Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__azobra:AZOBR_RS19590 Length = 405 Score = 249 bits (637), Expect = 8e-71 Identities = 150/387 (38%), Positives = 212/387 (54%), Gaps = 13/387 (3%) Query: 9 YARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNL 68 Y D+V RGEG Y++ T+G R+LD + + GH +P ++EA+ QA KL TS Sbjct: 20 YKPLDVVLARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQQASKLTLTSRA 79 Query: 69 FRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYE-KG-DKARTRIITFE 126 FR + L T + + NSGAEA E K +RK+ YE +G + + II Sbjct: 80 FRNDQLALFYEELAALTGSHKILPMNSGAEAVESAIKTVRKWGYEVRGVPENQAEIIVCS 139 Query: 127 QAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGE 186 FHGRT++ VS + GFGP GF VPFGD A+ A+T T + LEPIQGE Sbjct: 140 DNFHGRTISIVSFSTDPDARGGFGPFTPGFRTVPFGDAAALEAALTPNTVAVLLEPIQGE 199 Query: 187 GGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIG 246 G+ +LR +R++C E +++ LDEIQ G+GRTGKL A E G+ DV + K + Sbjct: 200 AGVVIPPAGYLRRVRDLCTERNVVMILDEIQTGLGRTGKLLAEEHEGVEADVTLIGKALS 259 Query: 247 GGF-PLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGL 305 GGF P+ A L+ + + G HGST+GGNPLA AV A + ++E G +D+ G Sbjct: 260 GGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAAMRVLVEEGMIDNAAAQGAY 319 Query: 306 LQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDV---VVALRANGLLSVPAGDNVVR 362 ++L G + N V + RG+GLML + P G ALRA G+L+ D+ +R Sbjct: 320 FLEQL-GAIRSN--VIREARGRGLMLAVELHPEAGGARRYCEALRARGVLAKDTHDHTIR 376 Query: 363 LLPPLNIGEAEVEEAV----AILAKTA 385 + PPL I +V+ A+ A+L TA Sbjct: 377 IAPPLVITREQVDWALEQFDAVLTGTA 403 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: 396 Number of extensions: 18 Number of successful extensions: 5 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