Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_025273703.1 HALAL_RS0109075 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q9K8V5 (384 letters) >NCBI__GCF_000527155.1:WP_025273703.1 Length = 425 Score = 192 bits (489), Expect = 1e-53 Identities = 129/396 (32%), Positives = 203/396 (51%), Gaps = 31/396 (7%) Query: 11 WDVTITSGKGTKLYDNQGNEYLDFVSGIAVCNLGHCHPKVVAAVEEQL--HSFWHVSNLF 68 W T+ +G+K+ D G EY+DF +G N GH +P++ + E L + H + + Sbjct: 18 WPTVFTTARGSKMSDEAGKEYIDFFAGAGSLNYGHNNPEIKKKLLEYLAEDNVIHTLDTY 77 Query: 69 HIPIQENVAA---LLTEQSGMD--AVFFCNSGAEANEAAIKLARKATGKHEIVTFTQSFH 123 +E + L+ + GMD +F +G A E A+KLARK TG+ +++FT FH Sbjct: 78 STAKREFLKTFDELILQPRGMDYKMMFPGPAGNNAVEGALKLARKYTGRETVISFTNGFH 137 Query: 124 GRTLGTMSATGQDKIKTGFGPMLETFHHVPFN--------DIAALKQVVNE------QTA 169 G TLG ++ TG + G G L +PF+ D L+ ++ + + A Sbjct: 138 GMTLGALAVTGNSMKRGGAGVPLNNTATMPFDGYMDGQTPDFLWLRTLLEDPGSGLDKPA 197 Query: 170 AIVLEVIQGEGGVNLIDPEFAASVNHVCQEHGILLIIDEIQTGIGRTGTAFAFQQYELTP 229 A+++E +QGEGG+N+ PE+ + VC +H +LLI+D+IQ G GRTG+ F+F++ + P Sbjct: 198 AVIVETVQGEGGINVASPEWLKGLQEVCHDHDVLLIVDDIQMGCGRTGSYFSFEEAGIKP 257 Query: 230 DIITVAKGL-GNGFPVGAMLGKQHLIDAFSAGSHGSTFGGNPLAMAAAQAVLTEVFQPN- 287 DIIT++K L G G P+ L ++ L D + G H TF G A A A L E + N Sbjct: 258 DIITLSKSLSGIGLPLAVTLMRREL-DVWDPGEHNGTFRGFAPAFVTATAAL-ETYWKND 315 Query: 288 -FLQAVQEKGKQL---LSGLNEALSGLEIVKEIRGNGLLVGIELQEEGAPFIKQLREKGL 343 F ++V +G+ L L + GL + RG + + E + ++GL Sbjct: 316 AFAKSVVAQGEWLHEQLEAIVREFPGLGLSTRGRGLARALEFSVAEHADETAAESFKQGL 375 Query: 344 LVLNAG--PNVIRLLPPLVVTSEELHEAVTQLKEVL 377 L+ G VI+ LPPL T EE E + +L+ L Sbjct: 376 LMETCGAEDEVIKFLPPLNTTQEEFIEGLDKLRAAL 411 Lambda K H 0.318 0.135 0.391 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: 407 Number of extensions: 16 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: 384 Length of database: 425 Length adjustment: 31 Effective length of query: 353 Effective length of database: 394 Effective search space: 139082 Effective search space used: 139082 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