Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase
Query= curated2:O66442 (376 letters) >FitnessBrowser__Marino:GFF3915 Length = 422 Score = 186 bits (471), Expect = 1e-51 Identities = 132/400 (33%), Positives = 212/400 (53%), Gaps = 42/400 (10%) Query: 8 YAR-LPVKFVRGKGVYLYDEEGKEYLDFVSGIGVNSLGHAYPKLTEALKEQVE-----KL 61 Y+R PV F R K +LY E+GKEYLDF++G G + GH L +AL E +E + Sbjct: 14 YSRAFPVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQG 73 Query: 62 LHVSNLYENPWQEELAHKLVKHFWTEGKVFFAN-SGTESVEAAIKLARKYWRDKGKNKWK 120 L + ++ + E ++ + K+ F +GT VEAA+KLARK K + Sbjct: 74 LDMFTTAKHDFMESYKKHILDPRGLDYKMQFTGPTGTNCVEAALKLARKV-----KGRSG 128 Query: 121 FISFENSFHGRTYGSLSATGQPKFHKGF--EPL-------VPGFSYAKLNDIDSVYKLLD 171 ISF N FHG T G+++ TG K H+G PL G+ ++ + + KLL Sbjct: 129 IISFTNGFHGVTMGAVATTGN-KHHRGGVGTPLGNVDFMFYDGYLGDDVDTLAIMDKLLS 187 Query: 172 EETAG------IIIEVIQGEGGVNEASEDFLSKLQEICKEKDVLLIIDEVQTGIGRTGEF 225 + ++G +I+E +QGEGG+N ++L L E+CK+ D+LLI+D++Q G GRTGEF Sbjct: 188 DGSSGFELPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEF 247 Query: 226 YAYQHFNLKPDVIALAKGLGG-GVPIGAILAREEVAQSFTPGSHGSTFGGNPLACRAGTV 284 ++++ +KPD++ ++K L G G+P+ +L + E+ + PG H TF GN +A Sbjct: 248 FSFEFAGIKPDIVTVSKSLSGYGLPMALVLFKPEL-DVWDPGEHNGTFRGNNMAFITARA 306 Query: 285 VVDEVEK---LLPHVREVGNYFKEKLKEL-----GKGKVKGRGLMLGLELERE--CKDYV 334 V+ K V+ + L+ + G+ K+KGRGLM G+E + Sbjct: 307 AVENYWKDDAFANEVKAKTEVLGDALQSICDKYPGQFKMKGRGLMRGIEAKHADITGPIT 366 Query: 335 LKALEKGLLINCTA--GKVLRFLPPLIIQKEHIDRAISVL 372 +A E GL+I + +V++ L PL +E + + ++L Sbjct: 367 KRAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALL 406 Lambda K H 0.318 0.139 0.409 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: 354 Number of extensions: 13 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: 376 Length of database: 422 Length adjustment: 31 Effective length of query: 345 Effective length of database: 391 Effective search space: 134895 Effective search space used: 134895 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