Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_092482996.1 BM299_RS08235 acetylornithine transaminase
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_900115975.1:WP_092482996.1 Length = 396 Score = 298 bits (764), Expect = 1e-85 Identities = 163/384 (42%), Positives = 225/384 (58%), Gaps = 8/384 (2%) Query: 18 HNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTS 77 H Y IG+ RGEG +WD DG +LD + + S GHCHP ++ A+ EQA RL S Sbjct: 16 HTYGRIGLAPVRGEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVS 75 Query: 78 RAFHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIV 137 ++ + A E + + +V NSGAEA E AIK RKW + G D+ EII Sbjct: 76 NLYYIEPQARLAELLVQNSCCDRVFFCNSGAEANEGAIKLARKWAKKQHGA--DKYEIIT 133 Query: 138 CADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQ 197 +FHGRTL + + P+ + F P PGF+ +PF D ALE+AI P+T A ++EP+Q Sbjct: 134 AEKSFHGRTLAAITATGQPKYQQGFEPLPPGFKYVPFNDPDALERAIGPHTCAVMLEPVQ 193 Query: 198 GEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKA 257 GE GV + Y VRELC N ++LV DE+Q GLGRTG+ LA QH +E D+ L KA Sbjct: 194 GEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEFLAYQHYDVEPDIITLAKA 253 Query: 258 LAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQG 317 L GGF P+ A+L+ V PG H +TFGGNPLACA AAM+ ++ +G+++N G Sbjct: 254 LGGGF-PIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAAMQTMLGDGVMQNCRAVG 312 Query: 318 ARLLEGLKDI--RANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTI 375 A E L+D+ + + ++EVRG GL+L +EL+ G C + KG+L + + + Sbjct: 313 AYFKEKLQDLARKYDFIKEVRGLGLLLGMELNRPGGDIVNRC---REKGLLINCVNNNVL 369 Query: 376 RIAPPLVITSDEVDWALEQFATTL 399 R PPLVI ++EVD ALE L Sbjct: 370 RFTPPLVIGTEEVDRALETVEAVL 393 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: 428 Number of extensions: 23 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: 396 Length adjustment: 31 Effective length of query: 373 Effective length of database: 365 Effective search space: 136145 Effective search space used: 136145 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 09 2024. 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