Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 204 bits (520), Expect = 3e-57 Identities = 125/383 (32%), Positives = 212/383 (55%), Gaps = 28/383 (7%) Query: 21 LALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRALYSDN 80 + + K G+ VWD D Y+D G +V++ GH +P + L +Q ++ S ++ Sbjct: 12 IEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGFYSNSVKIPL 71 Query: 81 LGKWEEKICKLANKEN--VLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMNGNF 138 + EK+ +++ K++ + N+G EA E A+K+A + K +IA G F Sbjct: 72 QVQLAEKLGEVSGKKDFQLFLCNSGAEANENALKLASFYNGRKK--------VIAFTGAF 123 Query: 139 HGRTLGSLSLSSQDSYKKGFGPL--LNNIHYADFGD---IEQLKKLINNQTTAIILEPIQ 193 HGRT SL+++ D+ K P+ N+ + F + +E+ K N+ +A+I+E IQ Sbjct: 124 HGRT--SLAVAVTDN-PKIVAPVNQTENVIFLPFNNEIALEETFKAQGNEISAVIIEGIQ 180 Query: 194 GEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKS 253 G GG+ F+Q++R LC+EYN + IAD +Q G GRTG ++ ++ E D+Y + K Sbjct: 181 GVGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKG 240 Query: 254 LGGGLYPISAVLANQDVMSVLTP--GTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALD 311 +G G +P++ + + S P G G+TFGGN LACA ++A L+V+ +++L++NA + Sbjct: 241 MGNG-FPVAGI----SIASKFKPWHGELGTTFGGNHLACAAALAVLEVMEKDNLIKNAEE 295 Query: 312 LGDRLLKHLQQIESELIVEVRGRGLFIGIELNV-AAQDYCEQMINKGVLCKETQGNIIRI 370 +G+ L+ L++ E +VEVRGRGL IGIEL A E + + E + N+IR+ Sbjct: 296 VGNYLIAELKKFEQ--VVEVRGRGLMIGIELPAELAHVKKELLFTHHIFTGEAKPNVIRL 353 Query: 371 APPLVIDKDEIDEVIRVITEVLE 393 P L + K DE + + ++ Sbjct: 354 LPALNLTKAHADEFLAAFEKAVK 376 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: 363 Number of extensions: 14 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: 382 Length adjustment: 30 Effective length of query: 364 Effective length of database: 352 Effective search space: 128128 Effective search space used: 128128 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