Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_027178271.1 G496_RS0104745 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YMS6 (388 letters) >NCBI__GCF_000429985.1:WP_027178271.1 Length = 391 Score = 333 bits (853), Expect = 7e-96 Identities = 167/391 (42%), Positives = 246/391 (62%), Gaps = 4/391 (1%) Query: 1 MKLAARVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGK 60 MK++ R+ + PS TLA+ AKA+ ++A+G ++ S + GEPDF TP H+ A KA DEG Sbjct: 1 MKISERLMRAKPSATLAVNAKAQELRAQGREIVSLAVGEPDFPTPKHVCEALKKAADEGF 60 Query: 61 TKYGAAAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIP 120 T+Y G P LR+A+A K + + EN I++NGGKHSLYNL +AL+DPGDEV+IP Sbjct: 61 TRYTPVPGMPALRKAVAEYYGKFYGVKAEAENTIISNGGKHSLYNLCMALVDPGDEVLIP 120 Query: 121 APYWLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVY 180 APYW+SYP MV L GK VIVPT AS G+ + E L + TPKTK+ +LN+PSNPTG Y Sbjct: 121 APYWVSYPPMVELADGKPVIVPTKASNGFLASVEDLEASSTPKTKVLILNTPSNPTGGHY 180 Query: 181 TPEEIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYS 240 + +AQ I+++ DE+Y++++Y+ A ++ + ++ + +K++S Sbjct: 181 PQAHLDEIAQWAKKRGIFIICDEVYDRLVYEPATFSTLSTFWEKNPEDVAVVGALSKSFS 240 Query: 241 MTGWRLGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALEDSQDCVEEMRQAFAKRR 300 MTGWR+G D++K+ IQG STSN+ + Q AIAA E D V+ MR+AF +RR Sbjct: 241 MTGWRVGTTLAHADLVKSIVKIQGQSTSNINSMTQKAAIAAYEGPWDLVDTMREAFQRRR 300 Query: 301 QVMLDRLNAIPGLSTAKPDGAFYLFPDIS----KTGLKSLEFCDALIEEHKVAVIPGIAF 356 + D + + PG+ +KPDGAFYLFP ++ + S C ++EE +A++PG AF Sbjct: 301 DIAYDIITSWPGVKCSKPDGAFYLFPVLNAFYDEETPDSASMCTKILEEAGIALVPGSAF 360 Query: 357 GADDNIRLSYATDLATIEKGLDRLEKFVRSR 387 G D IR SYA D ++ L+++ K + + Sbjct: 361 GDDRCIRFSYAVDDEILKSSLEKVGKVLMKK 391 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: 428 Number of extensions: 18 Number of successful extensions: 2 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: 391 Length adjustment: 30 Effective length of query: 358 Effective length of database: 361 Effective search space: 129238 Effective search space used: 129238 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