Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_012282524.1 HM1_RS06545 acetylornithine transaminase
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_000019165.1:WP_012282524.1 Length = 432 Score = 291 bits (744), Expect = 3e-83 Identities = 154/390 (39%), Positives = 233/390 (59%), Gaps = 15/390 (3%) Query: 10 KYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRI 69 KY Y L ++L KG+GA++WD + Y+D ++G +V + GHCHPK++ ALQ+Q+ + Sbjct: 12 KYVMNTYGRLPISLVKGQGARLWDADGREYLDFLAGLAVNSLGHCHPKVVDALQQQAATL 71 Query: 70 TMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARK-----WGADIKNI 124 VS + + + + + + + + V N+G EA E AIK+ARK WG+D Sbjct: 72 LHVSNLYWIEPQVQLAQVLVENSFADKVFFCNSGAEANEGAIKLARKYAKKTWGSD---- 127 Query: 125 DESSSEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQT 184 EII M +FHGRTL +++ ++Q Y+K + PL Y FGD++ L++ I+ T Sbjct: 128 ---KYEIITMEKSFHGRTLATVTATAQPKYQKDYEPLPQGFRYVPFGDLKALERAISPHT 184 Query: 185 TAIILEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTE 244 AI++EP+QGEGGVN+ F Q + +L +LLI DE+Q GLGRTGK+FA E Sbjct: 185 CAILVEPVQGEGGVNLAEPSFWQGLAKLAAANKLLLIFDEVQCGLGRTGKLFAHEHYGVT 244 Query: 245 PDIYLLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEH 304 P I L K+L GG P+ A+LA DV + PG H STFGGNPL A ++A +DVL + Sbjct: 245 PHIMTLAKALAGGA-PMGALLATDDVANAFQPGDHASTFGGNPLVAAAAVAVMDVLLNDG 303 Query: 305 LVQNALDLGDRLLKHLQQIESE--LIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKE 362 L+ N ++ + HL++++ + I EVRG GL + EL+ D + KG++ Sbjct: 304 LMDNCREMAAYFMGHLRRLQEKYPFITEVRGLGLMVACELDRPGADIVANCLEKGLIINC 363 Query: 363 TQGNIIRIAPPLVIDKDEIDEVIRVITEVL 392 T GN++R PPL+I+K ++DE + V+ EVL Sbjct: 364 TAGNVLRFLPPLIINKADVDEAVAVLEEVL 393 Lambda K H 0.317 0.136 0.396 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: 410 Number of extensions: 14 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: 394 Length of database: 432 Length adjustment: 31 Effective length of query: 363 Effective length of database: 401 Effective search space: 145563 Effective search space used: 145563 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 (21.6 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