Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Actinomyces naeslundii Howell 279, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [Caspi20]. 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_ALJK0100014912411437154,895RefSeq:NZ_ALJK01000149
NZ_ALJK0100014085747493,676RefSeq:NZ_ALJK01000140
NZ_ALJK0100003856550166,575RefSeq:NZ_ALJK01000038
NZ_ALJK0100005040343357,903RefSeq:NZ_ALJK01000050
NZ_ALJK0100006151471356,156RefSeq:NZ_ALJK01000061
NZ_ALJK0100019149431550,636RefSeq:NZ_ALJK01000191
NZ_ALJK0100009851490246,833RefSeq:NZ_ALJK01000098
NZ_ALJK0100015735331143,243RefSeq:NZ_ALJK01000157
NZ_ALJK0100023032292142,263RefSeq:NZ_ALJK01000230
NZ_ALJK0100002540380241,391RefSeq:NZ_ALJK01000025
NZ_ALJK0100002434313041,047RefSeq:NZ_ALJK01000024
NZ_ALJK0100000431291139,522RefSeq:NZ_ALJK01000004
NZ_ALJK0100014135294239,104RefSeq:NZ_ALJK01000141
NZ_ALJK0100018730271238,490RefSeq:NZ_ALJK01000187
NZ_ALJK0100002938340438,374RefSeq:NZ_ALJK01000029
NZ_ALJK0100000732281338,227RefSeq:NZ_ALJK01000007
NZ_ALJK0100010335340137,023RefSeq:NZ_ALJK01000103
NZ_ALJK0100005228280035,954RefSeq:NZ_ALJK01000052
NZ_ALJK0100001728260235,292RefSeq:NZ_ALJK01000017
NZ_ALJK0100016329280134,874RefSeq:NZ_ALJK01000163
NZ_ALJK0100020828280034,632RefSeq:NZ_ALJK01000208
NZ_ALJK0100011726260032,862RefSeq:NZ_ALJK01000117
NZ_ALJK0100004526240232,331RefSeq:NZ_ALJK01000045
NZ_ALJK0100004729290031,753RefSeq:NZ_ALJK01000047
NZ_ALJK0100022229260331,204RefSeq:NZ_ALJK01000222
NZ_ALJK0100017228222430,404RefSeq:NZ_ALJK01000172
NZ_ALJK0100019421210027,330RefSeq:NZ_ALJK01000194
NZ_ALJK0100001822200227,204RefSeq:NZ_ALJK01000018
NZ_ALJK0100002021190226,974RefSeq:NZ_ALJK01000020
NZ_ALJK0100007618160226,005RefSeq:NZ_ALJK01000076
NZ_ALJK0100023419170225,626RefSeq:NZ_ALJK01000234
NZ_ALJK0100012420180225,341RefSeq:NZ_ALJK01000124
NZ_ALJK0100007024202225,089RefSeq:NZ_ALJK01000070
NZ_ALJK0100015522200224,996RefSeq:NZ_ALJK01000155
NZ_ALJK0100022916141124,886RefSeq:NZ_ALJK01000229
NZ_ALJK0100009528270123,897RefSeq:NZ_ALJK01000095
NZ_ALJK0100007319180123,852RefSeq:NZ_ALJK01000073
NZ_ALJK0100006918180023,450RefSeq:NZ_ALJK01000069
NZ_ALJK0100015323200323,349RefSeq:NZ_ALJK01000153
NZ_ALJK0100007725240123,198RefSeq:NZ_ALJK01000077
NZ_ALJK0100015022220022,957RefSeq:NZ_ALJK01000150
NZ_ALJK0100020928250322,683RefSeq:NZ_ALJK01000209
NZ_ALJK0100016814110321,889RefSeq:NZ_ALJK01000168
NZ_ALJK0100008316160021,887RefSeq:NZ_ALJK01000083
NZ_ALJK0100004418170121,799RefSeq:NZ_ALJK01000044
NZ_ALJK0100005516114120,561RefSeq:NZ_ALJK01000055
NZ_ALJK0100021515150020,451RefSeq:NZ_ALJK01000215
