Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__PS:Dsui_3250 Length = 390 Score = 308 bits (788), Expect = 2e-88 Identities = 174/390 (44%), Positives = 229/390 (58%), Gaps = 4/390 (1%) Query: 2 IPVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHK 61 +P +M TYAR + F GEG +Y TDG+ +LD +G+AVN LGH +P LV A+ +QA + Sbjct: 1 MPHLMNTYARLPVAFSHGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAAR 60 Query: 62 LWHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTR 121 + HTSNL+R+ QE LA RL + + VFF NSG EA E KL R + ++KG A Sbjct: 61 VLHTSNLYRIPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQKGVDAPV- 119 Query: 122 IITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNA--VTDETAGIC 179 II E+AFHGRTLA +SA K GF PL+ GF VP+ DL+A+R A + + Sbjct: 120 IIVMEKAFHGRTLATLSATGNRKAQAGFEPLVSGFVRVPYNDLDAIRAAAELNPNVVAVL 179 Query: 180 LEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVM 239 LE +QGEGGI EF RGLR +CDE LL DE+QCGMGRTG F + AGI PDV Sbjct: 180 LEMVQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHAGILPDVA 239 Query: 240 AVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHV 299 +AKG+G G P+GAC+ KAA G HGST+GGNPLA A + + E ++ Sbjct: 240 TLAKGLGSGVPIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACIEEEKLRENA 299 Query: 300 QRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDN 359 G ++ L+ +A + + +RGKGLMLG+ G++V GLL + Sbjct: 300 VAQGEAIRRGLSEALAGVGGLVE-IRGKGLMLGIELDRPCGELVAKGLEAGLLINVTAEK 358 Query: 360 VVRLLPPLNIGEAEVEEAVAILAKTAKELV 389 VVRLLP L A+ +E V LA KE + Sbjct: 359 VVRLLPALTFSAADTQELVQRLAALIKEFL 388 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: 462 Number of extensions: 36 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: 390 Length adjustment: 30 Effective length of query: 359 Effective length of database: 360 Effective search space: 129240 Effective search space used: 129240 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