Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_012589872.1 MSIL_RS04290 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000021745.1:WP_012589872.1 Length = 400 Score = 456 bits (1172), Expect = e-133 Identities = 229/384 (59%), Positives = 273/384 (71%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 ++PTYARA + F+ GEG +L ATDG R+LDF G+AV LG+++P+LVEAL AQ KLWH Sbjct: 5 LLPTYARAHLAFDHGEGAWLTATDGERYLDFGGGIAVASLGYSHPHLVEALIAQGRKLWH 64 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSNLF + E LA RL EA+FAD VFFTNSGAEA E K RKY G + RI+T Sbjct: 65 TSNLFEIPQAERLAARLCEASFADFVFFTNSGAEAVEGAIKTARKYQSVSGHPEKFRIVT 124 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 F+ AFHGRTLA ++A K + GFGP L+GFD V FGDL+AV+ A+ +T + +EPIQ Sbjct: 125 FKGAFHGRTLATIAAGGNPKYLDGFGPKLEGFDSVEFGDLDAVKAAIGPQTGAVLVEPIQ 184 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GE GIR S EF+RGLR +CD HGLLL DE+QCG+GRTGKLFA+E G+TPD+MA+AKG Sbjct: 185 GEAGIRVASTEFMRGLRALCDAHGLLLVYDEVQCGVGRTGKLFAYELYGVTPDIMAIAKG 244 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 IGGGFPLGA LAT +A GMT GTHG+TYGGNPLAT++GNAVLD VL PGFLDHV +G Sbjct: 245 IGGGFPLGAFLATREAGKGMTVGTHGTTYGGNPLATSIGNAVLDVVLAPGFLDHVATVGA 304 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 L+ L L+ P VRG+GLMLGL V D V A RA +L +PAGDNV RLL Sbjct: 305 RLKQGLLTLIEAYPRSVANVRGEGLMLGLELRAPVADFVAAARAEKILVIPAGDNVARLL 364 Query: 365 PPLNIGEAEVEEAVAILAKTAKEL 388 PPL I EAE E V L L Sbjct: 365 PPLIISEAEAAEGVKRLGAACARL 388 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: 513 Number of extensions: 18 Number of successful extensions: 1 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: 400 Length adjustment: 31 Effective length of query: 358 Effective length of database: 369 Effective search space: 132102 Effective search space used: 132102 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