Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_018126051.1 B149_RS0115315 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YMS6 (388 letters) >NCBI__GCF_000375485.1:WP_018126051.1 Length = 390 Score = 322 bits (825), Expect = 1e-92 Identities = 160/391 (40%), Positives = 249/391 (63%), Gaps = 5/391 (1%) Query: 1 MKLAARVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGK 60 M+++ R+S++ PS TLA+ KA+ ++A+G ++ S + G+PDF TPAH+ AA ALDEG Sbjct: 1 MRISERLSRLKPSATLAVNTKAQELRAQGREIVSLAVGQPDFGTPAHVVEAAKAALDEGF 60 Query: 61 TKYGAAAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIP 120 T+Y G P+LREA+A + + EN I++NGGK LYNL++AL++PGDEV++P Sbjct: 61 TRYTPVPGIPELREAVADYYGRFYGITAVQENAIISNGGKQVLYNLLMALVNPGDEVLVP 120 Query: 121 APYWLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVY 180 APYW+SYP M+ L G+ V VPT+A + ++ E L A T +T++ VLNSPSNPTG Y Sbjct: 121 APYWVSYPAMIELAEGRCVTVPTEAENDFLVSVEGLEAARTERTRVLVLNSPSNPTGCCY 180 Query: 181 TPEEIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYS 240 T +++ +AQ +D ++++SDE+Y++++Y + ++ ++ + +K++ Sbjct: 181 TQDQLDGIAQWALDNGVFIISDEVYDRLVYAPVEPATLARFWQKHPESCALVGALSKSFC 240 Query: 241 MTGWRLGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALEDSQDCVEEMRQAFAKRR 300 MTGWRLG+ +++KA S IQG STSNV +F+Q + AL D VE+M++AF +RR Sbjct: 241 MTGWRLGWALAAEELVKAMSKIQGQSTSNVSSFSQKAGVVALAGEWDIVEQMKEAFVRRR 300 Query: 301 QVMLDRLNAIPGLSTAKPDGAFYLFPDI----SKTGLKSLEFCDALIEEHKVAVIPGIAF 356 + + + + G KPDGAFYLFP + ++ S C+ ++EE VA++PG AF Sbjct: 301 DIAHEIITSW-GAPCPKPDGAFYLFPVLDAFYTEDAPDSAAMCNKILEEAGVALVPGSAF 359 Query: 357 GADDNIRLSYATDLATIEKGLDRLEKFVRSR 387 G D IR SYA D T+ L R+ K + + Sbjct: 360 GDDRCIRFSYAVDDDTLRDALTRVGKVLTGK 390 Lambda K H 0.317 0.134 0.381 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: 372 Number of extensions: 20 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: 388 Length of database: 390 Length adjustment: 30 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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