Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_012113238.1 XAUT_RS06110 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000017645.1:WP_012113238.1 Length = 402 Score = 499 bits (1286), Expect = e-146 Identities = 247/378 (65%), Positives = 287/378 (75%) Query: 1 VIPVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAH 60 +I V+PTYAR D+ FERGEG +L TDGRRFLDF G+AVNVLGHA+PYL EAL+ QA Sbjct: 1 MITAVLPTYARIDLEFERGEGCWLVTTDGRRFLDFTGGIAVNVLGHAHPYLAEALSEQAK 60 Query: 61 KLWHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKART 120 KLWHTSNLFR+ G E LA R+ TFADT+FFTNSGAEA EC K+ RKY + G + Sbjct: 61 KLWHTSNLFRIPGGERLADRIKAVTFADTMFFTNSGAEALECAIKMARKYQFASGHPEKN 120 Query: 121 RIITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICL 180 RIITFE AFHGRTLA ++A K ++GFGP + GFD VPFGDL+A R AVT ETA I + Sbjct: 121 RIITFEGAFHGRTLATIAAGGNAKYLEGFGPAMPGFDQVPFGDLDAARAAVTPETAAILV 180 Query: 181 EPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMA 240 EP+QGEGG+R FL+GLR +CDE GLLL LDE+QCG+GRTGKLFAHEW G+TPD+MA Sbjct: 181 EPVQGEGGVRVPPSGFLKGLRALCDEKGLLLVLDEVQCGVGRTGKLFAHEWVGVTPDIMA 240 Query: 241 VAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQ 300 VAKGIGGGFP+GACLATE+AA GMT GTHGSTYGGNPLA AVGNAVLD VL GFLDHV Sbjct: 241 VAKGIGGGFPMGACLATEEAAKGMTLGTHGSTYGGNPLAMAVGNAVLDLVLADGFLDHVN 300 Query: 301 RIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNV 360 + L RLA + +P+V VRG+GL+LGL C D+V ALR G+L+ A DNV Sbjct: 301 AMSTRLVQRLAEVRDRHPSVIAEVRGQGLLLGLRCAVPAADLVTALREEGMLAPGASDNV 360 Query: 361 VRLLPPLNIGEAEVEEAV 378 VRLLPPL + E EV AV Sbjct: 361 VRLLPPLIVSEEEVGIAV 378 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: 531 Number of extensions: 22 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 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