Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_057508908.1 ABB28_RS12185 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YMS6 (388 letters) >NCBI__GCF_001431535.1:WP_057508908.1 Length = 397 Score = 206 bits (524), Expect = 9e-58 Identities = 123/387 (31%), Positives = 204/387 (52%), Gaps = 9/387 (2%) Query: 6 RVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGKTKYGA 65 R ++ P +++ A+A+A++ G DV GEPDF T A + A AL G T+Y A Sbjct: 15 RSHEIAPFHVMSLLARAQALEQAGHDVIHLEIGEPDFTTAAPVVRAGQAALAAGHTRYTA 74 Query: 66 AAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIPAPYWL 125 A G P LREAIA + LD P+ ++VT GG +L L+DPG ++ P + Sbjct: 75 ARGLPALREAIAGFYRSHYLLDIDPQRILVTPGGSGALLLASSLLVDPGRHWLLADPGYP 134 Query: 126 SYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVYTPEEI 185 + LV G + +VP DA T Y++TPE + + + +L SP+NPTG V + E+ Sbjct: 135 CNRHFLRLVEGGAQLVPVDAGTAYQLTPELVARHWNEHSVGALLASPANPTGTVLSAAEL 194 Query: 186 KALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYSMTGWR 245 L+Q + ++V DEIY + Y G S+ ++ + + N F+K + MTGWR Sbjct: 195 SRLSQSLHARGGHMVVDEIYHGLTY-GMDAASV----LQVDDSAFVLNSFSKYFGMTGWR 249 Query: 246 LGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALEDSQDCV-EEMRQAFAKRRQVML 304 LG+L P + + + + + AQ+ A+A +D + E+ R+AF +RR +L Sbjct: 250 LGWLVAPPAAVPELEKLAQNLYISASSIAQHAALACFQDEAMAIFEQRREAFRQRRDFLL 309 Query: 305 DRLNAIPGLSTAKPDGAFYLFPDISKTGLKSLEFCDALIEEHKVAVIPGIAFG---ADDN 361 L + +P GAFYL+ D+S + FC +E VA PG+ FG A+ + Sbjct: 310 PALRELGFRINVEPQGAFYLYADVSAFTDDAQAFCAHFLETEHVAFTPGLDFGFHRANQH 369 Query: 362 IRLSYATDLATIEKGLDRLEKFVRSRI 388 +RL+Y ++ +++ ++R+ + +R+ + Sbjct: 370 VRLAYTQEIPRLQEAVERIARGLRTLV 396 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: 340 Number of extensions: 17 Number of successful extensions: 3 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: 397 Length adjustment: 31 Effective length of query: 357 Effective length of database: 366 Effective search space: 130662 Effective search space used: 130662 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