Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-Nov-2024 from the annotated genome of Acidiphilium sp. PM PM, as obtained from RefSeq (annotation date: 14-AUG-2023). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AFPR0100051310910009114,367RefSeq:NZ_AFPR01000513
NZ_AFPR0100010565630262,154RefSeq:NZ_AFPR01000105
NZ_AFPR0100007559590059,921RefSeq:NZ_AFPR01000075
NZ_AFPR0100046448480054,335RefSeq:NZ_AFPR01000464
NZ_AFPR0100009243430046,989RefSeq:NZ_AFPR01000092
NZ_AFPR0100051436341141,581RefSeq:NZ_AFPR01000514
NZ_AFPR0100008338362040,854RefSeq:NZ_AFPR01000083
NZ_AFPR0100047548470139,405RefSeq:NZ_AFPR01000475
NZ_AFPR0100001939350439,405RefSeq:NZ_AFPR01000019
NZ_AFPR0100007139380138,729RefSeq:NZ_AFPR01000071
NZ_AFPR0100011133303036,397RefSeq:NZ_AFPR01000111
pAPM0135300534,426RefSeq:NZ_AFPR01000560
NZ_AFPR0100012136360034,225RefSeq:NZ_AFPR01000121
pAPM0136340232,808RefSeq:NZ_AFPR01000566
NZ_AFPR0100016235340132,181RefSeq:NZ_AFPR01000162
NZ_AFPR0100015029251331,860RefSeq:NZ_AFPR01000150
NZ_AFPR0100051724210330,680RefSeq:NZ_AFPR01000517
NZ_AFPR0100009327261027,998RefSeq:NZ_AFPR01000093
NZ_AFPR0100017621200127,749RefSeq:NZ_AFPR01000176
NZ_AFPR0100048322211027,663RefSeq:NZ_AFPR01000483
NZ_AFPR0100004127240327,474RefSeq:NZ_AFPR01000041
NZ_AFPR0100007726241127,272RefSeq:NZ_AFPR01000077
NZ_AFPR0100010321200126,692RefSeq:NZ_AFPR01000103
NZ_AFPR0100048923210226,191RefSeq:NZ_AFPR01000489
NZ_AFPR0100009129290025,540RefSeq:NZ_AFPR01000091
NZ_AFPR0100019419190025,100RefSeq:NZ_AFPR01000194
NZ_AFPR0100003330290125,061RefSeq:NZ_AFPR01000033
pAPM0220200024,646RefSeq:NZ_AFPR01000583
NZ_AFPR0100008521200123,952RefSeq:NZ_AFPR01000085
NZ_AFPR0100046218170123,667RefSeq:NZ_AFPR01000462
NZ_AFPR0100008824212123,627RefSeq:NZ_AFPR01000088
NZ_AFPR0100018819180123,153RefSeq:NZ_AFPR01000188
pAPM0329280122,612RefSeq:NZ_AFPR01000589
NZ_AFPR0100006518161122,213RefSeq:NZ_AFPR01000065
NZ_AFPR0100010019190021,754RefSeq:NZ_AFPR01000100
NZ_AFPR0100049515150020,565RefSeq:NZ_AFPR01000495
NZ_AFPR0100001618180020,431RefSeq:NZ_AFPR01000016
NZ_AFPR0100010818170120,106RefSeq:NZ_AFPR01000108
NZ_AFPR0100046720200019,907RefSeq:NZ_AFPR01000467
NZ_AFPR0100052416150119,382RefSeq:NZ_AFPR01000524
NZ_AFPR0100049117142119,350RefSeq:NZ_AFPR01000491
NZ_AFPR0100050816140218,664RefSeq:NZ_AFPR01000508
NZ_AFPR0100013616160018,424RefSeq:NZ_AFPR01000136
NZ_AFPR0100005719180117,792RefSeq:NZ_AFPR01000057
NZ_AFPR0100013018180017,577RefSeq:NZ_AFPR01000130
NZ_AFPR0100046121190217,502RefSeq:NZ_AFPR01000461
NZ_AFPR0100008020200017,488RefSeq:NZ_AFPR01000080
NZ_AFPR0100009820190116,732RefSeq:NZ_AFPR01000098
NZ_AFPR0100053815130216,597RefSeq:NZ_AFPR01000538
NZ_AFPR0100001719180116,590RefSeq:NZ_AFPR01000017
NZ_AFPR0100015216151016,552RefSeq:NZ_AFPR01000152
pAPM0322180416,479RefSeq:NZ_AFPR01000609
NZ_AFPR0100027715150016,341RefSeq:NZ_AFPR01000277
