Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Caulo:CCNA_00620 Length = 392 Score = 421 bits (1083), Expect = e-122 Identities = 218/382 (57%), Positives = 268/382 (70%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M TYARA+I RGEG +LY DGR +LD AAGVAVN LGH +P LV+AL QA LWH Sbjct: 4 LMNTYARANIDIVRGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWH 63 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SNL+R+ QE+LA +LT+ATFAD VFF NSGAEA E K R++ KG R R++T Sbjct: 64 ASNLYRLPAQEALATKLTDATFADRVFFANSGAEAVEAAIKTARRWQGAKGRPERYRVLT 123 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 F AFHGRTLA +SA Q K+ +GF PL D FD PF D+E A+T +TA I +EPIQ Sbjct: 124 FGNAFHGRTLATISATDQMKVREGFTPLYDAFDTTPFNDIEGAARAITPQTAAILVEPIQ 183 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GEGG+ + FL GLR +CD+H LLL LDE+Q G+GRTG LFAHE G+ PD++AVAKG Sbjct: 184 GEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHELYGVRPDIIAVAKG 243 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 +GGGFP+GACLATE AASGMT G+HGSTYGGNPLA AV +AVLD VL PGFL+ V+ Sbjct: 244 LGGGFPIGACLATEDAASGMTPGSHGSTYGGNPLACAVASAVLDAVLAPGFLETVRERAA 303 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 L+ L L+ + +F +G GLM GL + DVV LR G+++V AG +VVRLL Sbjct: 304 LVDALLERLLRRHSDLFVRAQGHGLMRGLQVRASARDVVAHLRDFGVMTVAAGADVVRLL 363 Query: 365 PPLNIGEAEVEEAVAILAKTAK 386 PPL I E E+ EA A L + A+ Sbjct: 364 PPLTISELEIAEAEARLLRAAE 385 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: 452 Number of extensions: 15 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: 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 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