Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_019557719.1 F612_RS0110440 aspartate aminotransferase family protein
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_000381085.1:WP_019557719.1 Length = 392 Score = 258 bits (660), Expect = 2e-73 Identities = 150/389 (38%), Positives = 224/389 (57%), Gaps = 18/389 (4%) Query: 18 HNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTS 77 + Y + V +G+G + D++G YLD +S + S GH HP I A+ +Q+ +L TS Sbjct: 7 NTYARLPVTFEKGDGATLQDSEGKMYLDAISGIAVTSLGHAHPFISEAICKQSQQLIHTS 66 Query: 78 RAFHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIV 137 +H + +++ L+G +V NSGAEA E+AIK +K+G++ +G+ + I+V Sbjct: 67 NLYHIKKQQMLADQLIELSGMEQVFFCNSGAEANEAAIKIAKKFGHQ-QGITNPT--IVV 123 Query: 138 CADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNT--VAFLVEP 195 ++FHGRT+ + + +P+ F P GF +PF + AA+E A++ N VA LVEP Sbjct: 124 MENSFHGRTMATLSATGNPKVHEGFQPLVGGFTRVPFDNVAAVE-ALSDNRDIVAILVEP 182 Query: 196 IQGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLG 255 IQGE GV +P GY +R++C ANN +L++DEIQTG+GRTG+ A QHE I DV L Sbjct: 183 IQGEGGVYVPQKGYLKALRKICDANNWLLMIDEIQTGMGRTGQWFAFQHENITPDVLTLA 242 Query: 256 KALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAAR 315 KAL G P+ A ++NN+ L PG HG+TFGGNPLACAV A + VL I A+ Sbjct: 243 KALGNG-VPIGACIANNKATDVLAPGNHGTTFGGNPLACAVGLAVIEVLKTHNYIPAIAK 301 Query: 316 QGARLLEGLKDIRANT--VREVRGRGLMLAVEL-HPEAGRARRYCEALQGKGILAKDTHG 372 +GA LL K + +RG+G M+ ++L P A + E +G+L T G Sbjct: 302 KGALLLNQFKSALTQQPGISSIRGQGYMIGIQLDRPCAELVKMALE----RGLLINVTRG 357 Query: 373 HTIRIAPPLVITSDEVDWALEQFATTLTQ 401 T+R+ P V++ + D + T L+Q Sbjct: 358 DTVRLLPSFVMSQQQTD----ELVTKLSQ 382 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: 384 Number of extensions: 21 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: 392 Length adjustment: 31 Effective length of query: 373 Effective length of database: 361 Effective search space: 134653 Effective search space used: 134653 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 10 2024. The underlying query database was built on Apr 09 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