Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate YP_004144436.1 Mesci_5288 class III aminotransferase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000185905.1:YP_004144436.1 Length = 452 Score = 225 bits (573), Expect = 2e-63 Identities = 149/403 (36%), Positives = 213/403 (52%), Gaps = 40/403 (9%) Query: 11 HMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIH 70 H + S T+ +G + D G ++D G +V+ LG+ HP +V A+K+Q++ L Sbjct: 45 HQSLSSPCLSTIAKAQGIWIEDTAGRRFMDF-HGNSVHHLGYGHPRLVAAIKKQLDELCF 103 Query: 71 CSNLYYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGG 130 + EP E A LA AP +L KV F G++++E A+K+AR TG K ++F Sbjct: 104 APRRFTCEPAVELAEKLAALAPGNLGKVLFTTGGSDAIEVALKIARAATGRFKTVSFWDA 163 Query: 131 FHGRTMGALSATWKPEFREPFE-PLVPEFEHV--------PYG------------DVNAV 169 FHG GA S + FR P++ EHV PYG ++ A Sbjct: 164 FHGAGFGAASVGGEATFRSHISGPMMTGTEHVAPWDGYRCPYGHDSLEASGLACANMIAY 223 Query: 170 EKAIDDDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFF 229 + D AAV+ EP++ A PP GF + +RE CD HG LLI DEV +G+G+TG+FF Sbjct: 224 VLGCEQDVAAVVAEPMR--ATPNPPPPGFWKRVREACDRHGTLLIFDEVPTGLGKTGKFF 281 Query: 230 AFEHEDVLPDIVCLAKGLGGGV-PVGATIARE--EVAEAFEPGDHGSTFGGNPLACAAVC 286 A EH+DV PDIV L K LGGGV P+ A IAR +V F G + T NP+ A Sbjct: 282 AHEHDDVTPDIVVLGKSLGGGVLPIAAIIARRDLDVTGGFAIGHY--THEKNPVTTRAAL 339 Query: 287 AAVSTVLEENLPEAAERKGKL---AMRILSEAEDVVEEVRGRGLMMGVEVGDDERAKDVA 343 + +LEE L E A G+ M+ L V +VRGRGLM+GVE+ +D + A Sbjct: 340 TTIDIILEEGLVERAAELGRHMLGRMQHLMARSPHVGDVRGRGLMVGVELVEDRDTRQPA 399 Query: 344 REM--------LDRGALVNVTSGDVIRLVPPLVIGEDELEKAL 378 R++ L++G ++ G+V+ L PPLVI + +L+ AL Sbjct: 400 RDLAERVFYACLEQGLSFKISQGNVLTLSPPLVISKTDLDGAL 442 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: 454 Number of extensions: 21 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: 389 Length of database: 452 Length adjustment: 32 Effective length of query: 357 Effective length of database: 420 Effective search space: 149940 Effective search space used: 149940 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 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