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Porphyromonas gingivalis Search Results

Record: 1 of 1  
MiniMap tRNA-Gln-1 IGR0022 IGR0027 IGR0025 IGR0021 IGR0023 IGR0020 IGR0026 IGR0024 PG0027 spoU, - PG0025 PG0028 PG0026.1 cdd, - PG0026 ispF, - PG0024 PG0021 PG0023 PG0022 PG0027 spoU, - PG0025 PG0028 PG0026.1 cdd, - PG0026 ispF, - PG0024 PG0021 PG0023 PG0022 PG0027 spoU, - PG0025 PG0028 cdd, - PG0026 ispF, - PG0024 PG0021 PG0023 PG0022 PG0026.1


LANL Gene ID: PG0024

GenBank Locus Tag: PG0028

DNA Molecule Name:
1  

GenBank ID:
34539905

Gene Name:
ispF  

Definition:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Cellular Location:
Cytoplasm [Evidence]

Gene Start:
34003

Gene Stop:
34488

Gene Length:
486

Molecular Weight*:
17635

pI*:
5.90

Net Charge*:
-3.61

EC:
4.6.1.12  

Functional Class:
Uncategorized  

Gene Ontology:
Biological process
  GO:0016114    terpenoid biosynthetic process

Molecular function
  GO:0008685    2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity


Pathway: pathway table
Sterol biosynthesis

Secondary Evidence:
Xu,J., Bjursell,M.K., Himrod,J., Deng,S., Carmichael,L.K.,
Chiang,H.C., Hooper,L.V. and Gordon,J.I.
A Genomic View of the Human-Bacteroides thetaiotaomicron Symbiosis
Science 299 (5615), 2074-2076 (2003)
PUBMED: 12663928

Comment:
TIGR ID: PG0028

Proteomic Data: Proteomic Data Search
TIGR Annotationconserved hypothetical protein TIGR00151, GroupJ (hypothetical proteins-Conserved)
ORF #PG-PP/PG-PPC1PG-PP/PG-PPC2
Spectral CountPeptide IntensitySpectral CountPeptide Intensity
ProqValProqValProqValProqVal
TIGRPG0028-0.920.035-1.660.00092-0.330.21-1.660.00092
LANLPG00240.530.320.800.37
ConsensusSP1IP1SP2IP2

Human Oral Microbiome Database:
View in HOMD Genome Viewer

 Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST; e.g.residues 6-158 are 68% similar to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase in Bacteroides thetaiotaomicron VPI-5482 (29349292|ref|NP_812795.1), residues 5-159 are 63% similar to (23957793|gb|AAN40806.1) IspF in Synechocystis sp., residues 6-158 are 54% similar to (7531255|sp|Q47956) 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (MECPS) in Haemophilus ducreyi, residues 6-159 are 50% similar to (AE002501) YgbB/YacN family protein in Neisseria meningitidis.

 Top Blast Hits:  Updated monthly
Click here to view the entire PsiBlast results.
 gi|34539905|ref|NP_904384.1|  2C-methyl-D-erythritol 2,4-cyc...   323   1e-87
 gi|154494056|ref|ZP_02033376.1|  hypothetical protein PARMER...   231   1e-59
 gi|60683225|ref|YP_213369.1|  putative 2-C-methyl-D-erythrit...   229   5e-59
 gi|126646545|ref|ZP_01719062.1|  2C-methyl-D-erythritol 2,4-...   229   5e-59
 gi|53715290|ref|YP_101282.1|  2-C-methyl-D-erythritol 2,4-cy...   228   8e-59
 gi|29349292|ref|NP_812795.1|  2-C-methyl-D-erythritol 2,4-cy...   225   8e-58
 gi|150009172|ref|YP_001303915.1|  2-C-methyl-D-erythritol 2,...   224   1e-57
 gi|156111362|gb|EDO13107.1|  hypothetical protein BACOVA_011...   222   5e-57
 gi|153809103|ref|ZP_01961771.1|  hypothetical protein BACCAC...   222   7e-57
 gi|156859626|gb|EDO53057.1|  hypothetical protein BACUNI_030...   221   9e-57


