Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013076538.1 BTUS_RS13030 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000092905.1:WP_013076538.1 Length = 450 Score = 205 bits (521), Expect = 2e-57 Identities = 144/410 (35%), Positives = 210/410 (51%), Gaps = 50/410 (12%) Query: 15 YSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL 74 + + PV + GEG + D G Y D V+ + +NV GH P + A+ +Q+ ++ HC+ L Sbjct: 26 FDQEPVIVERGEGVWLEDVRGRRYYDGVSSLWLNVHGHRVPELDRAIADQLGKIAHCTML 85 Query: 75 -YYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCT------KFIAF 127 N P E A L E +P LNKVF+ +SG E+VE AIK+A +F KFI Sbjct: 86 GQLNVPAVELAERLVEISPPGLNKVFYSDSGAEAVEIAIKMAYQFWQHVGHPEKRKFITM 145 Query: 128 EGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPY-----------------GDVNAVE 170 G +HG T+GA+S + + L+ E V Y ++ + Sbjct: 146 TGAYHGDTLGAVSVGAIDLYHRAYGGLLFETVRVLYPYCYRCPLNQEPKTCGFACLDLLR 205 Query: 171 KAID---DDTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTG 226 +A++ +TAA+IVEP +QG AG+ P GFLRE+R+LC +L+I DEV G GRTG Sbjct: 206 QALEAHGGETAALIVEPEMQGAAGMIAMPGGFLREVRDLCTRWDVLMIADEVAVGFGRTG 265 Query: 227 QFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAF--EPGD-----HGSTFGGN 278 + FA EH V PD + KGL GG +PV AT+ + V EAF EP + HG ++ GN Sbjct: 266 KMFACEHTGVSPDFLTCGKGLTGGYLPVAATLTTDRVYEAFLGEPWEEKTFYHGHSYTGN 325 Query: 279 PLACAAVCAAVSTVLEENLPEAAERKGKLAMRILSE--AEDVVEEVRGRGLMMGVEVGDD 336 PL CAA A + E L + + + L E V ++R +G+M+G+E+ D Sbjct: 326 PLGCAAALANLDLFDETQLVDRVRKNEAYLRKRLQELNGHPHVGDIRQKGMMVGIELVAD 385 Query: 337 ERAKD-----------VAREMLDRGALVNVTSGDVIRLVPPLVIGEDELE 375 K+ V R+ D G ++ GDV+ +PPL E +LE Sbjct: 386 RATKEPFPARRLMGAAVCRKARDEGMIIR-PLGDVVVFMPPLATPEGDLE 434 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: 499 Number of extensions: 31 Number of successful extensions: 8 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: 450 Length adjustment: 32 Effective length of query: 357 Effective length of database: 418 Effective search space: 149226 Effective search space used: 149226 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