Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Marino:GFF3099 Length = 404 Score = 257 bits (656), Expect = 5e-73 Identities = 141/393 (35%), Positives = 227/393 (57%), Gaps = 10/393 (2%) Query: 9 DKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR 68 D+ NY+P + +G G+++WD E +ID G +V GH HP ++ AL +Q+++ Sbjct: 12 DEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEK 71 Query: 69 ITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESS 128 I +S + ++ + + +C L E V N+G EA E A K+AR++ + + + Sbjct: 72 IWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWE--HHGKEK 129 Query: 129 SEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTT-AI 187 +EII+ +FHGRTL ++S+ Q Y +GF P IH+A+F D+E +KKLI+ + T AI Sbjct: 130 NEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAI 189 Query: 188 ILEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDI 247 ++EPIQGEGGV F+Q +R LC+E + LL+ DE+Q G+GR+G +A + PDI Sbjct: 190 VVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPDI 249 Query: 248 YLLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQ 307 K LGGG +P++A+L V + L GTHGST+GGN LACAV+ +D +++ +++ Sbjct: 250 LSSAKGLGGG-FPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILK 308 Query: 308 NALDLGDRLLKHLQQIESE--LIVEVRGRGLFIGIELNV----AAQDYCEQMINKGVLCK 361 D+L K + I + EVRG GL +G L A+D+ + +GV+ Sbjct: 309 GVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVL 368 Query: 362 ETQGNIIRIAPPLVIDKDEIDEVIRVITEVLEK 394 N+IR+AP L+I + +I+ + ++K Sbjct: 369 VAGANVIRLAPSLIIPEPDIELALERFEAAVKK 401 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: 374 Number of extensions: 15 Number of successful extensions: 6 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: 404 Length adjustment: 31 Effective length of query: 363 Effective length of database: 373 Effective search space: 135399 Effective search space used: 135399 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 Sep 17 2021. The underlying query database was built on Sep 17 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