Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_011160305.1 TX73_RS24410 acetylornithine transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000195775.1:WP_011160305.1 Length = 403 Score = 461 bits (1185), Expect = e-134 Identities = 223/384 (58%), Positives = 286/384 (74%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 ++P +ARAD+ FERGEG +L+ TDG R+LDF +GVAVN LGH +P+LVEAL QA KLWH Sbjct: 10 LLPVFARADVAFERGEGVWLHGTDGERYLDFTSGVAVNALGHCHPHLVEALQQQASKLWH 69 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SNLF+ E LA RL E +FAD VFF NSGAEA EC K+ R YH+ KG+ RTR+IT Sbjct: 70 VSNLFKSPEGERLAARLCEQSFADKVFFCNSGAEAVECALKMARHYHFSKGEPERTRVIT 129 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 FE AFHGRTL ++A K ++G+G L+GFD +P GDL+AV+ A+ TA I +EP+Q Sbjct: 130 FEGAFHGRTLGTLAATGSAKYLEGYGQPLEGFDQLPLGDLDAVKAAIGPNTAAILIEPLQ 189 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GEGG+R+ + F RGLRE+CD HGLLL DE+Q GMGRTG+LFA++ G+ PD+MA+AK Sbjct: 190 GEGGVRSPELAFFRGLRELCDAHGLLLVFDEVQTGMGRTGELFAYKRIGVAPDIMALAKA 249 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 +GGGFP+GACL+T +AA GM G HGST+GGNPLA AV NAVLD +L+PGF DHV+++ Sbjct: 250 LGGGFPIGACLSTAEAAKGMAPGAHGSTFGGNPLAVAVANAVLDVMLQPGFFDHVKKMSL 309 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 LL+ +LAG+V +P V +RG+GL+LGL +++ ALRA LLSV AGDNVVRLL Sbjct: 310 LLKQKLAGVVDRHPRVVSEIRGEGLLLGLKAVVPSPELIAALRAEKLLSVGAGDNVVRLL 369 Query: 365 PPLNIGEAEVEEAVAILAKTAKEL 388 PPL + EAE++EAV L + L Sbjct: 370 PPLIVNEAELDEAVGRLERACVTL 393 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: 490 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: 403 Length adjustment: 31 Effective length of query: 358 Effective length of database: 372 Effective search space: 133176 Effective search space used: 133176 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 10 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