Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_029767356.1 HALAL_RS0104185 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:O27392 (390 letters) >NCBI__GCF_000527155.1:WP_029767356.1 Length = 429 Score = 124 bits (311), Expect = 5e-33 Identities = 96/304 (31%), Positives = 144/304 (47%), Gaps = 27/304 (8%) Query: 22 PIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSSNIYYTR 81 P+ + +G+ + D++GNSYID +GHAHP+V A+ A+R +S + Sbjct: 38 PVYMESAQGSRMVDVDGNSYIDLVGSWGPMILGHAHPEVVSAVTTAAER--GTSFGTSSP 95 Query: 82 EQVELAKLLTAISPHDRVFFANSGAEANEGAIKLARKFTGKSEIIAAENSFHGRTLATVT 141 +VELA+ L A + ++V SG EA A++LAR TG+ ++I +HG A + Sbjct: 96 GEVELAEELVARTNCEQVRLVTSGTEATMSALRLARGATGRDKVIKFAGCYHGHGDAFLA 155 Query: 142 ATGQ--KKYSEPFRP-LPEGFKH----VPYGDIGAMADAV---GDETAAIILEPVQGEGG 191 A G P P +P VPY D+ A+ +A+ + AA+I E + G G Sbjct: 156 AAGSGVATLGTPDSPGVPASATADTIVVPYNDLDAVTEALQANEGQVAAVITEAIPGNMG 215 Query: 192 VIIPPEGYLKDVQELARQNDVLLILDEVQTGF--GRTGAMFASQLFGVEPDITTVAKAMG 249 + P + + + + LA ++ LLI DEV TGF GR G D+ T K MG Sbjct: 216 CVAPQDDFNERLYRLAHEHGSLLISDEVMTGFRVGRHGV-------SAPADLYTFGKVMG 268 Query: 250 GGYPIGAVLANERVAMAFEPGD---HGSTFGGNPWGCAAAIATIEVLMDE---KLPERAA 303 GG P A + P T GNP AA + T+ +L DE KL A Sbjct: 269 GGLPAAAFGGRRDLMEQLSPTGPIYQAGTLAGNPVTAAAGLTTLHLLTDEVYQKLDTLAE 328 Query: 304 KMGS 307 ++G+ Sbjct: 329 QIGT 332 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: 397 Number of extensions: 19 Number of successful extensions: 4 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: 429 Length adjustment: 31 Effective length of query: 359 Effective length of database: 398 Effective search space: 142882 Effective search space used: 142882 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 Apr 09 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