Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_089229566.1 B9O00_RS06850 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_900177295.1:WP_089229566.1 Length = 394 Score = 442 bits (1137), Expect = e-129 Identities = 221/379 (58%), Positives = 273/379 (72%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M TYARAD+ FERGEG YL+ TDGRR+LDF AG+AV GHA+P+LV+AL QA KLWH Sbjct: 5 MMNTYARADLAFERGEGSYLFGTDGRRYLDFTAGIAVTSCGHAHPHLVKALQDQAAKLWH 64 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSNLFR+ E LA+RL A+FAD VFF NSG EA+E AKL R+Y G R +IIT Sbjct: 65 TSNLFRIPAGERLAERLVAASFADKVFFCNSGVEAFEGAAKLARRYQNVTGSPQRWKIIT 124 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 +FHGR++AA+SAA K ++GFGP + G++ V F + +R A+ DETA I +EPIQ Sbjct: 125 VTGSFHGRSMAAISAAGNPKYLEGFGPRVPGYETVAFRNTNELRAAIDDETAAILVEPIQ 184 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GEGGIR +++LR LR ICDE GL+L DEIQCGMGRTGKLFA EWAGI PDVM +AKG Sbjct: 185 GEGGIRPAELDYLRELRTICDEFGLVLVFDEIQCGMGRTGKLFACEWAGIAPDVMMLAKG 244 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 +GGGFP+GA LA +K A G T G HG+T+GGNPLA AVGNAVLD +L GFLD VQ + G Sbjct: 245 LGGGFPIGAVLANDKTAVGFTPGVHGTTFGGNPLAMAVGNAVLDVILAEGFLDRVQEVAG 304 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 L+ RL + +P + VRG GLMLGL +++ ALR GLL+V A +NV+RLL Sbjct: 305 HLRSRLEAIAGRHPEQIEEVRGAGLMLGLKAARPNAELIGALREAGLLTVGAAENVIRLL 364 Query: 365 PPLNIGEAEVEEAVAILAK 383 PPL + E +EA AI+ K Sbjct: 365 PPLTLSSGEADEACAIIEK 383 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: 486 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: 394 Length adjustment: 31 Effective length of query: 358 Effective length of database: 363 Effective search space: 129954 Effective search space used: 129954 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