Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_017599949.1 D471_RS0118255 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000341125.1:WP_017599949.1 Length = 403 Score = 251 bits (640), Expect = 3e-71 Identities = 146/372 (39%), Positives = 200/372 (53%), Gaps = 9/372 (2%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +MP Y I G G +Y DGR++LD AG+AV+ LGH +P LV+A+ QA L H Sbjct: 15 LMPNYGVPPIALSLGRGCEIYDVDGRQYLDLIAGIAVSGLGHGHPALVKAVAHQAATLAH 74 Query: 65 TSNLFRVAGQESLAKRLTEATFADT-VFFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123 TSNLF + LA+RL D VFF NSG EA E KL+++ R + Sbjct: 75 TSNLFVHEREVELAERLVALLGGDAKVFFANSGTEANEAALKLVKR----AAGPGRHYFV 130 Query: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPI 183 + FHGRT +++ ++ + + FGP VP GD++A+ AV + EP Sbjct: 131 AATRGFHGRTSGSLALTGKDSIREPFGPYGMDVRFVPHGDIDALTEAVDTGCVAVFTEPT 190 Query: 184 QGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAK 243 QGE G+ +L G+R +CDE G LDEIQ G+GRTG+ FAH+ AG+ PDV+ +AK Sbjct: 191 QGEAGVVPAPEGYLAGVRAVCDETGAAFVLDEIQSGVGRTGQWFAHQDAGVRPDVLTLAK 250 Query: 244 GIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIG 303 G+GGG P+GAC+ A G HGST+GGNP+A A AVLD + G L H +G Sbjct: 251 GLGGGLPIGACVGFGDYADAFQKGDHGSTFGGNPVACAAALAVLDTIESEGLLAHTAVMG 310 Query: 304 GLLQDRLAGLVAENPAVFKGVRGKGLMLGLA-CGPAVGDVVVALRANGLLSVPAGDNVVR 362 LL ++L + ++P + +G RG GL L P V G L G +R Sbjct: 311 DLLAEQLDAI--DHP-LLEGQRGSGLWRALTLTAPVAAHVQDQAAVRGFLVNAVGPETIR 367 Query: 363 LLPPLNIGEAEV 374 L PPL I ++ Sbjct: 368 LAPPLVITPEQI 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: 473 Number of extensions: 24 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: 403 Length adjustment: 31 Effective length of query: 358 Effective length of database: 372 Effective search space: 133176 Effective search space used: 133176 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