Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_106717222.1 CU100_RS10730 ornithine--oxo-acid transaminase
Query= curated2:O27392 (390 letters) >NCBI__GCF_003010935.1:WP_106717222.1 Length = 396 Score = 293 bits (749), Expect = 8e-84 Identities = 159/397 (40%), Positives = 229/397 (57%), Gaps = 14/397 (3%) Query: 6 IIELERKFIMQTYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAIC 65 +I E + Y +VL G+G VWDI+GN Y+DC + + + GH HPK+ A+ Sbjct: 1 MISTESRLGAHNYKPLDVVLERGEGVHVWDIDGNRYLDCLSAYSAVNQGHCHPKILEAMV 60 Query: 66 HQAQRLIHSSNIYYTREQVELAKLLTAISPHDRVFFANSGAEANEGAIKLARKF------ 119 QA +L +S + + + L A++ ++ NSGAEA E AIK RK+ Sbjct: 61 EQAGKLTLTSRAFRNDQLALFYEELAALTGSHKILPMNSGAEAVETAIKAVRKWGYEVKG 120 Query: 120 --TGKSEIIAAENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHVPYGDIGAMADAVGDE 177 +EII ++FHGRT+ V + + F P GFK VP+GDI A + A+ Sbjct: 121 VPENAAEIIVCSDNFHGRTMGIVGFSTDPSARDNFGPFAPGFKVVPFGDIDAFSAALTPN 180 Query: 178 TAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAMFASQLFGV 237 T ++EP+QGE GVIIPP+GY V+EL +N++ LILDE+QTG GRTGA+ A G+ Sbjct: 181 TVGFLVEPIQGEAGVIIPPKGYFTKVRELCTENNITLILDEIQTGLGRTGALLAEAHEGI 240 Query: 238 EPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGDHGSTFGGNPWGCAAAIATIEVLMDE 296 E D+T + KA+ GG YP+ AVL+N V +PG HGSTFGGNP CA A A + VL +E Sbjct: 241 EADVTLIGKALSGGFYPVSAVLSNSDVLGVLKPGQHGSTFGGNPLACAIARAALRVLTEE 300 Query: 297 KLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEIDGECAGVVDAAREM---GV 353 + E + G YFL L+ + + VR++RG GLM+ +E+ E G E+ G+ Sbjct: 301 NMIENSRIEGEYFLEELKGI--RSNIVREVRGRGLMLAVELHPEAGGANRFCYELKARGI 358 Query: 354 LINCTAGKVIRIVPPLVIKKEEIDAAVDVLGHVISDL 390 L T G IRI PPLVIK++++D A++ V++ + Sbjct: 359 LAKDTHGDTIRIAPPLVIKRDQVDWALEQFNTVLTSM 395 Lambda K H 0.320 0.138 0.404 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: 413 Number of extensions: 16 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: 390 Length of database: 396 Length adjustment: 31 Effective length of query: 359 Effective length of database: 365 Effective search space: 131035 Effective search space used: 131035 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 Jul 26 2024. The underlying query database was built on Jul 25 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