Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Caulo:CCNA_02326 Length = 405 Score = 253 bits (646), Expect = 7e-72 Identities = 144/383 (37%), Positives = 218/383 (56%), Gaps = 8/383 (2%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 Y+ LA +GRGA++ E Y+DC++G + GH HP +++ L+ Q++++ VS Sbjct: 18 YNRAPLAFERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNI 77 Query: 76 LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMN 135 + + +C + + V N+GTEAVE A+K ARK+ + N +I + Sbjct: 78 YRIPEQEELADALCANSFADVVFFTNSGTEAVECALKTARKYHS--ANGQPERIDIYGFD 135 Query: 136 GNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTA-IILEPIQG 194 G+FHGRT +++ S SY GFGP L FGD + +K I + TTA II+EP+QG Sbjct: 136 GSFHGRTYAAVNASGNPSYVDGFGPRLPGYSQLTFGDHDAIKAAIASPTTAAIIVEPVQG 195 Query: 195 EGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEW-ENTEPDIYLLGKS 253 EGG PT + +RQLC+E+ VLLI DE+Q G+GRTGK+FA EW E EP I + K+ Sbjct: 196 EGGARSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLFAYEWAEGGEPHIMAVAKA 255 Query: 254 LGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLG 313 LGGG +PI A LA + +T HGSTFGGNPLA AV AAL+++ + N + Sbjct: 256 LGGG-FPIGACLATTEAAKGMTVAAHGSTFGGNPLAMAVGKAALEIIKSPETLDNVKTVS 314 Query: 314 DRLLKHLQQIES---ELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRI 370 + L ++ ++IV+VRG+G+ IG++L +D+ ++ +L N +R+ Sbjct: 315 GFFTQQLNGLKDRFPDVIVDVRGKGMLIGVKLIPNNRDFMVLARDEKLLIAGGGDNCVRL 374 Query: 371 APPLVIDKDEIDEVIRVITEVLE 393 PPL + +E E I + + E Sbjct: 375 LPPLNLTIEEASEAIAKLEKACE 397 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: 369 Number of extensions: 23 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: 394 Length of database: 405 Length adjustment: 31 Effective length of query: 363 Effective length of database: 374 Effective search space: 135762 Effective search space used: 135762 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