NZ_ALJK0100000519190019,610RefSeq:NZ_ALJK01000005
NZ_ALJK0100018819170219,290RefSeq:NZ_ALJK01000188
NZ_ALJK0100012912100219,088RefSeq:NZ_ALJK01000129
NZ_ALJK0100011914130118,778RefSeq:NZ_ALJK01000119
NZ_ALJK0100011212110118,615RefSeq:NZ_ALJK01000112
NZ_ALJK0100013915140118,283RefSeq:NZ_ALJK01000139
NZ_ALJK0100009715141017,933RefSeq:NZ_ALJK01000097
NZ_ALJK0100024016150117,581RefSeq:NZ_ALJK01000240
NZ_ALJK0100002715120317,330RefSeq:NZ_ALJK01000027
NZ_ALJK0100007515130216,796RefSeq:NZ_ALJK01000075
NZ_ALJK0100023810100016,655RefSeq:NZ_ALJK01000238
NZ_ALJK0100001919153116,417RefSeq:NZ_ALJK01000019
NZ_ALJK0100000821210016,391RefSeq:NZ_ALJK01000008
NZ_ALJK0100018215130216,288RefSeq:NZ_ALJK01000182
NZ_ALJK0100018413130016,052RefSeq:NZ_ALJK01000184
NZ_ALJK0100023914110316,003RefSeq:NZ_ALJK01000239
NZ_ALJK0100016116130315,990RefSeq:NZ_ALJK01000161
NZ_ALJK0100008111110015,885RefSeq:NZ_ALJK01000081
NZ_ALJK0100013314130115,826RefSeq:NZ_ALJK01000133
NZ_ALJK0100014316133015,625RefSeq:NZ_ALJK01000143
NZ_ALJK0100014814120215,141RefSeq:NZ_ALJK01000148
NZ_ALJK0100002813111115,060RefSeq:NZ_ALJK01000028
NZ_ALJK010002431291214,969RefSeq:NZ_ALJK01000243
NZ_ALJK0100014614110314,957RefSeq:NZ_ALJK01000146
NZ_ALJK0100010411100114,414RefSeq:NZ_ALJK01000104
NZ_ALJK0100021412120014,244RefSeq:NZ_ALJK01000214
NZ_ALJK0100016015130213,845RefSeq:NZ_ALJK01000160
NZ_ALJK0100020213110213,592RefSeq:NZ_ALJK01000202
NZ_ALJK0100006413120113,043RefSeq:NZ_ALJK01000064
NZ_ALJK010001521391312,382RefSeq:NZ_ALJK01000152
NZ_ALJK0100000612110112,186RefSeq:NZ_ALJK01000006
NZ_ALJK0100020012110111,665RefSeq:NZ_ALJK01000200
NZ_ALJK0100006714111211,477RefSeq:NZ_ALJK01000067
NZ_ALJK010002071010009,975RefSeq:NZ_ALJK01000207
NZ_ALJK010000101110019,203RefSeq:NZ_ALJK01000010
161 Undisplayed Contigs/Replicons52551413101845,664
Total:2,5922,302612293,114,341
Ortholog data available?No
Database Contents
Genes2,589
Pathways171
Enzymatic Reactions854
Transport Reactions55
Polypeptides2,535
Protein Complexes92
Enzymes505
Transporters231
Compounds684
Transcription Units2,095
tRNAs49
Protein Features2,683
GO Terms204
Database Version29.0
Sequence SourceGCF_000285995.1
Synonyms Actinomyces naeslundii Howell 279
Actinomyces naeslundii strain Howell 279
Actinomyces naeslundii str. Howell 279
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces naeslundii
Actinomyces naeslundii Howell 279
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00828754
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1115803
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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.