Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_086509625.1 BZY95_RS09090 aspartate aminotransferase family protein
Query= curated2:Q58131 (398 letters) >NCBI__GCF_002151265.1:WP_086509625.1 Length = 446 Score = 180 bits (457), Expect = 6e-50 Identities = 131/419 (31%), Positives = 210/419 (50%), Gaps = 42/419 (10%) Query: 18 YGRLPVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKKQAETLIHTSNI 77 + R P ++V +G D DG++ D L+G+ GHC P++ EA+ +Q + L ++ Sbjct: 29 FKRDPRIIVGAEGSYFTDADGRRIFDGLSGLWTCGAGHCRPEITEAVTRQLQQLDYSPAF 88 Query: 78 YYTIPQ-IKLAKKLVEL--SGLDRAFFCNSGAEANEGAIKFARKYVSKVLGREGGEIISM 134 + P+ +LA ++ L GLD F+ SG+E+ + A+K AR Y K +++ Sbjct: 89 QFGHPKAFELAHRIRGLMPQGLDHVFYTGSGSESADTALKIARAYWRKKGKPTKTKLVGR 148 Query: 135 YNAFHGRTLTTLA----ATPKPKYQDGFYP--LPPGF-------KYVPFNDIEALKEAI- 180 +HG ++ + + G LP K +P E +E + Sbjct: 149 AKGYHGVNFGGISLGGIGANRVLFGQGIDADHLPHTLLAENAFTKGMPERGAERAEELLE 208 Query: 181 ------TDKTAAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGR 234 AA+++EP+ G G+ K YL+ +R++CD +I+LIFDEV G GR G Sbjct: 209 LIALHDASNIAAVIVEPLAGSAGVIPPPKGYLQRLREICDQHDILLIFDEVITGFGRMGS 268 Query: 235 MFAFEHYGVEPDILTLAKAL-GGGVPIGAVVLKEEIAKA-LSYG--------DHGTTFGG 284 M E +GV PDIL +AK L G VP+GAV+++ EI + +G HG T+ G Sbjct: 269 MTGAEEFGVVPDILNVAKQLTNGAVPMGAVIVQGEIYHTFMEHGGPDYMLELPHGYTYSG 328 Query: 285 NPLACSAALASVEVIEELIKDDKVIEKGKYFIRKLENLIEKYNFIKEVRGLGLMIGAELE 344 +P+AC+AALA+++V+E +V E F L L + +I ++R GL ++E Sbjct: 329 HPVACAAALAALDVLENDRLIQRVREMSPVFEEALHGL-KGTRYISDIRNYGLAGALQIE 387 Query: 345 -FNGA------DIVKKMLEKGFLINCTSDTVLRFLPPLIVEKEHIDALINALDEVFTEI 396 + G +I K KGF + DT+ L P IVE++ ID L+NAL E +E+ Sbjct: 388 PYPGEPARRPFEIAMKCWNKGFYVRYGGDTIQLGL-PFIVERDEIDRLVNALGEAISEL 445 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: 485 Number of extensions: 32 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 446 Length adjustment: 32 Effective length of query: 366 Effective length of database: 414 Effective search space: 151524 Effective search space used: 151524 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