Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate GFF5065 PS417_25950 acetylornithine aminotransferase
Query= curated2:Q89RB7 (404 letters) >FitnessBrowser__WCS417:GFF5065 Length = 420 Score = 211 bits (537), Expect = 3e-59 Identities = 133/378 (35%), Positives = 191/378 (50%), Gaps = 11/378 (2%) Query: 26 VLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQL 85 V RG+G W+WD+D YLD +A S GH ++ A+ +Q L HN Sbjct: 38 VFVRGQGSWLWDSDDRAYLDFSQGNAANSLGHSPQVLIKALADQTQALINPGNGLHNRAQ 97 Query: 86 APFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFHGR 145 E + TGS + +NSGAEAVE+AIK RKWG +G II + HGR Sbjct: 98 LNLAERLCHRTGSDQAYLLNSGAEAVEAAIKLARKWGQLHRG---GAYRIISASAGSHGR 154 Query: 146 TLGIVGFSTD-PETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVII 204 + + S PE R F P PGF +PF D +AL A+ TVA L+EPIQGEAGVI Sbjct: 155 SFAAMSASAGGPENR--FEPQLPGFSHVPFNDLSALHAAVDAQTVAILLEPIQGEAGVIP 212 Query: 205 PPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGGFYP 264 Y V LC ++L+LDE+QTG+GR G LLAEQ G+ AD+ LGK L GG P Sbjct: 213 ATEHYLKGVERLCRELGILLILDEVQTGIGRCGTLLAEQQYGVRADIITLGKGLGGG-VP 271 Query: 265 VSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGL 324 ++A+L+ + G+ T GN L + A + ++E G +++ G L EGL Sbjct: 272 LAALLARGKAC-CFEVGELEGTHHGNALMASAGLAVLEAVLEHGFMDHVRESGLYLGEGL 330 Query: 325 KDIRANTVR-EVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIAPPLVI 383 + ++RG GLM + L ++ A +A +G++ + +R P L + Sbjct: 331 ARLAYRYDHGQLRGHGLMWGLTLSDDSADA--VVKAALHEGLIINAPQPNCLRFTPALTV 388 Query: 384 TSDEVDWALEQFATTLTQ 401 + +D L + A ++ Sbjct: 389 SKSNIDEMLLRLARAFSR 406 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: 442 Number of extensions: 16 Number of successful extensions: 3 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: 420 Length adjustment: 31 Effective length of query: 373 Effective length of database: 389 Effective search space: 145097 Effective search space used: 145097 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 Aug 03 2021. The underlying query database was built on Aug 03 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