Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_029933849.1 N746_RS0102830 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000711195.1:WP_029933849.1 Length = 392 Score = 305 bits (782), Expect = 1e-87 Identities = 168/388 (43%), Positives = 239/388 (61%), Gaps = 6/388 (1%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M TYAR ++F GEG LY G+ +LD +G+AV LGHA+P + +AL Q+ +L H Sbjct: 5 LMNTYARLPVMFTEGEGATLYDDQGKAYLDAVSGIAVCSLGHAHPAISQALCEQSKRLIH 64 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSNL+RV QE L + L + D VFF NSGAEA E K+ RK ++G + I+ Sbjct: 65 TSNLYRVENQEKLGEDLIRLSGMDRVFFGNSGAEANEAAIKIARKTGADRGIE-NPEILV 123 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDET--AGICLEP 182 E +FHGRT+A +SA +K+ +GFGPL+ GF VP+ +EAV A+ D I +EP Sbjct: 124 MENSFHGRTMATLSATGNKKVQEGFGPLVQGFVRVPYNQVEAVEKAIADHPNLVAILVEP 183 Query: 183 IQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVA 242 +QGEGG+ +L+ LR++CD+H LLL +DEIQ G+GRTGK FA++ I PDV+ +A Sbjct: 184 VQGEGGVFVPDAGYLKTLRQLCDQHNLLLMMDEIQTGVGRTGKWFAYQHEDILPDVLTLA 243 Query: 243 KGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRI 302 K +G G P+GACLA KAAS G HG+T+GGNPLA A G AV++ + + ++ V + Sbjct: 244 KALGNGVPIGACLARGKAASTFGPGNHGTTFGGNPLACAAGLAVINTLEQHDYISQVAKQ 303 Query: 303 GGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVV-VALRANGLLSVPAGDNVV 361 G + +A+ V + VRGKG M+G+ ++V +AL L++V GD V Sbjct: 304 GKQIMTAFRNALADQKGVVE-VRGKGYMIGIQLDRPCSELVKLALDKGLLINVTRGD-TV 361 Query: 362 RLLPPLNIGEAEVEEAVAILAKTAKELV 389 RLLPP I EA+ + V L++ E + Sbjct: 362 RLLPPFVISEAQTSQLVTDLSQLITEFL 389 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: 404 Number of extensions: 17 Number of successful extensions: 4 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: 392 Length adjustment: 31 Effective length of query: 358 Effective length of database: 361 Effective search space: 129238 Effective search space used: 129238 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 Apr 10 2024. The underlying query database was built on Apr 09 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