Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase
Query= curated2:Q8R7C1 (393 letters) >FitnessBrowser__Cola:Echvi_0577 Length = 413 Score = 272 bits (696), Expect = 1e-77 Identities = 149/401 (37%), Positives = 223/401 (55%), Gaps = 10/401 (2%) Query: 2 ITYEKKYLMDTYNRYPIMLVKGEGTRVWDSEGNAYLDFVAGIAVNSLGHCHPALVEAIKK 61 I E K+ Y+ P++L +GEG +WD EG Y DF++ + + GHCHP +++ + Sbjct: 12 IELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLID 71 Query: 62 QAETLIHCSNLYWNEKQIELARMISENSFGGKVFFANSGAEANEGAIKLARKYASLKYG- 120 QA TL S + N+ + ++E KV N+GAE E AIK+ARK+ K G Sbjct: 72 QAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGYEKKGI 131 Query: 121 -GKRYKIITAKNSFHGRTFGALTATGQEKYHKGFGPLLAGFKYVPLNDIEALYEAVDD-- 177 II AKN+FHGRT ++ + E K FGP GF +P +DI+AL + + Sbjct: 132 PENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSK 191 Query: 178 EVCAIMLEVIQGEGGIHEATPEYVKAVRKICDENDLLFILDEVQTGIGRTGKLFGYEHYG 237 + ++E IQGE G++ Y+K V +C ++ +LF+ DE+QTGI RTGKL +H G Sbjct: 192 NIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEG 251 Query: 238 VVPDIMTLAKGLGGGF-PIGAIVAKED-KAVFKPGDHASTFGGNPLACAAGIAVLNEVTK 295 V PD++ L K + GGF P+ A++A + V +PG H STFGGNPL + LN V Sbjct: 252 VKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMTALNVVKD 311 Query: 296 DGFLEGVDKKGKYFREGLETLQKKHKVVKEIRGKGLM----VGCEVDLEDASEIVLKALE 351 + E DK GK FRE ++ L K +V+ +RGKGL+ + D + A + L E Sbjct: 312 EKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVINDTEDSDTAWRLCLALKE 371 Query: 352 KGLLINSVSHNVLRFVPPLIVTEEEIDEALQILDDVLSEIR 392 GLL N++RF PPL++TEE++ + I++ + + Sbjct: 372 NGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNFK 412 Lambda K H 0.319 0.139 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: 495 Number of extensions: 25 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: 393 Length of database: 413 Length adjustment: 31 Effective length of query: 362 Effective length of database: 382 Effective search space: 138284 Effective search space used: 138284 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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