Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_000204645.1:WP_013518270.1 Length = 398 Score = 249 bits (637), Expect = 8e-71 Identities = 159/394 (40%), Positives = 219/394 (55%), Gaps = 20/394 (5%) Query: 18 HNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTS 77 + Y + + L RG+GV VWD +G +YLD L + + GH HP+++ A+ EQ +L TS Sbjct: 14 NTYGRVPIALERGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPALQEQIAKLIHTS 73 Query: 78 RAFHNDQLAPFYEEIAAL-TGSHKVLPM---NSGAEAVESAIKSVRKWGYEVKGVPDDQA 133 +H P EE+A L TG ++ N+G EA E AIK RK+G + KG+ ++ Sbjct: 74 NYYH----VPGQEELARLLTGRARMTNAFFCNTGLEANECAIKIARKYGVD-KGI--EKP 126 Query: 134 EIIVCADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAI--TPNTVAF 191 EI+V FHGR++ + + +P+ R FGP GF + D AL++A PN VA Sbjct: 127 EIVVYDHAFHGRSIATMTATGNPKVRNGFGPLLEGFIRVAPNDIEALQEATEGNPNVVAV 186 Query: 192 LVEPIQGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADV 251 L+EPIQGE G+ Y +VR+LC AN +L+LDE+Q G+GRTGK A Q GI DV Sbjct: 187 LMEPIQGEGGLHPMRVEYLQQVRKLCDANGWLLMLDEVQAGMGRTGKWFAHQWAGIVPDV 246 Query: 252 TLLGKALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIE 311 L K L G PV AVL++ L+PG HGSTFGGNPLA +R++ EEG+++ Sbjct: 247 MTLAKGLGSG-VPVGAVLAHGAASEVLKPGNHGSTFGGNPLAMRAGVETIRIMEEEGLLQ 305 Query: 312 NAARQGARLLEGLKDIRANT--VREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKD 369 NAA GA L GL+ + V EVRG+GL++ VEL G + G+L Sbjct: 306 NAADVGAHLKAGLQQALGSVPGVNEVRGQGLIIGVELDRPCG---VLIDRAAQAGLLLSV 362 Query: 370 THGHTIRIAPPLVITSDEVDWALEQFATTLTQDF 403 T IR+ P L +T E D + T L Q F Sbjct: 363 TADRVIRLVPALTLTRAEAD-EIVALLTPLVQAF 395 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: 469 Number of extensions: 27 Number of successful extensions: 7 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: 398 Length adjustment: 31 Effective length of query: 373 Effective length of database: 367 Effective search space: 136891 Effective search space used: 136891 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