Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_041457309.1 AVA_RS26830 ornithine--oxo-acid transaminase
Query= curated2:Q58131 (398 letters) >NCBI__GCF_000204075.1:WP_041457309.1 Length = 400 Score = 331 bits (849), Expect = 2e-95 Identities = 177/400 (44%), Positives = 259/400 (64%), Gaps = 8/400 (2%) Query: 1 MSQENWIDLEKKYHLQIYGRLPVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKV 60 M+ +++I+LE++Y Y L VV+ +G+G+ V+DI+GKKYLDFL+ N GHCHPK+ Sbjct: 1 MNTQDYIELEQQYGADNYHPLDVVITKGEGVWVWDIEGKKYLDFLSAYSALNQGHCHPKI 60 Query: 61 VEAIKKQAETLIHTSNIYYTIPQIKLAKKLVELSGLDRAFFCNSGAEANEGAIKFARKYV 120 ++A+ KQA+ + TS + K +KL ++SGL + NSGAEA E AIK RK+ Sbjct: 61 LQAMIKQAQQVTLTSRAFRNDQLGKFYQKLCQISGLPKVLPMNSGAEAVETAIKAIRKWA 120 Query: 121 SKVLG--REGGEIISMYNAFHGRTLTTLAATPKPKYQDGFYPLPPGFKYVPFNDIEALKE 178 KV G EII N F GRT++ ++ + + +YQDGF PL GFK +PF D +AL++ Sbjct: 121 YKVKGIPENQAEIIVCSNNFSGRTISLISFSTEEQYQDGFGPLTTGFKVIPFGDAQALEQ 180 Query: 179 AITDKTAAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAF 238 AIT TAA ++EP+QGEGGI V +LK +C +++L+FDE+Q G+GRTG+MFA Sbjct: 181 AITPNTAAFLVEPIQGEGGIIVPPHGFLKQAEQICRHHHVLLVFDEIQTGLGRTGKMFAH 240 Query: 239 EHYGVEPDILTLAKALGGG-VPIGAVVLKEEIAKALSYGDHGTTFGGNPLACSAALASVE 297 ++ V+PD +T+ KAL GG PI A + EE+ GDHG+TFGGNPLA + +A+++ Sbjct: 241 QYENVKPDGITVGKALSGGFYPISAFISTEEVMGIFQPGDHGSTFGGNPLAAAIGIAALD 300 Query: 298 VIEELIKDDKVIEKGKYFIRKLENLIEKYNFIKEVRGLGLMIGAEL--EFNGA-DIVKKM 354 V+ E +K ++ G+YFI KL+++ Y IKEVRG GL+IG EL E GA K + Sbjct: 301 VLIEEKLPEKALKLGEYFIEKLQSIESTY--IKEVRGKGLLIGMELYPEAGGARRFCKAL 358 Query: 355 LEKGFLINCTSDTVLRFLPPLIVEKEHIDALINALDEVFT 394 ++G L T D V+RF PPL++ ++ ID + ++ V T Sbjct: 359 AKEGLLAKETRDNVIRFAPPLVISEDEIDWALEKIERVLT 398 Lambda K H 0.320 0.141 0.409 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: 431 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: 398 Length of database: 400 Length adjustment: 31 Effective length of query: 367 Effective length of database: 369 Effective search space: 135423 Effective search space used: 135423 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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