGEHLMVKIRKTGENTKYVANELAKFCGVKSKNVSWAGLK
DRHAVTEQWLSVQVANSDELNFAKFEATHPGVEILEVTRHNKKLRPGDLQGNQFQVIATEVTDIDDVLARLEKVKLAGVP
NYFGSQRFGHEGNNVNEARRWGRDNVRTRDNSKRSFYLSAARSWIFNHIVSQRITEGYFSQPVDGDILLDRNDRIVNENV
TSEESIQKIQNGELSITAALAGDNQLPTTGTALTLEQPHLDAEPDLMALIRGNRMRHERRAIELHPENLTWSAEGDTLTL
NFSLTSGSFATVIVRELLQEIEVERTYSSND
>Mature_350_residues
SDIMSNFSWLYGKPVATGKLKQLPEHFIVKEILGFEFTGNGEHLMVKIRKTGENTKYVANELAKFCGVKSKNVSWAGLKD
RHAVTEQWLSVQVANSDELNFAKFEATHPGVEILEVTRHNKKLRPGDLQGNQFQVIATEVTDIDDVLARLEKVKLAGVPN
YFGSQRFGHEGNNVNEARRWGRDNVRTRDNSKRSFYLSAARSWIFNHIVSQRITEGYFSQPVDGDILLDRNDRIVNENVT
SEESIQKIQNGELSITAALAGDNQLPTTGTALTLEQPHLDAEPDLMALIRGNRMRHERRAIELHPENLTWSAEGDTLTLN
FSLTSGSFATVIVRELLQEIEVERTYSSND

Specific function: Responsible for synthesis of pseudouridine from uracil- 13 in transfer RNAs

COG id: COG0585

COG function: function code S; Uncharacterized conserved protein

Gene ontology:

Cell location: Cytoplasm [C]

Metaboloic importance: Unknown [C]

Operon status: Not Known

Operon components: None

Similarity: Contains 1 TRUD domain

Homologues:

Organism=Escherichia coli, GI1789102, Length=337, Percent_Identity=44.8071216617211, Blast_Score=279, Evalue=2e-76,

Paralogues:

None

Copy number: NA

Swissprot (AC and ID): TRUD_VIBF1 (Q5E330)

Other databases:

- EMBL:   CP000020
- RefSeq:   YP_205454.1
- ProteinModelPortal:   Q5E330
- SMR:   Q5E330
- STRING:   Q5E330
- GeneID:   3279153
- GenomeReviews:   CP000020_GR
- KEGG:   vfi:VF_2071
- NMPDR:   fig|312309.3.peg.2083
- eggNOG:   COG0585
- HOGENOM:   HBG541221
- OMA:   ALTRQWF
- PhylomeDB:   Q5E330
- ProtClustDB:   PRK00984
- BioCyc:   VFIS312309:VF2071-MONOMER
- HAMAP:   MF_01082
- InterPro:   IPR020103
- InterPro:   IPR001656
- InterPro:   IPR020119
- InterPro:   IPR011760
- PANTHER:   PTHR13326
- TIGRFAMs:   TIGR00094

Pfam domain/function: PF01142 TruD; SSF55120 PsdUridine_synth_cat_dom

EC number: 4.2.1.70

Molecular weight: Translated: 39610; Mature: 39479

Theoretical pI: Translated: 6.20; Mature: 6.20

Prosite motif: PS50984 TRUD; PS01268 UPF0024

Important sites: ACT_SITE 81-81

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.3 %Cys     (Translated Protein)
1.4 %Met     (Translated Protein)
1.7 %Cys+Met (Translated Protein)
0.3 %Cys     (Mature Protein)
1.1 %Met     (Mature Protein)
1.4 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MSDIMSNFSWLYGKPVATGKLKQLPEHFIVKEILGFEFTGNGEHLMVKIRKTGENTKYVA
CCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCEEEECCCCEEEEEEEECCCCHHHHH
NELAKFCGVKSKNVSWAGLKDRHAVTEQWLSVQVANSDELNFAKFEATHPGVEILEVTRH
HHHHHHHCCCCCCCEECCCCHHHHHHHHHHEEEECCCCCCCEEEEECCCCCCEEEEEHHC
NKKLRPGDLQGNQFQVIATEVTDIDDVLARLEKVKLAGVPNYFGSQRFGHEGNNVNEARR
CCCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCCHHCCCCCCCCCCCHHHHHH
WGRDNVRTRDNSKRSFYLSAARSWIFNHIVSQRITEGYFSQPVDGDILLDRNDRIVNENV
CCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCEEECCCC
TSEESIQKIQNGELSITAALAGDNQLPTTGTALTLEQPHLDAEPDLMALIRGNRMRHERR
CCHHHHHHHCCCCEEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEECCCCCHHHHCC
AIELHPENLTWSAEGDTLTLNFSLTSGSFATVIVRELLQEIEVERTYSSND
EEEECCCCEEEECCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCC
>Mature Secondary Structure 
SDIMSNFSWLYGKPVATGKLKQLPEHFIVKEILGFEFTGNGEHLMVKIRKTGENTKYVA
CHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCEEEECCCCEEEEEEEECCCCHHHHH
NELAKFCGVKSKNVSWAGLKDRHAVTEQWLSVQVANSDELNFAKFEATHPGVEILEVTRH
HHHHHHHCCCCCCCEECCCCHHHHHHHHHHEEEECCCCCCCEEEEECCCCCCEEEEEHHC
NKKLRPGDLQGNQFQVIATEVTDIDDVLARLEKVKLAGVPNYFGSQRFGHEGNNVNEARR
CCCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCCHHCCCCCCCCCCCHHHHHH
WGRDNVRTRDNSKRSFYLSAARSWIFNHIVSQRITEGYFSQPVDGDILLDRNDRIVNENV
CCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCEEECCCC
TSEESIQKIQNGELSITAALAGDNQLPTTGTALTLEQPHLDAEPDLMALIRGNRMRHERR
CCHHHHHHHCCCCEEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEECCCCCHHHHCC
AIELHPENLTWSAEGDTLTLNFSLTSGSFATVIVRELLQEIEVERTYSSND
EEEECCCCEEEECCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCC

PDB accession: NA

Resolution: NA

Structure class: Alpha Beta

Cofactors: NA

Metal ions: NA

Kcat value (1/min): NA

Specific activity: NA

Km value (mM): NA

Substrates: uracil; D-ribose 5-phosphate

Specific reaction: uracil + D-ribose 5-phosphate = pseudouridine 5'-phosphate + H2O

General reaction: NA

Inhibitor: NA

Structure determination priority: 10.0

TargetDB status: NA

Availability: NA

References: NA