InterPro Summary:  InterProScan

InterPro
IPR003526
Domain
MECDP-synthase
PF02542 [5-161]T 8.000026593468091E-85 PF02542 YgbB YgbB
TIGR00151 [6-160]T 1.2458712844667698E-94 TIGR00151 ispF ispF
PS01350 [39-54]T 8.0E-5 PS01350 ISPF ISPF
SSF69765 [5-159]T 6.0E-67 SSF69765 YgbB_synth YgbB_synth
InterPro
IPR010925
Family
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
PIRSF005911 [5-162]T 2.7000000000000804E-91 PIRSF005911 MECDP_synth MECDP_synth
noIPR
unintegrated
unintegrated
G3DSA:3.30.1330.50 [5-156]T 2.5000090991619998E-59 G3DSA:3.30.1330.50 G3DSA:3.30.1330.50 G3DSA:3.30.1330.50


COGS Summary:  COGS Search
BeTs to 10 clades of COG0245
COG name: Putative enzyme of deoxyxylulose pathway (terpenoid biosynthesis), YgbB family
Functional Class: R
The phylogenetic pattern of COG0245 is -----qvcebrhujgp-lin-
Number of proteins in this genome belonging to this COG is 1
Blocks Summary:  Blocks Search
No significant hit to the Blocks database.

 ProDom Summary:  Protein Domain Search
Residues 6-158 are 56% similar to a (PROTEIN YGBB INTERGENIC REGION) protein domain (PD006214 which is seen in YACN_BACSU.


Paralogs:  Local Blast Search
No paralogs found in P. gingivalis.

Pfam Summary:  Pfam Search
Residues 5 to 161 (E-value = 7.1e-88) place PG0024 in the YgbB family which is described as YgbB family (PF02542)

 Structural Feature(s):
Feature Type  Start  Stop
No predicted structural features.  
  
transmembrane  
42  
58

Top PDB Hits:
-74% similar to PDB:1T0A Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis (E_value = 6.9E_46);
-71% similar to PDB:1GX1 STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (E_value = 2.2E_44);
-71% similar to PDB:1H47 STRUCTURES OF MECP SYNTHASE IN COMPLEX WITH (I) CMP AND (II) CMP AND PRODUCT (E_value = 2.2E_44);
-71% similar to PDB:1H48 THE STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE IN COMPLEX WITH CMP AND PRODUCT (E_value = 2.2E_44);
-71% similar to PDB:1JY8 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) (E_value = 2.2E_44);

Gene Protein Sequence:
MKKPFRIGFGFDVHRLSEGYPLWMGGVRLEHSKGLEGHSDADVLIHAICD
ALLGAAALRDIGYHFPPSDPQYKGIDSKILLARVMELVRSQGYELGNIDA
TIAAEQPKLNPHIPDMQRVLAEVIQVEVSDISLKATTTEKLGFTGREEGI
SAYAVALLIAAV

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAGAAGCCTTTTCGAATAGGATTCGGTTTCGATGTACACCGCTTGTC
CGAAGGTTATCCTTTGTGGATGGGCGGTGTTCGTCTGGAACATTCCAAGG
GCTTGGAGGGACATTCCGATGCCGATGTGCTCATTCATGCTATTTGTGAT
GCCCTGCTGGGTGCTGCCGCTTTGCGTGATATCGGCTATCACTTTCCTCC
TTCGGATCCTCAATATAAGGGGATCGATAGTAAGATCCTGTTGGCTCGCG
TTATGGAATTGGTGCGTTCACAGGGTTATGAATTGGGTAATATCGATGCT
ACTATTGCGGCGGAACAGCCCAAACTGAATCCACATATACCGGATATGCA
GCGTGTCTTGGCTGAGGTGATACAGGTGGAGGTGTCGGATATTTCACTGA
AAGCCACAACGACGGAGAAACTTGGCTTCACAGGACGAGAGGAAGGCATT
TCCGCCTATGCCGTGGCCTTGCTCATTGCTGCCGTC

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