Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_000504245.1:WP_034272173.1 Length = 393 Score = 261 bits (667), Expect = 3e-74 Identities = 152/373 (40%), Positives = 205/373 (54%), Gaps = 17/373 (4%) Query: 19 NYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSR 78 NY + L RG+G V+D DGN YLD + + + GH HP ++ A+ EQ L TS Sbjct: 14 NYGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGHTSN 73 Query: 79 AFHND---QLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEI 135 + N LA +IA L+G KVL NSGAEAVE+AIK R G ++++ Sbjct: 74 LYINPVALSLAETLLDIAGLSG--KVLFCNSGAEAVEAAIKITRLTG---------KSKL 122 Query: 136 IVCADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEP 195 + C FHGRT+G + + P R F P PG +PFGD AALE A+ +T A VEP Sbjct: 123 VACDGGFHGRTMGALSVTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEP 182 Query: 196 IQGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLG 255 + GE GV+ P G+ RE+ TA +LVLDE+QTG+GR G A Q G+ DV L Sbjct: 183 VLGEGGVVPAPDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLA 242 Query: 256 KALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAAR 315 K L GG P+ AV+ + L+PGQHG+TFGGNP+ACA A +R + E+G++++ Sbjct: 243 KGLGGGL-PLGAVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVET 301 Query: 316 QGARLLEGLKDIRANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTI 375 G L G++ + V EVRG GL+ + L A A Q G L I Sbjct: 302 LGKDLAAGVRKLDHPLVSEVRGAGLLQGIGLTKPV--APTVATAAQRAGYLINPVQPDVI 359 Query: 376 RIAPPLVITSDEV 388 R+APPL+IT +V Sbjct: 360 RLAPPLIITERQV 372 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: 436 Number of extensions: 17 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: 404 Length of database: 393 Length adjustment: 31 Effective length of query: 373 Effective length of database: 362 Effective search space: 135026 Effective search space used: 135026 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 Jul 26 2024. The underlying query database was built on Jul 25 2024.
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