Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_043795594.1 ALVIN_RS09555 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000025485.1:WP_043795594.1 Length = 392 Score = 326 bits (836), Expect = 6e-94 Identities = 180/379 (47%), Positives = 241/379 (63%), Gaps = 4/379 (1%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M TY R + F+RGEG +L+ T+G+R+LD +G+AV LGHA+P + +AL QA +L H Sbjct: 5 LMATYNRLPVTFDRGEGVWLWDTNGKRYLDALSGIAVCGLGHAHPAVRDALCEQAGRLIH 64 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSN++ VA QE L LTE D VFF NSGAEA E KL R + + +G + I+ Sbjct: 65 TSNIYGVAEQERLGALLTEQAGMDRVFFANSGAEANEAAIKLARLHAHRRGIE-NPAILV 123 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDET--AGICLEP 182 E +FHGRTLA +SA K+ GF PL+ GF VP+ DL+A+ A T+ I +EP Sbjct: 124 AEHSFHGRTLATLSATGNRKVQAGFEPLVQGFVRVPYDDLDAIETAATNRPNIVAILIEP 183 Query: 183 IQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVA 242 IQGEGGIR S ++L LREICD G LL LDEIQ GMGRTG+LFA + AGI PDV+ +A Sbjct: 184 IQGEGGIRLPSDDYLVRLREICDRSGWLLMLDEIQTGMGRTGRLFAFQHAGIQPDVVTLA 243 Query: 243 KGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRI 302 KG+G G P+GACLA AA + G+HGST+GGNPLA VG AVL+ +++ ++ Sbjct: 244 KGLGNGMPIGACLARGAAAEVFSPGSHGSTFGGNPLACRVGRAVLETLIDENLTENAAAQ 303 Query: 303 GGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVR 362 G L D L + E + + +RG+GLM+G+ G++V GLL + V+R Sbjct: 304 GAYLLDSLRAALGETHGLVE-IRGRGLMVGIELDRPCGELVGRALDAGLLINVTAERVIR 362 Query: 363 LLPPLNIGEAEVEEAVAIL 381 LLPPL I A+++E VA L Sbjct: 363 LLPPLIIDRAQIDELVATL 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: 480 Number of extensions: 26 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: 392 Length adjustment: 31 Effective length of query: 358 Effective length of database: 361 Effective search space: 129238 Effective search space used: 129238 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