Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013459839.1 SULKU_RS04950 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:Q9X2A5 (385 letters) >NCBI__GCF_000183725.1:WP_013459839.1 Length = 427 Score = 126 bits (317), Expect = 1e-33 Identities = 105/349 (30%), Positives = 162/349 (46%), Gaps = 38/349 (10%) Query: 17 GKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLIHCSNLFWNRP---QM 73 G+G ++ D N Y+D+ + GH + A+ + + L + P + Sbjct: 41 GEGGYLIDIDENRYIDYVQSWGPLIFGHRDESIENAVIEAVKH-----GLSFGAPTEAES 95 Query: 74 ELAELL-SKNTFGGKVFFANTGTEANEAAIKIARKYGKKKSEKKYRILSAHNSFHGRTLG 132 ELAEL+ S K+ F ++GTEA +AI++AR + + K+ +HG + Sbjct: 96 ELAELIISIYDSIEKIRFVSSGTEAVMSAIRLARGFTGRDDIVKFT-----GCYHGHSDA 150 Query: 133 SLT--ATGQPKYQKPFEPLVPG-----FEYFEFNNVEDLRR--KMSEDVCAVFLEPIQGE 183 L +G + P P VP E+NN+E +++ + S + V +EPI G Sbjct: 151 LLVQAGSGAVTFGTPSSPGVPADFTKHTLLAEYNNIESVKKCFQDSPGIACVIIEPIAGN 210 Query: 184 SGIVPATKEFLEEARKLCDEYDALLVFDEVQCGMGRTGKLFAYQKYGVVPDVLTTAKGLG 243 G+VPA K+FL E R +CD+Y ALL+FDEV G R A G PD++T K +G Sbjct: 211 MGLVPANKDFLSELRAVCDQYGALLIFDEVMSGF-RACLHGAESITGTKPDLVTLGKVIG 269 Query: 244 GGVPIGA--------VIVNERANVLEPGDHGTTFGGNPLACRAGVTVIKEL-TKEGFLEE 294 GG+P+GA ++ V + G T GNP+A AG+ I +L T Sbjct: 270 GGMPVGAFGGRREIMAHLSPEGGVYQAG----TLSGNPVAMAAGLASINKLKTNARVFNV 325 Query: 295 VEEKGNYLMKKLQEMKEEYDVVADVRGMGLMIGIQFR-EEVSNREVATK 342 +EE+ LM E ++++ G M G F E V+N A K Sbjct: 326 LEERAKRLMNGFAEAAAKHNIGLQTDVRGSMFGFFFSGESVTNFAEALK 374 Lambda K H 0.318 0.138 0.402 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: 404 Number of extensions: 22 Number of successful extensions: 5 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: 385 Length of database: 427 Length adjustment: 31 Effective length of query: 354 Effective length of database: 396 Effective search space: 140184 Effective search space used: 140184 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 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