Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_013835847.1 THICY_RS06630 aspartate aminotransferase family protein
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_000214825.1:WP_013835847.1 Length = 390 Score = 256 bits (655), Expect = 6e-73 Identities = 152/371 (40%), Positives = 208/371 (56%), Gaps = 11/371 (2%) Query: 18 HNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTS 77 + Y + V GEG ++D N YLD +S + S GH HP I A+ EQ+ L TS Sbjct: 6 NTYGRLPVTFHYGEGALLYDEQDNAYLDAVSGIAVCSLGHAHPAIAQALCEQSKTLIHTS 65 Query: 78 RAFHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIV 137 +H + +++ A++G KV NSGAEA E+AIK RK+G+ KG+ A+IIV Sbjct: 66 NLYHVAKQQQLGDKLVAISGMDKVFFGNSGAEANEAAIKMARKYGHS-KGI--SHAQIIV 122 Query: 138 CADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAIT--PNTVAFLVEP 195 ++FHGRTL + + + F P GF +PF + A+ AI PN VA LVEP Sbjct: 123 MENSFHGRTLATLSATGSAKVHDGFYPLVEGFVRVPFDNVEAVANAIANNPNVVAILVEP 182 Query: 196 IQGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLG 255 +QGE GV +P GY +R LC ++++L++DEIQ G+GRTGK A QHEGI DV L Sbjct: 183 VQGEGGVHVPKPGYLKALRALCDEHDLLLMIDEIQAGIGRTGKWFAFQHEGILPDVLSLA 242 Query: 256 KALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAAR 315 KAL G P+ A L+ + PG HG+TFGGNPLACA A + L I+ A+ Sbjct: 243 KALGNG-VPIGASLARGKAAELFAPGNHGTTFGGNPLACAAGLAVIETLEYHNYIDLVAK 301 Query: 316 QGARLLEGLKDIRANT--VREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGH 373 QGA LL K AN V ++RG+G M+ ++L G + AL K +L T G Sbjct: 302 QGAELLAAFKTALANIPGVVDIRGKGYMIGIQLDRPCGDLVKM--ALADK-LLINVTRGD 358 Query: 374 TIRIAPPLVIT 384 T+R+ P V+T Sbjct: 359 TVRLLPTFVMT 369 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: 407 Number of extensions: 22 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: 390 Length adjustment: 31 Effective length of query: 373 Effective length of database: 359 Effective search space: 133907 Effective search space used: 133907 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 Apr 09 2024. 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