Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate YP_002826881.1 NGR_c23690 omega amino acid--pyruvate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000018545.1:YP_002826881.1 Length = 442 Score = 199 bits (505), Expect = 2e-55 Identities = 137/397 (34%), Positives = 203/397 (51%), Gaps = 45/397 (11%) Query: 34 EGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNEPQA-EAARLLAEAAP 92 +G +D AG+ GHC P + EA++EQ L + P+A E A L + AP Sbjct: 44 DGRTVLDGTAGLWCVNAGHCRPKITEAIREQAGELDYAPAFQLGHPKAFELANRLVDIAP 103 Query: 93 KDLNKVFFCNSGTESVECAIKLARKFTGCT------KFIAFEGGFHGRTMGALSATWKPE 146 + LN V + NSG+ESV+ A+K+A + + I E G+HG G +S Sbjct: 104 EGLNHVLYTNSGSESVDTALKVALAYHRAKGNGSRFRLIGRERGYHGVNFGGISVGGIVA 163 Query: 147 FREPFEPLVPEFEHVPYGDVNA------------------VEKAI---DDDT-AAVIVEP 184 R+ F L+ +H+P+ + A +E+ + D T AAVIVEP Sbjct: 164 NRKMFGTLLTGVDHLPHTHLPARNAFTRGEPEHGADLATELERIVTLHDASTIAAVIVEP 223 Query: 185 VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLA 244 V G GV IPP+G+L++LRE+C +HG+LLI DEV +G GR G FA ++ DV PDI+ A Sbjct: 224 VAGSTGVLIPPKGYLQKLREICTKHGILLIFDEVITGFGRLGTPFAAQYFDVKPDIITTA 283 Query: 245 KGLGGGV-PVGATIAREEVAEAFEPGD-------HGSTFGGNPLACAAVCAAVSTVLEEN 296 KG+ GV P+GA E+ +AF G HG T+ GNP+A AA + T EE Sbjct: 284 KGITNGVIPMGAVFVTSEIHDAFMSGPEHLIEFFHGYTYSGNPIASAAALGTLDTYKEEG 343 Query: 297 LPEAAERKGKLAMRILSEAEDV--VEEVRGRGLMMGVEV-----GDDERAKDVAREMLDR 349 L A L +D V ++R GL+ VE+ +RA + ++ Sbjct: 344 LLTRAAELASYWEEGLHSLKDCPQVIDIRNIGLIGAVELEPIAGEPTKRAFSAFLKAYEK 403 Query: 350 GALVNVTSGDVIRLVPPLVIGEDELEKALAELADALR 386 G L+ T+GD+I L PPL+I + ++++ +L D L+ Sbjct: 404 GLLIR-TTGDIIALSPPLIIEKSQIDELFDKLRDVLK 439 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: 391 Number of extensions: 18 Number of successful extensions: 7 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: 442 Length adjustment: 31 Effective length of query: 358 Effective length of database: 411 Effective search space: 147138 Effective search space used: 147138 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