Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_092344171.1 BLU87_RS01565 aspartate aminotransferase family protein
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_900107645.1:WP_092344171.1 Length = 460 Score = 219 bits (559), Expect = 9e-62 Identities = 144/406 (35%), Positives = 221/406 (54%), Gaps = 40/406 (9%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78 P+ + G+GA + D +GN YID+ +G V LGH HP V++A E +E + H ++ + Sbjct: 49 PMAMAKGKGATIEDVDGNIYIDMFSGAGVMALGHSHPDVLKASHEAIEDITHTLDIP-SP 107 Query: 79 PQAEAARLLAEAAPKDLNKVFFCN-SGTESVECAIKLARKFTGCTKFIAFEGGFHGRTMG 137 + + + + PK+L +VFF +G+++VE AIKLA+ TG IAFEG +HG T Sbjct: 108 IRQRMVKSMKKILPKELTRVFFGGPTGSDAVEQAIKLAKFNTGRYGVIAFEGSYHGMTGM 167 Query: 138 ALSATWKPEFREPFEPLVPEFEHVPYG-----------------DVNAVEKAIDDD---- 176 AL+ T R+ PL P + +PY +E+ + D Sbjct: 168 ALALTCDAHHRQGLGPLSPGVQFLPYPYEYRNPFGCPDEDLQLQAAENLERVLSDSHSGY 227 Query: 177 --TAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHE 234 AAVI+E VQGE G IP FL+ +RE+C +H +++I DE+Q+G+GRTG+ FAFEH Sbjct: 228 LKPAAVILESVQGEGGTIIPAPIFLQRVREICTKHDIVMICDEIQAGLGRTGKMFAFEHA 287 Query: 235 DVLPDIVCLAKGLGG-GVPVGATIAREEVAEAFEPGDHGSTFGGNPLACAAVCAAVSTVL 293 ++PDIV ++K LGG G P+ A REE+ + G TF GN +A AA AA+ + Sbjct: 288 GIVPDIVTMSKALGGIGFPISAIAYREEL-NTWPTGLTIGTFRGNMIAFAAGSAALEWMQ 346 Query: 294 EENLPEAAERKGKLAMRILSEAE---DVVEEVRGRGLMMGVEVGDDERAKDVAREMLD-- 348 + + E A G+ M L E E +V E RG G+M+ +E+ D+ +++ A + Sbjct: 347 DNGVIEHAAGLGEKCMVKLKELEAQSAIVGESRGLGMMLAIEMVKDKESREPAGDYAKLV 406 Query: 349 ------RGALVNVTS--GDVIRLVPPLVIGEDELEKALAELADALR 386 RG ++ V G+V RL+PPL+I ED K + +A ++ Sbjct: 407 RKHAHLRGVMIEVGGHHGNVARLLPPLIITEDLAMKGIEIIAGVIK 452 Lambda K H 0.318 0.137 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: 446 Number of extensions: 31 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: 389 Length of database: 460 Length adjustment: 32 Effective length of query: 357 Effective length of database: 428 Effective search space: 152796 Effective search space used: 152796 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