Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_085773604.1 B1812_RS08505 aspartate aminotransferase family protein
Query= curated2:Q58131 (398 letters) >NCBI__GCF_002117405.1:WP_085773604.1 Length = 452 Score = 184 bits (468), Expect = 3e-51 Identities = 130/407 (31%), Positives = 204/407 (50%), Gaps = 51/407 (12%) Query: 29 KGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKKQAETL------IHTSNIYYTIP 82 +G E++ +G++ LDF +G V+N+GH HP++V A+K++ + H S + Sbjct: 37 EGAELHTTEGRRILDFNSGYCVHNIGHNHPRLVAALKQELDAAGPAMLQSHVSGLAG--- 93 Query: 83 QIKLAKKLVELSG--LDRAFFCNSGAEANEGAIKFARKYVSKVLGREGGEIISMYNAFHG 140 +LA++L +G L +AFF SGAE E IKFAR + R G I+ N FHG Sbjct: 94 --ELAQQLCTRAGGRLAKAFFACSGAEGVETVIKFARAHT-----RRAG-ILYAENGFHG 145 Query: 141 RTLTTLAATPKPKYQDGFYPLPPGFKYVPFNDIEALKEAI-TDKTAAIMIEPVQGEGGIH 199 T L+ ++DGF PL P + PF D+ L+E + T + AA ++EP+QGE G+ Sbjct: 146 LTCGALSLMSNGFWKDGFGPLLPETESTPFGDLADLEEKLATKRFAAFVLEPIQGEAGVR 205 Query: 200 VADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYGVEPDILTLAKALGGG-V 258 + YL+ + LC +L DEVQ G RTG A +GVEPD++ LAKA+ GG + Sbjct: 206 APPEGYLEQAQALCRRYGTLLALDEVQTGFHRTGPFLAAHRFGVEPDMVVLAKAISGGLI 265 Query: 259 PIGAVVLKEEIAKALSYGD------HGTTFGGNPLACSAALASVEVIEELIKDDKVIEKG 312 P AV++ +EI ++ Y H TT+ N LA A L ++ ++E+ +KG Sbjct: 266 PCSAVLMTDEICHSV-YSSLKRAFVHTTTYSENGLAMRAGLTTLAILEDEELGACAEDKG 324 Query: 313 KYFIRKLENLIEKYNFIKEVRGLGLMIGAELE---------------------FNGADIV 351 + KL + Y ++++RG GL+ E F ++ Sbjct: 325 EALRAKLSEKLSGYEMVEDIRGFGLLSAIEFRPPRSLLLRAPFESFKAIHPGMFGQVVVM 384 Query: 352 KKMLEKGFLIN-CTSDTV-LRFLPPLIVEKEHIDALINALDEVFTEI 396 + + G L C +D + L+ PPLIV ID + A+ V ++ Sbjct: 385 RLFRDHGVLSQICGNDFLSLKVAPPLIVSDAQIDQYVEAIGAVVADM 431 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: 442 Number of extensions: 21 Number of successful extensions: 6 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: 452 Length adjustment: 32 Effective length of query: 366 Effective length of database: 420 Effective search space: 153720 Effective search space used: 153720 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: 51 (24.3 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