Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_050463092.1 AKL27_RS12160 acetylornithine transaminase
Query= BRENDA::A0A3B6MXE9 (473 letters) >NCBI__GCF_001189915.1:WP_050463092.1 Length = 400 Score = 216 bits (549), Expect = 1e-60 Identities = 138/389 (35%), Positives = 210/389 (53%), Gaps = 16/389 (4%) Query: 60 MVFSKGEGSHILDPEGNKYIDFLSAYSAVNQGHCHPKVLRALIEQAERLTLSSRAFYNDK 119 ++F++G G + D G +Y+D+L ++ GH ++ AL QA++L S AFYN Sbjct: 20 LIFTEGSGMWMTDHTGKRYLDYLQGWAVNALGHSPQCMVDALTAQAKKLINPSPAFYNAP 79 Query: 120 FPVFAEYLTSMFGYDMMLPMNTGAEGVETAIKLARKWGYEKKNIPKNEAL----IVSCCG 175 A+ LT +D + N+GAE E AIKLARKWG KKN P +E I++ Sbjct: 80 SIELADLLTENSVFDRVFFANSGAEANEGAIKLARKWG--KKN-PDSEGQDRFEIITFDH 136 Query: 176 CFHGRTLGVISMSCDNDATRGFGPLVPGHLKVDFGDIDGLEKIFKEHGDRICGFLFEPIQ 235 FHGRT+ +S S F P VPG K + D+ +E++ + + + EP+Q Sbjct: 137 SFHGRTIATMSASGKPGWDTMFAPQVPGFKKAELNDLTSVERLITK---KTVAVMLEPVQ 193 Query: 236 GEAGVIIPPDGYLKAVRDLCSRHNILMIDDEIQTGIARTGKMLACDWEDVRPDMVILGKA 295 GE GVI +++ +R L + N+L+I DE+QTG RTG++ A D+ PD++ LGK Sbjct: 194 GEGGVIPATREFMQGLRRLTKQANLLLIVDEVQTGFGRTGELFAYQLSDIEPDIMTLGKG 253 Query: 296 LGAGVVPVSAVLADKDIMLCIKPGEHGSTFGGNPLASAVAVASLKVVKDEGLVERAAELG 355 +G G VP++A+LA ++I C + GE G T+ GNPL +AV A LK + G ++ + G Sbjct: 254 IGGG-VPLAALLAREEI-ACFEAGEQGGTYNGNPLMTAVGAAVLKELLKPGFLQSVKDQG 311 Query: 356 QEFRDQLQKVQQKFPHIIREIRGRGLLNAVDLCSKALYPASAYDICIKLKERGILAKPTH 415 Q +L K+ K H RG GLL A+ L K + P + L G+L Sbjct: 312 QYLSSELIKLSDK--HGFEGERGEGLLRALKL-GKDIGP-QIVEAARDLNPIGLLINSPR 367 Query: 416 DTIIRLAPPLSISSEELAEASKALSDVLE 444 ++R P L++S +E+ + LSDVL+ Sbjct: 368 PNLLRFMPSLNVSKDEIDQMLSMLSDVLK 396 Lambda K H 0.321 0.137 0.409 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: 381 Number of extensions: 25 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: 473 Length of database: 400 Length adjustment: 32 Effective length of query: 441 Effective length of database: 368 Effective search space: 162288 Effective search space used: 162288 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: 51 (24.3 bits)
This GapMind analysis is from Jul 25 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