Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_013076222.1 BTUS_RS11380 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000092905.1:WP_013076222.1 Length = 401 Score = 310 bits (795), Expect = 4e-89 Identities = 162/378 (42%), Positives = 224/378 (59%), Gaps = 1/378 (0%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M TY R + RGEG +L+ DG ++LDFAAG+AV +LGH++P + EA+ QA L H Sbjct: 15 LMHTYGRWPVAMVRGEGVWLWDADGNQYLDFAAGIAVTILGHSHPAVAEAIADQARTLLH 74 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SNLF + Q LA L + D VFF NSG EA E KL R++ Y G R+ +IT Sbjct: 75 CSNLFYIPQQVELANWLVNHSALDQVFFCNSGTEASEAAIKLARRWAYHNGVPERSTVIT 134 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 E +FHGRTL A++A Q K +GFGPLL G VP GD++A+ A+ + +E +Q Sbjct: 135 LEHSFHGRTLGALTATAQPKYQEGFGPLLGGVRHVPVGDVKALEEALDGTVCAVMMEMVQ 194 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GEGG+ ++++ +R +CD +LL +DE+Q GMGRTG FA+E G+ PD+ +AKG Sbjct: 195 GEGGVMPVPTDYVQEVRALCDRRNVLLVIDEVQTGMGRTGTFFAYEQFGVEPDICTLAKG 254 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 + G P+GA LA A G+HGST+GGNPLA A ++ V + + R G Sbjct: 255 LANGVPVGAVLAKRPVAEAFVPGSHGSTFGGNPLAMRAALATVEVVEKERLWEKAARRGA 314 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 L+ RLA + +P F+ +RG GLM+G+ V A GLL AG N VRLL Sbjct: 315 YLRGRLANALGNHPH-FREIRGMGLMIGVVLDEGASQVAEACLKRGLLVTVAGGNTVRLL 373 Query: 365 PPLNIGEAEVEEAVAILA 382 PPL + E E++ AV L+ Sbjct: 374 PPLIVEEPEIDMAVERLS 391 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: 421 Number of extensions: 24 Number of successful extensions: 2 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: 401 Length adjustment: 31 Effective length of query: 358 Effective length of database: 370 Effective search space: 132460 Effective search space used: 132460 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