Summary This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Actinomyces sp. oral taxon 877 F0543, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 22.0) [Karp16, Karp11] using MetaCyc version 22.0 [Caspi18]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KE95231357534064,849RefSeq:NZ_KE952313
NZ_KE95231440380249,963RefSeq:NZ_KE952314
NZ_KE95242542400247,526RefSeq:NZ_KE952425
NZ_KE95250952520047,269RefSeq:NZ_KE952509
NZ_KE95252034303141,123RefSeq:NZ_KE952520
NZ_KE95253123210239,349RefSeq:NZ_KE952531
NZ_KE95254228280038,928RefSeq:NZ_KE952542
NZ_KE95255342365138,580RefSeq:NZ_KE952553
NZ_KE95256434320237,510RefSeq:NZ_KE952564
NZ_KE95257534321135,561RefSeq:NZ_KE952575
NZ_KE95231532311035,539RefSeq:NZ_KE952315
NZ_KE95232625232034,388RefSeq:NZ_KE952326
NZ_KE95233732310134,081RefSeq:NZ_KE952337
NZ_KE95234828252134,041RefSeq:NZ_KE952348
NZ_KE95235928280032,868RefSeq:NZ_KE952359
NZ_KE95237034330132,368RefSeq:NZ_KE952370
NZ_KE95238121170431,817RefSeq:NZ_KE952381
NZ_KE95239227215130,392RefSeq:NZ_KE952392
NZ_KE95240325250030,053RefSeq:NZ_KE952403
NZ_KE95241425220328,425RefSeq:NZ_KE952414
NZ_KE95242613130027,943RefSeq:NZ_KE952426
NZ_KE95243729261227,461RefSeq:NZ_KE952437
NZ_KE95244825250026,873RefSeq:NZ_KE952448
NZ_KE95245935330225,935RefSeq:NZ_KE952459
NZ_KE95246921191125,132RefSeq:NZ_KE952469
NZ_KE95248021173125,059RefSeq:NZ_KE952480
NZ_KE95249123191324,579RefSeq:NZ_KE952491
NZ_KE95250120180223,534RefSeq:NZ_KE952501
NZ_KE95250722190322,987RefSeq:NZ_KE952507
NZ_KE95250818171022,319RefSeq:NZ_KE952508
NZ_KE95251019190022,271RefSeq:NZ_KE952510
NZ_KE95251119170222,132RefSeq:NZ_KE952511
NZ_KE95251218180021,675RefSeq:NZ_KE952512
NZ_KE95251325193321,555RefSeq:NZ_KE952513
NZ_KE95251422200221,514RefSeq:NZ_KE952514
NZ_KE95251526195221,439RefSeq:NZ_KE952515
NZ_KE95251616150121,393RefSeq:NZ_KE952516
NZ_KE95251719181021,222RefSeq:NZ_KE952517
NZ_KE95251823230020,972RefSeq:NZ_KE952518
NZ_KE95251919172020,843RefSeq:NZ_KE952519
NZ_KE95252119171120,747RefSeq:NZ_KE952521
NZ_KE95252218170120,411RefSeq:NZ_KE952522
NZ_KE95252317160120,359RefSeq:NZ_KE952523
NZ_KE95252417141220,295RefSeq:NZ_KE952524
NZ_KE95252616140220,279RefSeq:NZ_KE952526
NZ_KE95252518170120,276RefSeq:NZ_KE952525
NZ_KE95252717160120,247RefSeq:NZ_KE952527
NZ_KE95252823211119,765RefSeq:NZ_KE952528
NZ_KE95252918160219,424RefSeq:NZ_KE952529
NZ_KE95253015150018,865RefSeq:NZ_KE952530
NZ_KE95253220180217,947RefSeq:NZ_KE952532
NZ_KE95253315150017,836RefSeq:NZ_KE952533
NZ_KE9525341290317,578RefSeq:NZ_KE952534
NZ_KE95253518150317,277RefSeq:NZ_KE952535
NZ_KE95253616131217,083RefSeq:NZ_KE952536
NZ_KE95253723220116,942RefSeq:NZ_KE952537
NZ_KE95253815140116,937RefSeq:NZ_KE952538
NZ_KE9525401190216,747RefSeq:NZ_KE952540
NZ_KE95254116150116,614RefSeq:NZ_KE952541
NZ_KE95254317160116,443RefSeq:NZ_KE952543
NZ_KE95254411110016,222RefSeq:NZ_KE952544
NZ_KE95254514130116,014RefSeq:NZ_KE952545
NZ_KE95254614120215,967RefSeq:NZ_KE952546
NZ_KE95254713110215,732RefSeq:NZ_KE952547
NZ_KE95254818171014,759RefSeq:NZ_KE952548
NZ_KE95254914100414,340RefSeq:NZ_KE952549
NZ_KE95255013120114,271RefSeq:NZ_KE952550
NZ_KE95255413120113,965RefSeq:NZ_KE952554
NZ_KE95255512120013,695RefSeq:NZ_KE952555
NZ_KE95256617160111,559RefSeq:NZ_KE952566
NZ_KE9525681291211,364RefSeq:NZ_KE952568
NZ_KE95257312110110,368RefSeq:NZ_KE952573
NZ_KE95257411110010,224RefSeq:NZ_KE952574
200 Undisplayed Contigs/Replicons6286217141931,494
Total:2,3802,096542302,713,514
Ortholog data available?Yes
Database Contents
Genes2,380
Pathways146
Enzymatic Reactions749
Transport Reactions41
Polypeptides2,162
Protein Complexes22
Enzymes393
Transporters243
Compounds655
Transcription Units1,608
tRNAs49
Protein Features2,396
GO Terms8,488
Database Version29.0
Synonyms Actinomyces sp. oral taxon 877 str. F0543
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. oral taxon 877
Actinomyces sp. oral taxon 877 F0543
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436890
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1227264
Environmentsupragingival plaque biofilm of a molar
Geographic LocationUSA
Collection Date2008
HostHomo sapiens
Human Microbiome Body Sitenot-specified

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.