Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_012336169.1 M446_RS31620 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000019365.1:WP_012336169.1 Length = 397 Score = 488 bits (1256), Expect = e-142 Identities = 242/384 (63%), Positives = 292/384 (76%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 ++PTYARA + FERGEG +L A DG R+LDF AG+AVN LGHA+P+LVEALT QA K+WH Sbjct: 5 LLPTYARAKVSFERGEGAWLVARDGSRYLDFGAGIAVNALGHAHPHLVEALTEQARKVWH 64 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SNLF + E LA+RL +ATFAD VFF+NSGAEA E K+ RKYH G R RI+T Sbjct: 65 VSNLFEIPEGERLAQRLIDATFADVVFFSNSGAEANEAAIKMARKYHAAGGHPERFRIVT 124 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 FE AFHGRTLA ++A Q+K I+GFGP ++GFD VP+GDL+A+ +A+T ETA + +EPIQ Sbjct: 125 FEGAFHGRTLATIAAGGQQKYIEGFGPKVEGFDQVPYGDLDALAHAITPETAALMIEPIQ 184 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GEGG+R S EFLR LR +CD HGLLL +DE+Q GMGRTGKLFAHEW+G+TPD+++ AKG Sbjct: 185 GEGGLRVVSPEFLRTLRGLCDRHGLLLIMDEVQTGMGRTGKLFAHEWSGVTPDILSAAKG 244 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 IGGGFP+GACLAT +AA GM G+HG+T+GGNPLA AVGNAVLD VL PGFL+ V+R G Sbjct: 245 IGGGFPMGACLATREAARGMVVGSHGTTFGGNPLAMAVGNAVLDVVLAPGFLEQVRRTGL 304 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 LL+ RLA L +P V VRG+GLM GL C + A RA LL +PAGDNVVRLL Sbjct: 305 LLKQRLAALKDRHPGVIAEVRGEGLMTGLRCVVPNTEFAAAARAEHLLVIPAGDNVVRLL 364 Query: 365 PPLNIGEAEVEEAVAILAKTAKEL 388 PPL IGEAEV EAV L + L Sbjct: 365 PPLIIGEAEVAEAVNRLEAASSSL 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: 499 Number of extensions: 16 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: 397 Length adjustment: 31 Effective length of query: 358 Effective length of database: 366 Effective search space: 131028 Effective search space used: 131028 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 25 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