Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Pedo557:CA265_RS15205 Length = 378 Score = 228 bits (580), Expect = 3e-64 Identities = 140/386 (36%), Positives = 215/386 (55%), Gaps = 38/386 (9%) Query: 21 LALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRALYSDN 80 L + +G ++D ++ +ID I+G V N GHCHP ++KA+QEQ++ T + +Y + Sbjct: 2 LEFVRAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAE--TYMHLMVYGEY 59 Query: 81 LGKWEEKICKLANKENVLP--------MNTGTEAVETAIKMARKWGADIKNIDESSSEII 132 + + K ++LP +N+GTEAVE A+K+A+++ I Sbjct: 60 VQTPQVNFAKAL--ADILPESLSCTYFLNSGTEAVEGAMKLAKRY--------TGRKGFI 109 Query: 133 AMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPI 192 A +HG T G+ SL D Y G+GP L ++ + + ++ L+K I N+ A+ +EPI Sbjct: 110 ACKNAYHGSTQGAESLMESDFYSSGYGPFLPHVSFIEHNNLADLEK-ITNEIAAVFIEPI 168 Query: 193 QGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGK 252 QGE G+ + ++Q +R C E LLI DEIQ G GR+GKMFA E N PD+ LL K Sbjct: 169 QGEAGIRVSDLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAK 228 Query: 253 SLGGGLYPISAVLANQDVMSVLTPGT---HGSTFGGNPLACAVSMAALDVLNEEHLVQNA 309 +GGG+ PI A +++ ++MSVL+ H +TFGG+P+ CA +A L L ++H+V Sbjct: 229 GIGGGM-PIGAFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEV 287 Query: 310 LDLGDRLLKHLQQIESELIVEVRGRGLFIGI-----ELNVAAQDYCEQMINKGVLCKETQ 364 + G +L K L ++ I E+RG+GL + + E+N D C I GVL Sbjct: 288 EEKG-QLFKQL--LQHPAIKEIRGKGLMLAVEFENFEINKKIIDAC---ILDGVLSDWFL 341 Query: 365 --GNIIRIAPPLVIDKDEIDEVIRVI 388 N +RIAPPL+I K+EI E +I Sbjct: 342 HCSNSMRIAPPLIITKEEIAEACTII 367 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: 327 Number of extensions: 17 Number of successful extensions: 8 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: 378 Length adjustment: 30 Effective length of query: 364 Effective length of database: 348 Effective search space: 126672 Effective search space used: 126672 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