Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_010960134.1 MCA_RS04000 aspartate aminotransferase family protein
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000008325.1:WP_010960134.1 Length = 462 Score = 236 bits (601), Expect = 1e-66 Identities = 144/385 (37%), Positives = 225/385 (58%), Gaps = 33/385 (8%) Query: 23 VPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVE-RLIHCSNLYYNEPQA 81 V +G ++DD+ EY+DL++G V LG HP VV A+K+ ++ +L + + Sbjct: 42 VRAQGPYLYDDQDREYLDLLSGFGVFALGRNHPQVVGALKDVLDAQLPDLVQMDVSLLSG 101 Query: 82 EAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGGFHGRTMGALSA 141 + + + P DL+++F+CNSG E+VE AIK AR T K + E GFHG T+GALS Sbjct: 102 LLSEKILQRCPGDLSRMFYCNSGAEAVEAAIKFARYTTKREKIVYCEHGFHGLTLGALSL 161 Query: 142 TWKPEFREPFEPLVPEFEHVPYGDVNAVEKAI-DDDTAAVIVEPVQGEAGVRIPPEGFLR 200 + FR+ F PL+P + VP+ D+ A+E A+ +D AA IVEP+QG+ GV +P EG+L Sbjct: 162 NGEQVFRDGFGPLLPACKAVPFNDLGALEAALRHNDVAAFIVEPIQGK-GVNLPDEGYLA 220 Query: 201 ELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAR 259 E LC +HG L + DE+Q+G+GRTG+F+A EH V PD++ +AK L GG +PVGA + Sbjct: 221 EAARLCRKHGALFVADEIQTGIGRTGKFWAIEHWGVEPDMILMAKALSGGFIPVGAVAMK 280 Query: 260 EEVAEA-FEPGD----HGSTFGGNPLACAAVCAAVSTVLEENLPEAAERKGK---LAMRI 311 + + EA F D HGSTF N +A AA A + + EE L E A + G+ +R Sbjct: 281 KHIMEAVFNRMDRAVVHGSTFSKNNMAMAAGIATLEVLAEERLVENAAKLGEQIISGIRA 340 Query: 312 LSEAEDVVEEVRGRGLMMGVEVGDDE----RAKDVAREMLDRG--------------ALV 353 +++ +++ VRG+G+M+ VE G + +A E ++G ++ Sbjct: 341 MTDRYELLHAVRGKGMMIAVEFGAPKSFSLKAAWSLLETANKGLFSQMITIPLFKNHRIL 400 Query: 354 NVTSG---DVIRLVPPLVIGEDELE 375 + +G +V++ +PPLVIG+ + + Sbjct: 401 SQVAGHGMNVVKFLPPLVIGQRDAD 425 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: 396 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 389 Length of database: 462 Length adjustment: 32 Effective length of query: 357 Effective length of database: 430 Effective search space: 153510 Effective search space used: 153510 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: 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