Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_013840422.1 DESRU_RS01825 acetylornithine transaminase
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_000215085.1:WP_013840422.1 Length = 399 Score = 295 bits (756), Expect = 1e-84 Identities = 166/377 (44%), Positives = 221/377 (58%), Gaps = 8/377 (2%) Query: 18 HNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTS 77 + Y + + L +GEG WVWD DG +YLD + + S GH HPK+ A+ QA L S Sbjct: 16 NTYGRLPMALVKGEGPWVWDADGRKYLDFVGGLAVNSLGHAHPKVAEAISRQAATLLHCS 75 Query: 78 RAFHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIV 137 + + + + + + K NSGAEA E AIK RK Y K + +Q E+I Sbjct: 76 NIYWIEPQVKLAKLLVENSCASKAFFCNSGAEANEGAIKLARK--YAKKNLGPNQYEVIS 133 Query: 138 CADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQ 197 ++FHGRTL V + + + F P PGFR +PF D AALE+ I P T A ++EP+Q Sbjct: 134 ATNSFHGRTLATVTATGQTKYQKGFEPLPPGFRHVPFNDLAALEENIRPQTCAVMLEPVQ 193 Query: 198 GEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKA 257 GE GVI GY V +LC ++L+ DE+Q GLGRTGK LA QH G+E D+ L KA Sbjct: 194 GEGGVIPADPGYLAGVAQLCRDKGLLLIFDEVQCGLGRTGKFLAHQHYGVEPDIITLAKA 253 Query: 258 LAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQG 317 L GGF P+ A+L+ EV G +PG H STFGGNPLA A A AAM L+++G+ ENAA+ G Sbjct: 254 LGGGF-PIGALLAKEEVAGAFQPGDHASTFGGNPLATAAALAAMEALLQDGVQENAAKVG 312 Query: 318 ARLLEGLKDIRA--NTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTI 375 E L + A + VREVRG GLML +EL E C +G+L T+G+ + Sbjct: 313 QYFKEKLSGLTAKHSFVREVRGLGLMLGLELSIEGKDIVAKC---LEQGLLINCTNGNVL 369 Query: 376 RIAPPLVITSDEVDWAL 392 R PPL+IT ++VD AL Sbjct: 370 RFLPPLIITEEDVDHAL 386 Lambda K H 0.319 0.136 0.405 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: 437 Number of extensions: 24 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: 404 Length of database: 399 Length adjustment: 31 Effective length of query: 373 Effective length of database: 368 Effective search space: 137264 Effective search space used: 137264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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