Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_040912231.1 ON01_RS05315 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:O66442 (376 letters) >NCBI__GCF_000224785.1:WP_040912231.1 Length = 425 Score = 201 bits (510), Expect = 4e-56 Identities = 142/404 (35%), Positives = 219/404 (54%), Gaps = 41/404 (10%) Query: 5 MNNYAR-LPVKFVRGKGVYLYDEEGKEYLDFVSGIGVNSLGHAYPKLTEALKEQVEK--L 61 + +Y+R P F + KG L+D +GKEYLDF +G G + GH + + E ++ + Sbjct: 22 VRSYSRGWPTVFEKAKGYKLWDTDGKEYLDFFAGAGGLNYGHNDDAMQAKMIEYIQNNGI 81 Query: 62 LH---VSNLYENPWQEELAHKLVKHFWTEGKVFFAN-SGTESVEAAIKLARKYWRDKGKN 117 LH + + E ++K + KV F +GT SVE+A+K+ARK Sbjct: 82 LHSLDMGTTSRKEFLERFKEVILKPRNLDYKVMFPGPTGTNSVESALKIARKV-----TG 136 Query: 118 KWKFISFENSFHGRTYGSLSATGQP-KFHKGFEPL-----VPGFSYAK-LNDIDSVYKLL 170 + ISF N+FHG T GSLS T K H PL +P Y + N I + + L Sbjct: 137 RDTVISFTNAFHGMTIGSLSVTANSFKRHGAGVPLHHSVSMPFDEYVEDQNTIAYLERFL 196 Query: 171 DEETAG------IIIEVIQGEGGVNEASEDFLSKLQEICKEKDVLLIIDEVQTGIGRTGE 224 ++ +G II+E +QGEGG+N AS D+L K++++CK+ D+LLI+D++Q G GRTG Sbjct: 197 EDRGSGVALPAAIILETVQGEGGINAASMDWLKKVEDLCKQWDILLIVDDIQAGCGRTGT 256 Query: 225 FYAYQHFNLKPDVIALAKGLGG-GVPIGAILAREEVAQSFTPGSHGSTFGGNPLACRAGT 283 F++++ + PD++ L+K +GG G+P+ L + E Q + PG H TF GN LA T Sbjct: 257 FFSFEPAGIDPDIVCLSKSIGGAGLPMALTLIKPEHDQ-WGPGEHNGTFRGNNLAFIGAT 315 Query: 284 VVVD--EVEKLLPHVREVGNYFKEKLKELG------KGKVKGRGLMLGLELERE--CKDY 333 + E + +RE G +E ++EL +GRGLM G+ L + D Sbjct: 316 QALSYWENDDFGKSIREKGELLREGIEELVAKYPELDAHHRGRGLMQGIALGKPELTDDI 375 Query: 334 VLKALEKGLLINCTAG---KVLRFLPPLIIQKEHIDRAISVLRE 374 +A ++GL++ TAG +V++FLPPLII KE + + +L E Sbjct: 376 CAEAFQRGLIVE-TAGPDDEVVKFLPPLIIDKEALKEGLKILDE 418 Lambda K H 0.318 0.139 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: 385 Number of extensions: 19 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: 376 Length of database: 425 Length adjustment: 31 Effective length of query: 345 Effective length of database: 394 Effective search space: 135930 Effective search space used: 135930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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