Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012676480.1 PERMA_RS05260 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000021565.1:WP_012676480.1 Length = 428 Score = 165 bits (417), Expect = 3e-45 Identities = 124/343 (36%), Positives = 173/343 (50%), Gaps = 25/343 (7%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78 P+ + G+G+RVWD +GNEYID V +LGH + +V A+K+ S E Sbjct: 35 PLFIQKGKGSRVWDVDGNEYIDYVLSWGPLILGHANDQIVNAIKQVAN--YGTSFGAPTE 92 Query: 79 PQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGGFHGRTMGA 138 + E A+ + +A P + V F NSGTE+ AI+LAR +TG K + FEG +HG Sbjct: 93 LEIEMAKAVVDAVPS-IEMVRFVNSGTEATMSAIRLARGYTGKKKIVKFEGCYHGHVDSL 151 Query: 139 L--SATWKPEFREPFEPLVPE-FEHV----PYGDVNAVEKAID---DDTAAVIVEPVQGE 188 L + + P P +PE F ++ PY +++AVE+ DD A VI+EPV G Sbjct: 152 LVSAGSGVATLSIPGTPGIPEEFANLTIVLPYNNIDAVEETFKKHGDDIACVIIEPVAGN 211 Query: 189 AGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGLG 248 GV P + + + LRE+ E+G LLI DEV +G R A E + PD+ L K +G Sbjct: 212 MGVVAPSKEYHQRLREITKEYGALLIWDEVMTGF-RLAYGGAQELYGIEPDLTTLGKVIG 270 Query: 249 GGVPVGATIAREEVAEAFEPGD---HGSTFGGNPLACAAVCAAVSTVLEENLPEAAERKG 305 GG+PVGA + E+ E P T GNPLA A + + E+N +RKG Sbjct: 271 GGLPVGAYGGKREIMEYVAPVGPVYQAGTLSGNPLAMAGGLRQLQILKEKNPYPDLDRKG 330 Query: 306 KL---AMRILSEAEDVVEEVRGRGLMMGV-----EVGDDERAK 340 K +R LSE + V G M+ EV D E AK Sbjct: 331 KKLEEGLRYLSEKYGIPATVNRVGSMITAFFTDKEVVDFETAK 373 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: 394 Number of extensions: 20 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: 428 Length adjustment: 31 Effective length of query: 358 Effective length of database: 397 Effective search space: 142126 Effective search space used: 142126 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