Align Acetylornithine aminotransferase, chloroplastic/mitochondrial; ACOAT; Acetylornithine transaminase; AOTA; Protein HOPW1-1-INTERACTING 1; EC 2.6.1.11 (characterized)
to candidate NP_661271.1 CT0367 acetylornithine aminotransferase
Query= SwissProt::Q9M8M7 (457 letters) >NCBI__GCF_000006985.1:NP_661271.1 Length = 400 Score = 298 bits (762), Expect = 3e-85 Identities = 159/395 (40%), Positives = 240/395 (60%), Gaps = 9/395 (2%) Query: 62 IEEEAKVIVGTYARAPVVLSSGKGCKLFDPEGKEYLDCASGIAVNALGHGDPDWLRAVTE 121 +E E ++ YAR P+ ++SGKG L+ G+ YLD +G+ VNA+G+GD +A+TE Sbjct: 8 LETEKQLFFHNYARLPLDIASGKGSFLYTASGERYLDMIAGVGVNAIGYGDKRLEQAITE 67 Query: 122 QAGVLAHVSNVYYTIPQIELAKRLVASSFADRVFFCNSGTEANEAAIKFSRKFQRFTHPE 181 QA HVSN++ PQ +LA +L+ S +VFFCNSGTEA EAAIK +R+F Sbjct: 68 QASKYIHVSNLFMQKPQFDLAAKLLEISRMSKVFFCNSGTEAIEAAIKLARRFAARNGDT 127 Query: 182 DKEVATGFIAFTNSFHGRTLGALALTSKEQYRTPFEPIMPGVTFLEYGNIQAATDLIR-- 239 DK T ++ TN FHGRT GAL+LT+K +Y FEP++P +++ +++ DL R Sbjct: 128 DK---TQVLSLTNCFHGRTYGALSLTAKPKYVDGFEPLVPETGMIDFNDVE---DLERKV 181 Query: 240 SGKIAAVFVEPIQGEGGIYSATKEFLQSLRSACDAAGSLLVFDEVQCGLGRTGLMWAYEA 299 S + AAVFVE +QGEGGI+ ++ F+ L+ L+V DE+Q G GRTG ++Y Sbjct: 182 SNRTAAVFVEFVQGEGGIHKVSEAFIAKLKELAKEHDFLIVADEIQAGCGRTGAFFSYMP 241 Query: 300 FGVTPDIMTVAKPLAGGLPIGAVLVTEKVAETINYGDHGSTFAGSPLVCSAAIAVMDKVS 359 F + PD++ VAKPL GGLP+GA++ +EKVAE G HG+TF G+P+ C+A +A+++ + Sbjct: 242 FDIQPDLVCVAKPLGGGLPLGAIIGSEKVAEVFTPGSHGTTFGGNPVACAAGLAMIEAIL 301 Query: 360 KPSFLSSVSNKGRYFRDLLVKKLGGNSHVKEVRGEGLIIGVELDVPASSLVDACRDSGLL 419 + + G R K ++ + E+R GL+IGV + A V+ G+L Sbjct: 302 ADGLMQNALEVGSMMRTAFEKMAEKHAQILEIRQYGLMIGVTVHREAKYYVEEALKRGVL 361 Query: 420 ILTAGKGNVVRIVPPLVISEEEIERAVEIMSQNLT 454 + A NV+R++PPL IS+EE + ++ + T Sbjct: 362 V-NATSNNVIRLLPPLSISKEEAQLCLDTLDAIFT 395 Lambda K H 0.318 0.135 0.385 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: 417 Number of extensions: 14 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: 457 Length of database: 400 Length adjustment: 32 Effective length of query: 425 Effective length of database: 368 Effective search space: 156400 Effective search space used: 156400 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 (21.7 bits) S2: 51 (24.3 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