Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_018243099.1 RL_RS18215 aspartate aminotransferase family protein
Query= curated2:O66442 (376 letters) >NCBI__GCF_000009265.1:WP_018243099.1 Length = 441 Score = 193 bits (491), Expect = 7e-54 Identities = 140/416 (33%), Positives = 209/416 (50%), Gaps = 49/416 (11%) Query: 8 YARLPVKFVRGKGVYLYDEEGKEYLDFVSGIGVNSLGHAYPKLTEALKEQVEKLLHVSNL 67 + + P FV K +Y +G++ LD +G+ + GH PK+TEA++EQ +L + Sbjct: 24 FKKEPRLFVGAKDMYYTTHDGRQVLDGTAGLWCVNAGHCRPKITEAIREQAGELDYAPAF 83 Query: 68 Y-ENPWQEELAHKLVKHFWTEG--KVFFANSGTESVEAAIKLARKYWRDKGK-NKWKFIS 123 +P ELA++LV EG V + NSG+ESVE A+K+A Y R KG ++++ I Sbjct: 84 QLGHPKAFELANRLVD-IAPEGLNHVLYTNSGSESVETALKVALAYHRVKGNGSRFRLIG 142 Query: 124 FENSFHGRTYGSLSATGQPKFHKGFEPLVPGFSYAK---------------------LND 162 E +HG +G +S G K F L+ G + + Sbjct: 143 RERGYHGVNFGGISVGGIVTNRKMFGTLLTGVDHMPHTHQPGKNNFTRGEPEHGGDIATE 202 Query: 163 IDSVYKLLDEET-AGIIIEVIQGEGGVNEASEDFLSKLQEICKEKDVLLIIDEVQTGIGR 221 ++ + L D T A +I+E + G GV + +L KL+EIC + +LLI DEV TG GR Sbjct: 203 LERIVTLHDASTVAAVIVEPVAGSTGVLIPPKGYLQKLREICTKHGILLIFDEVITGFGR 262 Query: 222 TGEFYAYQHFNLKPDVIALAKGLGGGV-PIGAILAREEVAQSFTPGS-------HGSTFG 273 G +A Q++++KPD+I AKGL GV P+GA+ E+ +F G HG T+ Sbjct: 263 LGAPFAAQYYDVKPDMITAAKGLTNGVIPMGAVFVTSEIHDAFMNGPEHMIEFFHGYTYS 322 Query: 274 GNPLACRAGTVVVD--EVEKLLPHVREVGNYFKEKLKEL----GKGKVKGRGLMLGLELE 327 GNP+A A +D + E LL E+ +Y+ + L L ++ GL+ +EL+ Sbjct: 323 GNPIASAAALATLDTYKEEGLLTRAAELSDYWADALHSLKDCPNVIDIRNTGLIGAIELD 382 Query: 328 -------RECKDYVLKALEKGLLINCTAGKVLRFLPPLIIQKEHIDRAISVLREIL 376 + LKA E GLLI T G ++ PPLII+K HID LR IL Sbjct: 383 PIAGEPTKRAFTAFLKAYESGLLIR-TTGDIIALSPPLIIEKHHIDELFGKLRTIL 437 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: 372 Number of extensions: 23 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: 441 Length adjustment: 31 Effective length of query: 345 Effective length of database: 410 Effective search space: 141450 Effective search space used: 141450 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 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