Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_011780353.1 MVAN_RS15790 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_000015305.1:WP_011780353.1 Length = 408 Score = 229 bits (585), Expect = 8e-65 Identities = 135/385 (35%), Positives = 219/385 (56%), Gaps = 23/385 (5%) Query: 20 KLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR---ITMVSRAL 76 + +A+ RG V + Y+D SG V N GHCHP++++A+Q Q+ R + + R + Sbjct: 30 EFVVAEARGCTVTTADGRSYLDMTSGIGVANVGHCHPRVVEAIQAQAARYAHVNVYGRFV 89 Query: 77 YSDNLGKWEEKICKLANK--ENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAM 134 + + + E++ A + ++G E+ E A+K+ARK + +A Sbjct: 90 VPEQV-ELVERLTGAAGAGFDMAYLTSSGAESTECAMKLARK--------HTGRPKFVAF 140 Query: 135 NGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQG 194 +HGRTLG+LS+S ++ ++ F PLL+ + + + + ++++T A+I+EPIQG Sbjct: 141 ERAYHGRTLGALSVSWREEWRAPFEPLLDEVMFVPYDSLTAAAAAVDDRTAAVIVEPIQG 200 Query: 195 EGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSL 254 EGG+ +P F+ +R+LC+ LLI DE+Q G+GR+G+ FA + + PDI + K++ Sbjct: 201 EGGIRVPSDDFLPGLRELCDATGALLIVDEVQGGMGRSGRWFAHQHTDVRPDIITMAKAV 260 Query: 255 GGGLYPISAVLANQDVMSVLT--PGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDL 312 GGGL P+ AVLA+ ++ + P +H +T GGNP+ACA +AA DV+ + L+ ++ Sbjct: 261 GGGL-PLGAVLASAELFATFVDPPLSHLTTMGGNPVACAAGIAAFDVI-ADGLLDRVVEA 318 Query: 313 GDRLLKHLQQIESE---LIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKE--TQGNI 367 G+ L L + E L+V+VRGRGL+ IEL+V A +M GVL Q Sbjct: 319 GEYLRTGLAALCDEFAGLLVDVRGRGLWCAIELSVDANPVVARMQQLGVLVGSVLNQSGT 378 Query: 368 IRIAPPLVIDKDEIDEVIRVITEVL 392 +RI PPLVI EID + V+ VL Sbjct: 379 VRIMPPLVISDAEIDTFVGVLRTVL 403 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: 366 Number of extensions: 22 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: 408 Length adjustment: 31 Effective length of query: 363 Effective length of database: 377 Effective search space: 136851 Effective search space used: 136851 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 24 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