Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Caulo:CCNA_02326 Length = 405 Score = 389 bits (999), Expect = e-113 Identities = 201/384 (52%), Positives = 252/384 (65%), Gaps = 2/384 (0%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M Y RA + FERG G L +T+G +LD AG+A N LGHA+P LVE L AQA KLWH Sbjct: 14 IMGVYNRAPLAFERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWH 73 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SN++R+ QE LA L +FAD VFFTNSG EA EC K RKYH G R I Sbjct: 74 VSNIYRIPEQEELADALCANSFADVVFFTNSGTEAVECALKTARKYHSANGQPERIDIYG 133 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAV-TDETAGICLEPI 183 F+ +FHGRT AAV+A+ + GFGP L G+ + FGD +A++ A+ + TA I +EP+ Sbjct: 134 FDGSFHGRTYAAVNASGNPSYVDGFGPRLPGYSQLTFGDHDAIKAAIASPTTAAIIVEPV 193 Query: 184 QGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWA-GITPDVMAVA 242 QGEGG R+ + L GLR++CDEHG+LL DE+QCGMGRTGKLFA+EWA G P +MAVA Sbjct: 194 QGEGGARSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLFAYEWAEGGEPHIMAVA 253 Query: 243 KGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRI 302 K +GGGFP+GACLAT +AA GMT HGST+GGNPLA AVG A L+ + P LD+V+ + Sbjct: 254 KALGGGFPIGACLATTEAAKGMTVAAHGSTFGGNPLAMAVGKAALEIIKSPETLDNVKTV 313 Query: 303 GGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVR 362 G +L GL P V VRGKG+++G+ P D +V R LL GDN VR Sbjct: 314 SGFFTQQLNGLKDRFPDVIVDVRGKGMLIGVKLIPNNRDFMVLARDEKLLIAGGGDNCVR 373 Query: 363 LLPPLNIGEAEVEEAVAILAKTAK 386 LLPPLN+ E EA+A L K + Sbjct: 374 LLPPLNLTIEEASEAIAKLEKACE 397 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: 468 Number of extensions: 21 Number of successful extensions: 3 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: 405 Length adjustment: 31 Effective length of query: 358 Effective length of database: 374 Effective search space: 133892 Effective search space used: 133892 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