Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_027489918.1 LRK54_RS03035 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q8R7C1 (393 letters) >NCBI__GCF_021560695.1:WP_027489918.1 Length = 467 Score = 184 bits (467), Expect = 5e-51 Identities = 128/434 (29%), Positives = 210/434 (48%), Gaps = 63/434 (14%) Query: 17 PIMLVKGEGTRVWDSEGNAYLDFVAGIAVNSLGHCHPALVEAIKKQAETLIHCSNLYWNE 76 P + GEG+ ++D+ G +LD + + G+ + L + +K+Q + L ++ Y ++ Sbjct: 37 PKIFRHGEGSYMFDTAGTPFLDLQMWYSAVNFGYGNKRLNDTLKRQIDLLPQVASQYLHQ 96 Query: 77 KQIELARMIS---ENSFG--GKVFFANSGAEANEGAIKLARKYASLKYGGKRYKIITAKN 131 +IELA+ ++ + FG G+V F GA+A E ++KL R Y + GK + + Sbjct: 97 TRIELAKTVALDAKKKFGLDGRVHFNVGGAQAIEDSLKLVRNYKN----GKSL-MFAFEG 151 Query: 132 SFHGRTFGALTATGQEKYHKGFGPLLAGFKYVP--------------------LNDIEAL 171 +HGRT GA + T +Y + FG ++P +N L Sbjct: 152 GYHGRTLGASSITSSYRYRRRFGHFGERAMFLPFPYPFRRPKGMTAEEYSDACVNQFARL 211 Query: 172 YEAVDD----------EVCAIMLEVIQGEGGIHEATPEYVKAVRKICDENDLLFILDEVQ 221 +E + E A +E IQG GG + K ++K+ D+ +L ++DE+Q Sbjct: 212 FETEYNGVWDPKTNQCEYAAFYVEPIQGTGGYVVPPMNFFKDLKKVLDQYGILLVVDEIQ 271 Query: 222 TGIGRTGKLFGYEHYGVVPDIMTLAKGLGGGF-PIGAIVAKED---KAVFKPGDHASTFG 277 G RTGKL+ EH+GV PD++ K L G P+ + A+E+ +F PG STF Sbjct: 272 MGFWRTGKLWSIEHFGVTPDVIVFGKALTNGLNPLSGLWAREEMINPTIFPPGSTHSTFN 331 Query: 278 GNPLACAAGIAVLNEVTKDGFLEGVDKKGKYFREGLETLQKKHKVVKEIRGKGLMVGCEV 337 NPL A G+ V+ + + + V KG +F EGL LQKKHK + ++ G GL + E+ Sbjct: 332 SNPLGTALGLEVIKMGYELDYEKTVPVKGAHFLEGLRGLQKKHKEIGDVDGLGLALRAEI 391 Query: 338 DLED-----------------ASEIVLKALEKGLL--INSVSHNVLRFVPPLIVTEEEID 378 ED A ++ + GL+ + NV+ F P L +T EEID Sbjct: 392 CTEDGFTPNKALLDRMVDIGLAGDLTHNGKKIGLVLDVGGWYKNVITFAPSLDITHEEID 451 Query: 379 EALQILDDVLSEIR 392 A+ +LD +L++ + Sbjct: 452 LAISLLDQLLTKAK 465 Lambda K H 0.319 0.139 0.405 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: 496 Number of extensions: 34 Number of successful extensions: 6 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: 393 Length of database: 467 Length adjustment: 32 Effective length of query: 361 Effective length of database: 435 Effective search space: 157035 Effective search space used: 157035 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 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