Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_037570915.1 BS73_RS08925 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000744815.1:WP_037570915.1 Length = 395 Score = 273 bits (698), Expect = 6e-78 Identities = 159/379 (41%), Positives = 218/379 (57%), Gaps = 12/379 (3%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M Y I RGEG +++ DG+R+ D AG+AVN LGH +P +V A+T Q + L H Sbjct: 15 LMNNYGTPRIPLARGEGAHVWDADGKRYTDLVAGIAVNALGHGHPAVVGAVTEQINTLGH 74 Query: 65 TSNLFRVAGQESLAKRLTEATFAD-TVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123 SNLF L++RL E VFF NSGAEA E K+ R R ++ Sbjct: 75 VSNLFIAEPPVRLSERLLELFGRPGRVFFCNSGAEANEGAFKIGRL-------TGRRHMV 127 Query: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPI 183 FHGRT+ A+S Q GF PL + VP+GD+EA+R AVT+ETA +EP+ Sbjct: 128 ATTGGFHGRTMGALSLTGQPGKQDGFAPLPGDVEFVPYGDVEALRAAVTEETAFFIVEPV 187 Query: 184 QGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAK 243 QGE G +L REI G LL +DE+Q G+GRTG FAH+ AGI PDV+ +AK Sbjct: 188 QGENGAVPAPDGYLEAAREITRAKGALLVVDEVQTGIGRTGHWFAHQAAGIEPDVVTLAK 247 Query: 244 GIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIG 303 G+GGG P+GA +A AA + G HG+T+GGNP+ A G AVLD + + G LDHV+R+G Sbjct: 248 GLGGGLPIGATVAFGAAAELLQPGQHGTTFGGNPVCCAAGLAVLDTIAQDGLLDHVKRVG 307 Query: 304 GLLQDRLAGLVAENPAVFKGVRGKGLMLGLA-CGPAVGDVVVALRANGLLSVPAGDNVVR 362 L+ +G+ + + VRG GL+LG+ P V A + G L G ++VR Sbjct: 308 ERLR---SGIESIGDPLVARVRGTGLLLGIVLTEPLAPQVQAAAQRAGFLVNATGPDLVR 364 Query: 363 LLPPLNIGEAEVEEAVAIL 381 L+PPL + E + + +A+L Sbjct: 365 LVPPLTLPEVDADAFLAVL 383 Lambda K H 0.321 0.139 0.414 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: 474 Number of extensions: 30 Number of successful extensions: 4 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: 389 Length of database: 395 Length adjustment: 31 Effective length of query: 358 Effective length of database: 364 Effective search space: 130312 Effective search space used: 130312 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