Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_043771338.1 U743_RS05875 acetylornithine/succinylornithine family transaminase
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_000733765.1:WP_043771338.1 Length = 408 Score = 245 bits (625), Expect = 2e-69 Identities = 144/386 (37%), Positives = 202/386 (52%), Gaps = 6/386 (1%) Query: 19 NYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSR 78 NY P V RGEG VW DG +D + S GHCHP+++AA+ EQA L S Sbjct: 21 NYAPADFVPVRGEGARVWTADGRELIDLGGGIAVNSLGHCHPELIAALTEQAGMLWHVSN 80 Query: 79 AFHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVC 138 N E++ A T + + NSGAEA E+A+K R++ G + + EI+ Sbjct: 81 VVTNVPALALAEKLCAETFAERAFFCNSGAEANEAALKLARRYASLKHG--EHKHEIVSF 138 Query: 139 ADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQG 198 +++FHGRTL V P+ HFGP G R +P+ D AA E AI P T A +VEP+QG Sbjct: 139 SNSFHGRTLFTVSVGGQPKYSEHFGPLPGGIRHLPYNDIAAAEAAIGPQTCAVIVEPLQG 198 Query: 199 EAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKAL 258 E GV+ + +R C ++ +LV DE+Q+G+GRTG L A + DV K L Sbjct: 199 EGGVMPADPAFLAALRAACDRHDALLVFDEVQSGVGRTGSLYAYMQTEVTPDVLSTAKGL 258 Query: 259 AGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGA 318 GGF P+ A+L+ E+ L G HG+TFGGNPL CAVA+ + ++ E + ++G Sbjct: 259 GGGF-PIGAMLTTAEIAAYLPAGTHGTTFGGNPLGCAVAKRVLDIITEPDFLHGVQQRGL 317 Query: 319 RLLEGLKDI--RANTVREVRGRGLML-AVELHPEAGRARRYCEALQGKGILAKDTHGHTI 375 + L+D+ R VRG GL+L AV P GRA A Q G+ + Sbjct: 318 AMRAALQDMAARHGIFAGVRGSGLLLGAVTAEPWRGRAGEIVRAGQAAGVWCLVAGPDVV 377 Query: 376 RIAPPLVITSDEVDWALEQFATTLTQ 401 R APPL I E+ L + + L++ Sbjct: 378 RFAPPLNIDEAELQDGLARLDSALSK 403 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: 448 Number of extensions: 17 Number of successful extensions: 4 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: 408 Length adjustment: 31 Effective length of query: 373 Effective length of database: 377 Effective search space: 140621 Effective search space used: 140621 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 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