Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_026606891.1 METAC_RS0109860 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000427445.1:WP_026606891.1 Length = 402 Score = 443 bits (1139), Expect = e-129 Identities = 226/377 (59%), Positives = 271/377 (71%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 ++PTYARAD+ FERG+G +L +T G RFLDF G+AV LG+ +P+LV AL Q KLWH Sbjct: 5 LLPTYARADLAFERGDGAWLTSTTGERFLDFGGGIAVASLGYNHPHLVAALNEQGGKLWH 64 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSNLF++ E LA RL EA+FAD VFFTNSGAEA E K RKY G + +T Sbjct: 65 TSNLFQIPQAERLAARLVEASFADYVFFTNSGAEAVEGAIKTARKYQSVCGRPEKFHAVT 124 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 FE AFHGRTLA ++A K I GFGP ++GFD VPFGDL AV A+ +T I +EPIQ Sbjct: 125 FEGAFHGRTLATIAAGGNPKYIDGFGPKVEGFDPVPFGDLAAVEAAIGPQTGMILVEPIQ 184 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GEGGIR S EFLRGLR++CD H LLL DE+Q G+GRTGKLFA+E G+ PDVMA+AKG Sbjct: 185 GEGGIRVASPEFLRGLRQLCDRHDLLLVFDEVQSGVGRTGKLFAYELYGVAPDVMAIAKG 244 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 IGGGFPLGA LAT +A GMT G+HG+TYGGNPLAT++G AVLD VL PGF+DHV +G Sbjct: 245 IGGGFPLGAFLATREAGKGMTVGSHGTTYGGNPLATSIGGAVLDVVLAPGFMDHVALMGL 304 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 L+ LA L PAV +RG+GLM G+A V + A RA LL +PAGDNV RLL Sbjct: 305 KLKQSLAELKDRYPAVIAEIRGEGLMRGIALKVPVNEFAAAARAEKLLVIPAGDNVARLL 364 Query: 365 PPLNIGEAEVEEAVAIL 381 PPL +GEAE+ EA+A L Sbjct: 365 PPLIVGEAEISEAIARL 381 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: 508 Number of extensions: 17 Number of successful extensions: 1 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: 402 Length adjustment: 31 Effective length of query: 358 Effective length of database: 371 Effective search space: 132818 Effective search space used: 132818 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