Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_085122464.1 B9O00_RS09970 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_900177295.1:WP_085122464.1 Length = 389 Score = 271 bits (694), Expect = 2e-77 Identities = 170/378 (44%), Positives = 211/378 (55%), Gaps = 5/378 (1%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M +R VF RGEG +L+ GRR+LDF G AVN LGH L AL QA L + Sbjct: 8 LMTITSRPATVFVRGEGSWLFDGHGRRYLDFVQGWAVNCLGHCPLVLARALCEQAATLIN 67 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 S F A LA+ L A+ D FF NSGAEA E KL RK+ A I+T Sbjct: 68 CSPAFYNAPMVRLAEALKAASGLDRSFFANSGAEANEGAIKLARKWGALHRGGAH-EIVT 126 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 FEQ FHGRTLA +SA+ + F P + GF VP GDL AV A+ +TA + LEPIQ Sbjct: 127 FEQGFHGRTLATMSASGKAAWKGLFEPKVPGFPKVPLGDLAAVEAAIGPDTAAVMLEPIQ 186 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GE G+ FL+ LR + G+LL LDEIQ GMGRTG+LF ++ G TPD++ + KG Sbjct: 187 GEAGVIPAGDGFLKELRALTQAKGVLLILDEIQTGMGRTGRLFHYQHLGFTPDILTLGKG 246 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 +GGG PL A LA E G G T+ GNPL TA G AVL+ V PGFL+ V G Sbjct: 247 LGGGVPLSALLAREDVCC-FEPGDQGGTFNGNPLMTAAGLAVLEAVTAPGFLERVTATGA 305 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVV-ALRANGLLSVPAGDNVVRL 363 L + LA L + F GVRG+GL+L L G VG +V A A GLL +R Sbjct: 306 YLAEGLAALSRRHG--FGGVRGRGLLLALDLGRPVGPALVEAALAEGLLINAPRPECLRF 363 Query: 364 LPPLNIGEAEVEEAVAIL 381 +P L + EV+ +A L Sbjct: 364 MPALTVSREEVDSLLATL 381 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: 483 Number of extensions: 31 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: 389 Length adjustment: 30 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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 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