Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 451 bits (1160), Expect = e-131 Identities = 226/377 (59%), Positives = 278/377 (73%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 ++P + R D++FE+GEG +L A+DGRRFLDF AGVAVN LGHA+P LV AL AQA KLWH Sbjct: 6 LLPVFDRTDVIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWH 65 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SNL+RV GQE +A+RL +A+FADT FF N+GAEA E K+ R+YH+ G R RI+ Sbjct: 66 CSNLYRVPGQERVAERLIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVA 125 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 +FHGRT+A ++AA K ++GFGP+ GFD VP+GDLEA R A+ TA + +EP+Q Sbjct: 126 CTGSFHGRTIATLAAAGTPKYLEGFGPVAQGFDHVPYGDLEAARGAIGSNTAALLVEPVQ 185 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GEGGIR +LRGLR + D+ GLLL +DE+Q G+GRTGKLFAHEW+GI PDVM +AKG Sbjct: 186 GEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVMGLAKG 245 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 +GGGFP+GA LATEKAAS MT GTHG T+GGNPLA AV AVLD+V+ PGFL+ VQ + Sbjct: 246 LGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERVQAVAA 305 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 LL+ RL L P VRG+GLMLGL P + L A GLL+V AGDNVVRL+ Sbjct: 306 LLRGRLDDLARRYPGAIAQVRGQGLMLGLKTVPVNTEFNAKLFAAGLLAVGAGDNVVRLV 365 Query: 365 PPLNIGEAEVEEAVAIL 381 PPL IGEAEVE AV I+ Sbjct: 366 PPLIIGEAEVERAVEII 382 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: 497 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: 388 Length adjustment: 30 Effective length of query: 359 Effective length of database: 358 Effective search space: 128522 Effective search space used: 128522 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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