Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013451594.1 CALNI_RS07435 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000183405.1:WP_013451594.1 Length = 422 Score = 152 bits (383), Expect = 2e-41 Identities = 112/304 (36%), Positives = 159/304 (52%), Gaps = 24/304 (7%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78 P+ + G+G++++D +G EYID V + GH ++ +VER++ + Sbjct: 30 PIFIDRGKGSKIYDVDGKEYIDYVCSWGPLIHGHADDDIIT----EVERVLK-KGTTFGA 84 Query: 79 P---QAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGGFHGRT 135 P + E A+ + E P + V +SGTE+V AI+LAR +TG K I FEG +HG + Sbjct: 85 PTVLELELAKKVVEMVPS-IEMVRMVSSGTEAVMSAIRLARGYTGRDKIIKFEGCYHGHS 143 Query: 136 MGAL--SATWKPEFREPFEPLVPE--FEHV---PYGDVNAVEKAI---DDDTAAVIVEPV 185 L + + F +P P VP +H Y D+N+V++ + A VIVEPV Sbjct: 144 DSLLVKAGSGALTFGQPSSPGVPADLAKHTLIADYNDLNSVKQLFINNKNQIACVIVEPV 203 Query: 186 QGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLAK 245 G GV +P EGFL LR+LC G LLI DEV +G R A E+ +V+PDI L K Sbjct: 204 AGNMGVVLPEEGFLSGLRDLCSNEGALLIFDEVITGF-RLAPGGAQEYFNVMPDITTLGK 262 Query: 246 GLGGGVPVGATIAREEVAEAFEPGD---HGSTFGGNPLACAAVCAAVSTVLEENLPEAAE 302 LGGG+PVGA R+E+ E P T GNPLA AA A ++ L EN Sbjct: 263 ILGGGLPVGAYGGRKEIMEKISPLGPVYQAGTLSGNPLAMAAGIANLNK-LNENFYYELR 321 Query: 303 RKGK 306 +K + Sbjct: 322 KKSQ 325 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: 402 Number of extensions: 20 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: 422 Length adjustment: 31 Effective length of query: 358 Effective length of database: 391 Effective search space: 139978 Effective search space used: 139978 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