NZ_AFPR0100019314112116,277RefSeq:NZ_AFPR01000193
NZ_AFPR0100052016140215,858RefSeq:NZ_AFPR01000520
NZ_AFPR0100016513130015,492RefSeq:NZ_AFPR01000165
NZ_AFPR0100054215150015,435RefSeq:NZ_AFPR01000542
NZ_AFPR0100044111110015,259RefSeq:NZ_AFPR01000441
NZ_AFPR0100048712120014,735RefSeq:NZ_AFPR01000487
NZ_AFPR0100053713130014,544RefSeq:NZ_AFPR01000537
pAPM0112110114,330RefSeq:NZ_AFPR01000564
NZ_AFPR0100011912120014,241RefSeq:NZ_AFPR01000119
NZ_AFPR0100015716150114,178RefSeq:NZ_AFPR01000157
NZ_AFPR0100018214120214,082RefSeq:NZ_AFPR01000182
NZ_AFPR0100015913130014,023RefSeq:NZ_AFPR01000159
NZ_AFPR0100009914131013,954RefSeq:NZ_AFPR01000099
NZ_AFPR0100024220191013,701RefSeq:NZ_AFPR01000242
NZ_AFPR0100016714140013,446RefSeq:NZ_AFPR01000167
pAPM0313120113,365RefSeq:NZ_AFPR01000599
NZ_AFPR0100020910100013,252RefSeq:NZ_AFPR01000209
NZ_AFPR0100014811110013,076RefSeq:NZ_AFPR01000148
NZ_AFPR0100027111100113,014RefSeq:NZ_AFPR01000271
NZ_AFPR0100004812110112,981RefSeq:NZ_AFPR01000048
NZ_AFPR010004691091012,895RefSeq:NZ_AFPR01000469
NZ_AFPR0100050416160012,849RefSeq:NZ_AFPR01000504
NZ_AFPR0100006213120112,754RefSeq:NZ_AFPR01000062
NZ_AFPR0100002912110112,694RefSeq:NZ_AFPR01000029
NZ_AFPR0100031318170112,446RefSeq:NZ_AFPR01000313
NZ_AFPR0100003813110212,392RefSeq:NZ_AFPR01000038
NZ_AFPR0100047410100012,049RefSeq:NZ_AFPR01000474
NZ_AFPR0100020413120111,942RefSeq:NZ_AFPR01000204
NZ_AFPR010001261090111,662RefSeq:NZ_AFPR01000126
NZ_AFPR0100016912100211,628RefSeq:NZ_AFPR01000169
pAPM0117150211,193RefSeq:NZ_AFPR01000577
NZ_AFPR0100013813120111,081RefSeq:NZ_AFPR01000138
NZ_AFPR0100010611110010,779RefSeq:NZ_AFPR01000106
NZ_AFPR0100011612102010,556RefSeq:NZ_AFPR01000116
NZ_AFPR0100018513110210,273RefSeq:NZ_AFPR01000185
NZ_AFPR010000581010009,954RefSeq:NZ_AFPR01000058
pAPM051110019,664RefSeq:NZ_AFPR01000619
NZ_AFPR010000281111009,294RefSeq:NZ_AFPR01000028
NZ_AFPR010001981311209,027RefSeq:NZ_AFPR01000198
NZ_AFPR01000156119118,535RefSeq:NZ_AFPR01000156
534 Undisplayed Contigs/Replicons1,2891,263262081,871,395
Total:3,4983,149522973,929,465
Ortholog data available?No
Database Contents
Genes3,498
Pathways307
Enzymatic Reactions1,649
Transport Reactions52
Polypeptides3,780
Protein Complexes124
Enzymes854
Transporters319
Compounds1,504
Transcription Units2,718
tRNAs45
Protein Features3,934
GO Terms4,567
Database Version29.0
Sequence SourceGCF_000219295.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acidiphilium
unclassified Acidiphilium
Acidiphilium sp. PM
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469446
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1043206
Geographic LocationSpain
Annotation ProviderNCBI RefSeq
Annotation Date2023-08-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.5
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

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