Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_028950007.1 Q385_RS0101715 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_000619805.1:WP_028950007.1 Length = 388 Score = 251 bits (641), Expect = 2e-71 Identities = 142/397 (35%), Positives = 227/397 (57%), Gaps = 18/397 (4%) Query: 2 LDLYEHTDKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKA 61 ++L E +KY +NY L KG G ++D + Y+D +SG +V G+ HPK+ A Sbjct: 1 MNLIEEANKYLFQNYGRLPYFFEKGEGCYLYDEKGKKYLDMLSGIAVNALGYNHPKLTDA 60 Query: 62 LQEQSQRITMVSRALYSDNLGKWEEKICKLANKEN----VLPMNTGTEAVETAIKMARKW 117 + +Q +I +S Y K + ++ K+ ++ + V N+G E+ E IK+ R++ Sbjct: 61 ICQQVSKIIHISNLFYI----KPQIEVAKILSENSFGGKVFFCNSGAESNEALIKLVRRY 116 Query: 118 GADIKNIDESSSEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLK 177 D K + EII G+FHGRTL +++ ++Q Y +GF PL+ YA F DI +K Sbjct: 117 FYDKK---QDKYEIITFEGSFHGRTLATVTATAQPKYHEGFYPLVGGFKYAKFNDINSVK 173 Query: 178 KLINNQTTAIILEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFA 237 LI ++T AI++E +QGEGGVN FI+++ LC E ++L DE+Q G+GRTGK+FA Sbjct: 174 NLITDKTAAILIELVQGEGGVNPADKEFIKDLYNLCKEKDILFTVDEVQTGIGRTGKLFA 233 Query: 238 MEWENTEPDIYLLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAAL 297 + +PDI L K LGGG+ PI A++A + PGTH STFGGN L S A Sbjct: 234 YQHFEIQPDIISLAKGLGGGV-PIGAIIAKDKIAKSFVPGTHASTFGGNYL----STVAA 288 Query: 298 DVLNEEHLVQNALDLGDRLLKHLQQIESELIVEVRGRGLFIGIEL--NVAAQDYCEQMIN 355 V+ EE L + LD ++ +L++ V+G GL +G++L ++ A++ ++ + Sbjct: 289 KVVLEEVLSEGFLDKVQKVGDYLKESLKVFGYPVKGLGLMVGMDLPKDIPAKEVMKKALE 348 Query: 356 KGVLCKETQGNIIRIAPPLVIDKDEIDEVIRVITEVL 392 KG++ N +R PPL+I + ++DE + ++ EVL Sbjct: 349 KGLIVGTAGENTLRFVPPLIITEKQVDEAVDILKEVL 385 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: 368 Number of extensions: 15 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: 388 Length adjustment: 31 Effective length of query: 363 Effective length of database: 357 Effective search space: 129591 Effective search space used: 129591 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 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