Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012505186.1 PAES_RS02955 aspartate aminotransferase family protein
Query= curated2:P59316 (400 letters) >NCBI__GCF_000020625.1:WP_012505186.1 Length = 397 Score = 559 bits (1441), Expect = e-164 Identities = 270/395 (68%), Positives = 333/395 (84%) Query: 3 TPAINLETEKQLFFHNYARLPLDIASGKGSFLYTASGERYLDMIAGVGVNAIGYGDKRLE 62 T +N ETE +LFFHNYARLPL I GKG +L+ + RYLDMI+G+GVNA+GYGD+RL Sbjct: 2 TSILNKETEHELFFHNYARLPLAITHGKGVYLFDENSNRYLDMISGIGVNALGYGDERLI 61 Query: 63 QAITEQASKYIHVSNLFMQKPQFDLAAKLLEISRMSKVFFCNSGTEAIEAAIKLARRFAA 122 +AI +QA K IH SNLFM +PQF LA+KLL+IS +SKVFF NSGTEAIEAA+KL+R++A+ Sbjct: 62 EAIHDQAKKIIHASNLFMLEPQFKLASKLLDISGLSKVFFANSGTEAIEAAMKLSRKWAS 121 Query: 123 RNGDTDKTQVLSLTNCFHGRTYGALSLTAKPKYVDGFEPLVPETGMIDFNDVEDLERKVS 182 +G T K ++LSL+NCFHGRTYGA+SLTAKPKY++GF+PL+P TG I FND+EDL+RK++ Sbjct: 122 LSGSTGKKEILSLSNCFHGRTYGAMSLTAKPKYLEGFDPLLPGTGSIAFNDIEDLKRKIT 181 Query: 183 NRTAAVFVEFVQGEGGIHKVSEAFIAKLKELAKEHDFLIVADEIQAGCGRTGAFFSYMPF 242 + TAAVF+EFVQGEGGIH++S F+ +LK+L + H+FLIVADEIQAGCGRTG FFSYM F Sbjct: 182 SNTAAVFIEFVQGEGGIHQISREFVEELKKLRETHNFLIVADEIQAGCGRTGKFFSYMHF 241 Query: 243 DIQPDLVCVAKPLGGGLPLGAIIGSEKVAEVFTPGSHGTTFGGNPVACAAGLAMIEAILA 302 DI PDLVCVAKPLGGGLPLGA+IGS KV +VF G+HGTTFGGNPVACAAG A+IE + + Sbjct: 242 DIDPDLVCVAKPLGGGLPLGAVIGSRKVQDVFAAGNHGTTFGGNPVACAAGHALIETLYS 301 Query: 303 DGLMQNALEVGSMMRTAFEKMAEKHAQILEIRQYGLMIGVTVHREAKYYVEEALKRGVLV 362 +M++AL GS ++ A K+AE H QI EIRQYGLMIG+TV+R+A YYV+E+LKR VLV Sbjct: 302 KKIMEHALATGSWIKAALTKLAETHTQIQEIRQYGLMIGITVNRDAAYYVQESLKRRVLV 361 Query: 363 NATSNNVIRLLPPLSISKEEAQLCLDTLDAIFTEE 397 NATS NVIRLLPPL+I+ EEAQ C+D LD IF+EE Sbjct: 362 NATSQNVIRLLPPLTITVEEAQQCIDCLDEIFSEE 396 Lambda K H 0.320 0.136 0.386 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: 454 Number of extensions: 17 Number of successful extensions: 1 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: 400 Length of database: 397 Length adjustment: 31 Effective length of query: 369 Effective length of database: 366 Effective search space: 135054 Effective search space used: 135054 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