Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1332 Length = 398 Score = 263 bits (673), Expect = 5e-75 Identities = 144/397 (36%), Positives = 221/397 (55%), Gaps = 8/397 (2%) Query: 1 MLDLYEHTDKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIK 60 M E + Y + +AL +G+G +VWD+ YID + G +V GH H K++ Sbjct: 1 MTAFIEAASPHVMNTYGRVPIALERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVP 60 Query: 61 ALQEQSQRITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGAD 120 ALQ+Q ++ S + K K+ +L+ +NV N+G EA E A+K+ARK+G D Sbjct: 61 ALQDQIAKLIHTSNYYHVPLQEKLATKLVELSGMQNVFFCNSGLEANEAALKIARKFGVD 120 Query: 121 IKNIDESSSEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLI 180 K I + EI+ FHGR++ ++S + GFGPL+ DIE +K+ Sbjct: 121 -KGI--AKPEIVVYEKAFHGRSIATMSATGNPKIHNGFGPLVEGFVRVPMNDIEAIKQAT 177 Query: 181 --NNQTTAIILEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAM 238 N A+ E IQGEGG+N ++Q++R+LC+E L++ DE+Q G+GRTGK FA Sbjct: 178 EGNPNVVAVFFETIQGEGGINGMRIEYLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAH 237 Query: 239 EWENTEPDIYLLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALD 298 +W PD+ L K LG G+ PI AV+A +VL PG HG+TFGGNPLA + + Sbjct: 238 QWAGIVPDVMPLAKGLGSGV-PIGAVVAGPKAANVLQPGNHGTTFGGNPLAMRAGVETIR 296 Query: 299 VLNEEHLVQNALDLGDRLLKHLQQIESEL--IVEVRGRGLFIGIELNVAAQDYCEQMINK 356 ++ E+ L+ NA +GD L LQ+ L + E+RG+GL +GIELN + Sbjct: 297 IMEEDGLLHNAAQVGDHLRAALQRELGSLPGVKEIRGQGLMLGIELNKPCGALIGRAAEA 356 Query: 357 GVLCKETQGNIIRIAPPLVIDKDEIDEVIRVITEVLE 393 G+L T ++IR+ PPL++ E D ++ ++T +++ Sbjct: 357 GLLLSVTADSVIRLVPPLILTTAEADAIVAILTPLVK 393 Lambda K H 0.317 0.136 0.396 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: 392 Number of extensions: 18 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: 394 Length of database: 398 Length adjustment: 31 Effective length of query: 363 Effective length of database: 367 Effective search space: 133221 Effective search space used: 133221 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