Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000009985.1:WP_083763404.1 Length = 384 Score = 475 bits (1223), Expect = e-139 Identities = 238/383 (62%), Positives = 290/383 (75%) Query: 6 MPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHT 65 MPTYARAD+ FERGEG YL+ DGRR+LDFAAGVAVN LGH +P LV+ALTAQA K+WHT Sbjct: 1 MPTYARADLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHT 60 Query: 66 SNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITF 125 SNL+RVAGQES+A +L E +FADTVFF NSGAEA EC K+ R++H+ G+ R RII Sbjct: 61 SNLYRVAGQESVAAKLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICA 120 Query: 126 EQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQG 185 E AFHGRTLA V+A Q+K ++GF P +DGFD VP+G+L A+R ++T+ETA I +EP+QG Sbjct: 121 EGAFHGRTLATVAAGGQKKHLEGFAPAVDGFDHVPYGNLNALRASITEETAAILVEPVQG 180 Query: 186 EGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGI 245 EGGI G ++LR LR DE GLLL DE+Q GMGRTG LFAHE AGI PD+M VAKG+ Sbjct: 181 EGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQAGIAPDIMGVAKGL 240 Query: 246 GGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGL 305 GGGFP+GACLAT KAASGM GTHGST+GGNPLA AV VLD + EPGFL+HVQ + L Sbjct: 241 GGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAEPGFLEHVQAMAAL 300 Query: 306 LQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLLP 365 L+ ++ A P V + VRG GLMLG+ ++V L GLL+V AGDN+VRLLP Sbjct: 301 LRSKVEDTAARFPGVVEEVRGLGLMLGIKPRMPNTEMVARLAEGGLLTVGAGDNIVRLLP 360 Query: 366 PLNIGEAEVEEAVAILAKTAKEL 388 PL I +A+V+EAV ILA+ E+ Sbjct: 361 PLIINDAQVDEAVGILARAFDEV 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: 504 Number of extensions: 21 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: 384 Length adjustment: 30 Effective length of query: 359 Effective length of database: 354 Effective search space: 127086 Effective search space used: 127086 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