Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Burk376:H281DRAFT_04057 Length = 394 Score = 277 bits (708), Expect = 4e-79 Identities = 159/375 (42%), Positives = 226/375 (60%), Gaps = 8/375 (2%) Query: 11 RADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNLFR 70 R +IVF G+G +LY +G+R+LDF G AVN LGH + ++EAL QA L++ S F Sbjct: 17 RPEIVFTHGKGSWLYDNNGKRYLDFIQGWAVNCLGHCDEGMIEALNQQAKLLFNPSPAFY 76 Query: 71 VAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQAFH 130 LA LT+ + D VFF NSGAEA E KL RK+ + D A IITF+ +FH Sbjct: 77 NEPMAKLAALLTQHSCFDKVFFANSGAEANEGAIKLARKWGKKFKDGA-FEIITFDHSFH 135 Query: 131 GRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGEGGIR 190 GRTLA +SA+ + + P + GF D+ +V + +T + LEPIQGEGG+ Sbjct: 136 GRTLATMSASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKTVAVMLEPIQGEGGVI 195 Query: 191 AGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIGGGFP 250 + EF++ LRE+ +H +LL +DE+Q G GR G LFA+E +G+ PD+M + KGIGGG P Sbjct: 196 PATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGTLFAYELSGVEPDIMTLGKGIGGGVP 255 Query: 251 LGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQDRL 310 L A LA + A AG G TY GNPL TAVG +V+ ++ PGFL+ V+ G L+ +L Sbjct: 256 LAALLAKAEVAV-FEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGVRARGEYLRAKL 314 Query: 311 AGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVA----LRANGLLSVPAGDNVVRLLPP 366 L E FKG RG+GL+ L G +G+ +V ++ +GLL A N++R +P Sbjct: 315 LELSEERG--FKGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLLLNAARPNLLRFMPA 372 Query: 367 LNIGEAEVEEAVAIL 381 LN+ E+++ +A+L Sbjct: 373 LNVTNEEIDQMMAML 387 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: 405 Number of extensions: 23 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: 394 Length adjustment: 31 Effective length of query: 358 Effective length of database: 363 Effective search space: 129954 Effective search space used: 129954 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