Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_037575525.1 BS73_RS23310 ornithine--oxo-acid transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000744815.1:WP_037575525.1 Length = 391 Score = 231 bits (588), Expect = 3e-65 Identities = 143/379 (37%), Positives = 201/379 (53%), Gaps = 7/379 (1%) Query: 9 YARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNL 68 Y +V E EG ++ T GRR+LD AG + GH +P L+ A Q ++ TS Sbjct: 9 YHPLPVVIESAEGAWVTDTAGRRYLDLLAGYSALNFGHRHPRLIAAAERQLGRVTLTSRA 68 Query: 69 FRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYE-KGDKART-RIITFE 126 F+ ++L + + V N+GAEA E K R++ Y KG A T +I+ Sbjct: 69 FQHDLFAPFCEQLADLCGMEAVLPMNTGAEAVETAIKTARRWAYRVKGVPADTAKIVAAR 128 Query: 127 QAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGE 186 FHGRT V + E+ GFGP GF+LVP+GD+EA+ AV D TA + LEPIQGE Sbjct: 129 GNFHGRTTTIVGFSDDEEARDGFGPFTPGFELVPYGDVEALSAAVDDRTAAVLLEPIQGE 188 Query: 187 GGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIG 246 G+ +L R I +E G+LL DEIQ G+GRTG+ FA E G+ PD + K +G Sbjct: 189 AGVIVPPPGYLAEARRITEERGVLLIADEIQSGLGRTGRTFACEHEGVVPDAYILGKALG 248 Query: 247 GG-FPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGL 305 GG P+ A +++ T G+HGST+GGNPLA AV V+ + + +G Sbjct: 249 GGVLPISAVVSSRAVMDVFTPGSHGSTFGGNPLACAVALEVIALLRTGAYQRRAAELGAR 308 Query: 306 LQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVG---DVVVALRANGLLSVPAGDNVVR 362 L LA L A+ VRG+GL G+ PAVG ++ L A G+L+ + +R Sbjct: 309 LHRELAEL-ADGDWPVTAVRGRGLWAGVDVSPAVGTGREICERLMARGVLAKDTHGSTIR 367 Query: 363 LLPPLNIGEAEVEEAVAIL 381 + PPL I E ++ A+A L Sbjct: 368 VAPPLVISEEDLSWALAQL 386 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: 443 Number of extensions: 24 Number of successful extensions: 5 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: 391 Length adjustment: 31 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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 26 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