Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_011952251.1 SWIT_RS07135 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000016765.1:WP_011952251.1 Length = 396 Score = 409 bits (1050), Expect = e-119 Identities = 216/388 (55%), Positives = 262/388 (67%), Gaps = 3/388 (0%) Query: 2 IPVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHK 61 I +MP Y R + RGEG YL G R+LDFA+G+AVN+LGH +P LV+A+ QA Sbjct: 3 ITPLMPVYPRCGVRPVRGEGCYLIGERGERYLDFASGIAVNILGHGHPDLVKAIADQAAT 62 Query: 62 LWHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTR 121 L HTSNL+ E+ A++L + TFADTVFFTNSGAEA EC K R+YHY G RT+ Sbjct: 63 LMHTSNLYGSPQGEAFAQKLVDKTFADTVFFTNSGAEAVECAIKTARRYHYVNGSPERTK 122 Query: 122 IITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLE 181 II+F AFHGRTL +SA Q K+ GF PLL GF +VPF DLEA R AV TAG +E Sbjct: 123 IISFSNAFHGRTLGTISATSQPKMRDGFEPLLPGFQVVPFNDLEAARAAVDATTAGFLVE 182 Query: 182 PIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAV 241 P+QGEGG+ EFL+GLR+ICDE GLLL LDE+QCG RTG FAHE GITPD+MAV Sbjct: 183 PVQGEGGMTPSKPEFLKGLRQICDEQGLLLILDEVQCGYCRTGTFFAHEQYGITPDIMAV 242 Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301 AKGI GGFPLGACLATE+AA GM GTHGSTYGGNPLA A G AV + FL +V+ Sbjct: 243 AKGIAGGFPLGACLATEEAAKGMVFGTHGSTYGGNPLAMAAGEAVFKVAVNDEFLANVRA 302 Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAV--GDVVVALR-ANGLLSVPAGD 358 G L+ + L+ + VF VRG GLM+G+ AV V LR +GLL+V AG+ Sbjct: 303 TGDRLRQAIEQLIPNHDGVFDSVRGLGLMIGIKLKDAVEARAFVAHLRDHHGLLTVAAGE 362 Query: 359 NVVRLLPPLNIGEAEVEEAVAILAKTAK 386 NVVR+LPPL I E+ + E + L+ A+ Sbjct: 363 NVVRILPPLVIEESHIAECIEKLSAGAR 390 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: 509 Number of extensions: 18 Number of successful extensions: 2 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: 396 Length adjustment: 31 Effective length of query: 358 Effective length of database: 365 Effective search space: 130670 Effective search space used: 130670 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