Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_027457970.1 K420_RS0110205 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000519045.1:WP_027457970.1 Length = 390 Score = 313 bits (803), Expect = 4e-90 Identities = 172/388 (44%), Positives = 236/388 (60%), Gaps = 6/388 (1%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 VM TYAR + F G+G + T+G+ +LD +G+AV+ LGHA+P LV+A+ AQA ++ H Sbjct: 4 VMNTYARLPVTFSHGKGCRITDTEGKEYLDALSGIAVSTLGHAHPRLVDAIAAQAGRMLH 63 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSNL+R+ QE LA +L E + VFF NSGAEA E KL R Y ++KG + T I+ Sbjct: 64 TSNLYRIREQEQLADKLCELSGMQEVFFGNSGAEANEAAIKLARFYGHKKGVELPT-IVV 122 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGIC---LE 181 E+AFHGRT+A +SA K GF PL+ GF VP+GDL A+R AV + I LE Sbjct: 123 MEKAFHGRTMATLSATGNRKTQAGFEPLVSGFVRVPYGDLNAIR-AVAEHNKNIVAVMLE 181 Query: 182 PIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAV 241 IQGEGGI + RG+RE+CD H ++ DE+QCGMGRTGK F ++ AG+ PDV + Sbjct: 182 IIQGEGGIHLADPVYYRGVRELCDAHDWMMICDEVQCGMGRTGKWFGYQQAGVLPDVATL 241 Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301 AKG+ G +GAC+A+ KAA G HGST+GGNPLA+ + + E G LD+ R Sbjct: 242 AKGLASGVAIGACMASGKAAGLFGPGNHGSTFGGNPLASTAALTTIAVMEEEGLLDNAAR 301 Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVV 361 IG L++ +L G A +RG GLM+G+ G++V + GLL + ++ Sbjct: 302 IGSLIR-QLFGEALAGVAGVVDIRGHGLMIGIELDRPCGELVGKALSEGLLINVTSEKII 360 Query: 362 RLLPPLNIGEAEVEEAVAILAKTAKELV 389 RLLPPL + + E VA A K+ + Sbjct: 361 RLLPPLIFSDDDARELVARTAPLIKDFL 388 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: 466 Number of extensions: 31 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: 390 Length adjustment: 30 Effective length of query: 359 Effective length of database: 360 Effective search space: 129240 Effective search space used: 129240 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 09 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