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Ureaplasma urealyticum Search Results

Record: 1 of 1  
MiniMap IGR5 IGR3 IGR514 IGR513 IGR4 IGR2 IGR1 IGR6 IGR7 IGR515 rpL34,rpmH, - UU604 rnpA, - UU603 UU602 rpL31, - UU002 rpiB, - UU006 UU008 rpL10, - UU010 UU007 hemK, - UU004 prfA, - UU003 dnaA, - UU001 mgtE, - UU009 rpL34,rpmH, - UU604 rnpA, - UU603 UU602 rpL31, - UU002 rpiB, - UU006 UU008 rpL10, - UU010 UU007 hemK, - UU004 prfA, - UU003 dnaA, - UU001 mgtE, - UU009 Type: tandem, Name:  - 4 Type: tandem, Name:  - 377 Type: tandem, Name:  - 3 Type: tandem, Name:  - 375 Type: tandem, Name:  - 1 Type: tandem, Name:  - 429 Type: tandem, Name:  - 376 Type: tandem, Name:  - 6 Type: tandem, Name:  - 2 Type: tandem, Name:  - 390 Type: tandem, Name:  - 5 rnpA, - UU603 UU602 rpL34,rpmH, - UU604 rpL31, - UU002 rpiB, - UU006 UU008 rpL10, - UU010 UU007 hemK, - UU004 prfA, - UU003 dnaA, - UU001 mgtE, - UU009 hemK, - UU005 hemK, - UU005
* Calculated from Protein Sequence

Gene ID: UU004

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
hemK  

Definition:
protoporphyrinogen oxidase N-terminal residues

Gene Start:
3014

Gene Stop:
3886

Gene Length:
873

Molecular Weight*:
34153

pI*:
8.20

Net Charge*:
3.68

EC:
1.3.3.4  

Functional Class:
biosynthesis of cofactors, prosthetic groups, and carriers; heme and porphyrin  

Pathway: pathway table
Porphyrin and chlorophyll metabolism

Secondary Evidence:
Dailey TA, Meissner P, Dailey HA. 1994. Expression of a cloned protoporphyrinogen oxidase. J Biol Chem 269(2):813-5. Medline: 8288631.

Labbe P, Camadro JM, Chambon H. 1985. Fluorometric assays for coproporphyrinogen oxidase and protoporphyrinogen oxidase. Anal Biochem 149(1):248-60. Medline: 3907404.

Sasarman A, Chartrand P, Lavoie M, Tardif D, Proschek R, Lapointe C. 1979. Mapping of a new hem gene in Escherichia coli K12. J Gen Microbiol. 113(2):297-303. Medline: 390093.

Comment:
Protoporphyrinogen oxidases have some domain similarities to N-6 Adenine-specific DNA methylases, however we believe the correct/primary EC number has been assigned to UU004. These enzymes are typically constituted of 425-455 residues in bacteria; UU004 appears to represent only the first 254-284 of the residues whereas UU005 represents the remaining C-terminal residues (incorrect internal stop?). Protoporphyrinogen oxidase is the enzyme that catalyzes in the penultimate step in the heme biosynthetic pathway.

See UU274, a predicted hemN sequence.

Blast Summary:  PSI-Blast Search
Best hits in gapped BLAST are to hemK homologs, for example residues 55-260 are 28% similar to HEMK_BACSU. The protoporphyrinogen oxidases of Aquifex and Borrelia are also similar. Within the STDGEN database, UU004 is similar to MG259 and to CT024, both predicted protoporphyrinogen oxidases. (CT024 is at this time defined as an adenine methylase in GenBank, but as a protoporphyrinogen oxidase in this database). Residues 64-254 are 34% similar to residues 64-243 of MG259. Residues 49-284 are 27% similar to residues 45-273 of CT024.


COGS Summary:  COGS Search
The phylogenetic pattern of COG0500 is EHgpCMYU.
Cog name: SAM-dependent methyltransferases.
Functional class: R.
BeTs to -hg-cmyu.
Number of proteins in this genome belonging to this COG is 2



Blocks Summary:  Blocks Search
Residues 143-163 and 185-194 are similar to blocks BL01261B and C, which comprise uncharacterized proteins e.g. Y064_SYNY3 and Y438_METJA. Residues 185-193 are similar to block BL00092, N-6 Adenine-specific DNA methylase.






ProDom Summary:  Protein Domain Search
Residues 69-192 are 34% similar to a methyltransferase domain of Y259_MYCGE, a possible hemK product. Residues 192-260 are also weakly similar to a predicted hemK domain as seen in HEMK_BACSU. Several other weak similarities are observed.


Paralogs:  Local Blast Search
UU004 is paralogously related to UU305 and UU098: residues 85-131 are 25% similar to a stretch of UU305 (for which a function has not yet been assigned); residues 84-134 are 29% similar to UU098, a predicted type I restriction enzyme M protein (hsdM).


Pfam Summary:  Pfam Search
No significant hits to the Pfam 11.0 database

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
184  
290

PDB Hit:


Gene Protein Sequence:
MTYHQLIFQAYSLLEKKLRNPQVAFQLLYGLDNKINDSYSFSNNRLTIVN
SNLEYTYFKLLDEFINGKPLVRILGYGYFCAKRFYVDKNVFAFRVETELL
IDVVNKVIQQSTYKIKNVIDVCCGSGVLGLSTKMNFNQLNVSLLDISIDA
INNCKKNAKYHNLTDVNFIHKSMQEYFLNTKKRFDLIICNPPYIKSNYEL
NREVLDYDPINALIDFDHKDGISFYLFIINNIKSIANEKFTIIFEIGFDQ
KEILEKVIKKNEFPLFYYFINDYNNLCRILIISNIKYENL$

Gene Nucleotide Sequence:  Sequence Viewer
ATGACCTACCATCAATTAATTTTTCAAGCATACTCACTACTTGAAAAAAA
ATTACGTAATCCACAAGTAGCATTTCAGTTGCTGTACGGATTAGATAATA
AAATTAACGATTCTTATAGTTTTTCAAATAACCGCTTAACAATTGTAAAT
TCTAATTTAGAATATACATATTTTAAACTATTAGATGAATTTATTAATGG
AAAACCATTAGTGAGAATTTTAGGATATGGCTATTTTTGTGCAAAGCGCT
TTTATGTTGATAAAAATGTTTTTGCTTTTCGTGTTGAAACTGAATTATTA
ATAGATGTTGTTAATAAAGTAATTCAACAATCCACTTATAAAATTAAAAA
TGTTATTGATGTTTGTTGTGGTAGTGGTGTTTTAGGGTTAAGTACAAAAA
TGAATTTTAATCAATTGAATGTTTCATTATTAGATATTTCTATTGATGCA
ATTAATAATTGCAAAAAAAATGCTAAATATCATAACTTAACAGATGTAAA
TTTTATTCATAAAAGTATGCAAGAATACTTTTTAAACACAAAAAAACGGT
TTGATTTAATTATCTGTAATCCCCCATATATCAAAAGTAATTATGAATTA
AATCGTGAAGTCTTAGATTATGACCCCATTAATGCACTTATTGATTTCGA
TCACAAAGATGGAATTAGTTTTTATTTATTTATAATAAATAACATTAAAT
CAATTGCTAATGAGAAATTCACTATTATTTTTGAAATTGGTTTTGATCAA
AAAGAAATTTTAGAAAAAGTTATTAAAAAAAATGAATTTCCTCTTTTTTA
CTACTTTATAAATGATTATAATAATCTATGTAGAATTTTAATAATAAGTA
ATATTAAATATGAAAATTTATAG


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