Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1332 Length = 398 Score = 322 bits (826), Expect = 9e-93 Identities = 173/389 (44%), Positives = 238/389 (61%), Gaps = 4/389 (1%) Query: 3 PVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKL 62 P VM TY R I ERG+G ++ +G+ ++D G+AVN LGH + LV AL Q KL Sbjct: 10 PHVMNTYGRVPIALERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVPALQDQIAKL 69 Query: 63 WHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRI 122 HTSN + V QE LA +L E + VFF NSG EA E K+ RK+ +KG A+ I Sbjct: 70 IHTSNYYHVPLQEKLATKLVELSGMQNVFFCNSGLEANEAALKIARKFGVDKGI-AKPEI 128 Query: 123 ITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAV--TDETAGICL 180 + +E+AFHGR++A +SA K+ GFGPL++GF VP D+EA++ A + Sbjct: 129 VVYEKAFHGRSIATMSATGNPKIHNGFGPLVEGFVRVPMNDIEAIKQATEGNPNVVAVFF 188 Query: 181 EPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMA 240 E IQGEGGI +E+L+ LR++CDE G L+ +DE+QCGMGRTGK FAH+WAGI PDVM Sbjct: 189 ETIQGEGGINGMRIEYLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAHQWAGIVPDVMP 248 Query: 241 VAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQ 300 +AKG+G G P+GA +A KAA+ + G HG+T+GGNPLA G + + E G L + Sbjct: 249 LAKGLGSGVPIGAVVAGPKAANVLQPGNHGTTFGGNPLAMRAGVETIRIMEEDGLLHNAA 308 Query: 301 RIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNV 360 ++G L+ L + P V K +RG+GLMLG+ G ++ GLL D+V Sbjct: 309 QVGDHLRAALQRELGSLPGV-KEIRGQGLMLGIELNKPCGALIGRAAEAGLLLSVTADSV 367 Query: 361 VRLLPPLNIGEAEVEEAVAILAKTAKELV 389 +RL+PPL + AE + VAIL K ++ Sbjct: 368 IRLVPPLILTTAEADAIVAILTPLVKAIL 396 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: 496 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: 398 Length adjustment: 31 Effective length of query: 358 Effective length of database: 367 Effective search space: 131386 Effective search space used: 131386 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