Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase
Query= curated2:C3P3K3 (396 letters) >FitnessBrowser__PS:Dsui_3250 Length = 390 Score = 261 bits (666), Expect = 3e-74 Identities = 149/383 (38%), Positives = 216/383 (56%), Gaps = 8/383 (2%) Query: 17 NNYHPLPIVISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTS 76 N Y LP+ S EG + D +G Y+D LS + GH HPK++NA+ QA RV TS Sbjct: 6 NTYARLPVAFSHGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARVLHTS 65 Query: 77 RAFHSDQLGPWYEKVAKLTNKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIV 136 + +++A L+ E V N+G EA E AIK AR + + K V+A IIV Sbjct: 66 NLYRIPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQ-KGVDA--PVIIV 122 Query: 137 CEDNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAA--ITPNTAAFILEP 194 E FHGRT+ +S + N + + GF P++ G + +PY DL+A++AA + PN A +LE Sbjct: 123 MEKAFHGRTLATLSATGNRKAQAGFEPLVSGFVRVPYNDLDAIRAAAELNPNVVAVLLEM 182 Query: 195 IQGEAGINIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILG 254 +QGE GI++ F + +C +++ L + DE+Q G+GRTG F + PD+ L Sbjct: 183 VQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHAGILPDVATLA 242 Query: 255 KALGGGVFPISCAAANRDILGVFEPGSHGSTFGGNPLACAVSIAALEVLEEEKLTERSLQ 314 K LG GV PI G+F+PG+HGSTFGGNPLACA ++ + +EEEKL E ++ Sbjct: 243 KGLGSGV-PIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACIEEEKLRENAVA 301 Query: 315 LGEKLVGQLKEIDNPM--ITEVRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHENVIR 372 GE + L E + + E+RGKGL +GIEL+ P + AGLL T E V+R Sbjct: 302 QGEAIRRGLSEALAGVGGLVEIRGKGLMLGIELDRPCGELVAKGLEAGLLINVTAEKVVR 361 Query: 373 IAPPLVISEEDLEWAFQKIKAVL 395 + P L S D + Q++ A++ Sbjct: 362 LLPALTFSAADTQELVQRLAALI 384 Lambda K H 0.317 0.136 0.402 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: 404 Number of extensions: 21 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: 396 Length of database: 390 Length adjustment: 31 Effective length of query: 365 Effective length of database: 359 Effective search space: 131035 Effective search space used: 131035 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