Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_043743690.1 AMB_RS07030 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::Q8YMS6 (388 letters) >NCBI__GCF_000009985.1:WP_043743690.1 Length = 384 Score = 174 bits (440), Expect = 5e-48 Identities = 120/388 (30%), Positives = 185/388 (47%), Gaps = 14/388 (3%) Query: 4 AARVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGKTKY 63 AAR + P I + + A A +A G DV G+P P + AAA+A+ Y Sbjct: 5 AARRGAIAPFIVMDVMRDAAARQAAGADVIHLEVGQPSGQAPPKVLDAAARAVRTEPLGY 64 Query: 64 GAAAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIPAPY 123 A G LRE IAR + + PE V VT G + +A +PGD V + AP Sbjct: 65 TLALGRDSLRERIARHYHQAYGVSVVPERVCVTTGSSAAFLLAFLAAFEPGDRVAVAAPG 124 Query: 124 WLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVYTPE 183 + +Y ++ +G + V+VP S+ ++IT E L + + V+ SPSNPTG + + Sbjct: 125 YPAYRNILESLGVECVLVPVGPSSRWQITAEVL-AGVEGRLDGVVVASPSNPTGSMLSAH 183 Query: 184 EIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYSMTG 243 E+ LA I ++SDEIY I Y A + G ++ N F+K Y+MTG Sbjct: 184 EVAELAGWCELHGIRLISDEIYHGITYGRAAATAAGMAAAP---HAVVINSFSKYYAMTG 240 Query: 244 WRLGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALEDSQDCVEEMR---QAFAKRR 300 WRLG++ P D+ ++ + + + T +Q A E DC++E+ A+ R Sbjct: 241 WRLGWMVLPEDLARSVECLTQNLYISPPTLSQ----VAAESVFDCIDELEARVAAYRANR 296 Query: 301 QVMLDRLNAIPGLSTAKPDGAFYLFPDISKTGLKSLEFCDALIEEHKVAVIPGIAFGADD 360 +++ L A DGAFYL+ D+S+ S EFC ++ E VA PG+ F + Sbjct: 297 DILVAELPKAGFDRLAPSDGAFYLYADVSEMTNDSREFCARMLAETGVACTPGVDFDPIE 356 Query: 361 ---NIRLSYATDLATIEKGLDRLEKFVR 385 +R SYA + + RL+ + R Sbjct: 357 GHRTLRFSYAGSAEHMAEAARRLKAWRR 384 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: 334 Number of extensions: 12 Number of successful extensions: 4 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: 384 Length adjustment: 30 Effective length of query: 358 Effective length of database: 354 Effective search space: 126732 Effective search space used: 126732 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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