Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_011952251.1 SWIT_RS07135 acetylornithine transaminase
Query= curated2:C3P3K3 (396 letters) >NCBI__GCF_000016765.1:WP_011952251.1 Length = 396 Score = 238 bits (608), Expect = 2e-67 Identities = 141/372 (37%), Positives = 205/372 (55%), Gaps = 9/372 (2%) Query: 28 KAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRAFHSDQLGPW 87 + EG ++ G RY+D S + GH HP ++ A+ DQA + TS + S Q + Sbjct: 19 RGEGCYLIGERGERYLDFASGIAVNILGHGHPDLVKAIADQAATLMHTSNLYGSPQGEAF 78 Query: 88 YEKVAKLTNKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCEDNFHGRTMG 147 +K+ T + V N+GAEAVE AIKTARR+ Y E R +II + FHGRT+G Sbjct: 79 AQKLVDKTFADTVFFTNSGAEAVECAIKTARRYHYVNGSPE--RTKIISFSNAFHGRTLG 136 Query: 148 AVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITPNTAAFILEPIQGEAGINIPPAG 207 +S +S + + GF P+LPG V+P+ DLEA +AA+ TA F++EP+QGE G+ Sbjct: 137 TISATSQPKMRDGFEPLLPGFQVVPFNDLEAARAAVDATTAGFLVEPVQGEGGMTPSKPE 196 Query: 208 FLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALGGGVFPISCA 267 FLK ++C ++ +L + DE+Q G RTG FA + +TPD+ + K + GG FP+ Sbjct: 197 FLKGLRQICDEQGLLLILDEVQCGYCRTGTFFAHEQYGITPDIMAVAKGIAGG-FPLGAC 255 Query: 268 AANRDILGVFEPGSHGSTFGGNPLACAVSIAALEVLEEEKLTERSLQLGEKL---VGQLK 324 A + G+HGST+GGNPLA A A +V ++ G++L + QL Sbjct: 256 LATEEAAKGMVFGTHGSTYGGNPLAMAAGEAVFKVAVNDEFLANVRATGDRLRQAIEQLI 315 Query: 325 EIDNPMITEVRGKGLFIGIELNE--PARPYCEQLK-AAGLLCKETHENVIRIAPPLVISE 381 + + VRG GL IGI+L + AR + L+ GLL ENV+RI PPLVI E Sbjct: 316 PNHDGVFDSVRGLGLMIGIKLKDAVEARAFVAHLRDHHGLLTVAAGENVVRILPPLVIEE 375 Query: 382 EDLEWAFQKIKA 393 + +K+ A Sbjct: 376 SHIAECIEKLSA 387 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: 396 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: 396 Length of database: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 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 10 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