Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_000009985.1:WP_083763404.1 Length = 384 Score = 235 bits (599), Expect = 2e-66 Identities = 127/382 (33%), Positives = 210/382 (54%), Gaps = 6/382 (1%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 Y+ LA +G GA ++ + Y+D +G +V GHCHP+++KAL Q+ ++ S Sbjct: 4 YARADLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHTSNL 63 Query: 76 LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMN 135 K+ + + + V N+G EA+E +IKMAR+ N II Sbjct: 64 YRVAGQESVAAKLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGN--PQRYRIICAE 121 Query: 136 GNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGE 195 G FHGRTL +++ Q + +GF P ++ + +G++ L+ I +T AI++EP+QGE Sbjct: 122 GAFHGRTLATVAAGGQKKHLEGFAPAVDGFDHVPYGNLNALRASITEETAAILVEPVQGE 181 Query: 196 GGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLG 255 GG+ +++ +R +E+ +LLI DE+Q G+GRTG +FA E PDI + K LG Sbjct: 182 GGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQAGIAPDIMGVAKGLG 241 Query: 256 GGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDR 315 GG +P+ A LA S + PGTHGSTFGGNPLA AV+ LD++ E +++ + Sbjct: 242 GG-FPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAEPGFLEHVQAMAAL 300 Query: 316 LLKHLQQIESE---LIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRIAP 372 L ++ + ++ EVRG GL +GI+ + + ++ G+L NI+R+ P Sbjct: 301 LRSKVEDTAARFPGVVEEVRGLGLMLGIKPRMPNTEMVARLAEGGLLTVGAGDNIVRLLP 360 Query: 373 PLVIDKDEIDEVIRVITEVLEK 394 PL+I+ ++DE + ++ ++ Sbjct: 361 PLIINDAQVDEAVGILARAFDE 382 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: 329 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: 394 Length of database: 384 Length adjustment: 30 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 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 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