Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000504245.1:WP_034272173.1 Length = 393 Score = 267 bits (682), Expect = 4e-76 Identities = 154/379 (40%), Positives = 216/379 (56%), Gaps = 12/379 (3%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M Y + RG+G ++ DG +LD G+AVN LGHA+P +VEA++ Q L H Sbjct: 11 MMDNYGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGH 70 Query: 65 TSNLFRVAGQESLAKRLTE-ATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123 TSNL+ SLA+ L + A + V F NSGAEA E K+ R +++++ Sbjct: 71 TSNLYINPVALSLAETLLDIAGLSGKVLFCNSGAEAVEAAIKITRL-------TGKSKLV 123 Query: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPI 183 + FHGRT+ A+S Q + F PLL G VPFGD A+ +AV +TA + +EP+ Sbjct: 124 ACDGGFHGRTMGALSVTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEPV 183 Query: 184 QGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAK 243 GEGG+ FLR REI G LL LDE+Q G+GR G FA + AG+TPDV+ +AK Sbjct: 184 LGEGGVVPAPDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLAK 243 Query: 244 GIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIG 303 G+GGG PLGA + + + G HG+T+GGNP+A A G+AV+ + E G LDHV+ +G Sbjct: 244 GLGGGLPLGAVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVETLG 303 Query: 304 GLLQDRLAGLVAENPAVFKGVRGKGLMLGLA-CGPAVGDVVVALRANGLLSVPAGDNVVR 362 +D AG+ + + VRG GL+ G+ P V A + G L P +V+R Sbjct: 304 ---KDLAAGVRKLDHPLVSEVRGAGLLQGIGLTKPVAPTVATAAQRAGYLINPVQPDVIR 360 Query: 363 LLPPLNIGEAEVEEAVAIL 381 L PPL I E +V + +A L Sbjct: 361 LAPPLIITERQVADFLAAL 379 Lambda K H 0.321 0.139 0.414 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 493 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 389 Length of database: 393 Length adjustment: 31 Effective length of query: 358 Effective length of database: 362 Effective search space: 129596 Effective search space used: 129596 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory