Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_013530929.1 MESCI_RS15715 D-amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000185905.1:WP_013530929.1 Length = 321 Score = 162 bits (411), Expect = 7e-45 Identities = 91/275 (33%), Positives = 151/275 (54%), Gaps = 4/275 (1%) Query: 5 YMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIP 64 ++DG+++P ++AK+S+ D GFL+ D ++ + +NGR FRL H+DR + + + IP Sbjct: 32 FLDGQYLPMSQAKISVLDWGFLHSDATYDTVHVWNGRFFRLDLHLDRFLGGLEKLRMTIP 91 Query: 65 ITKEEFMEIILETLRKNNLRDAYIRPIVTRGIG-DLGLDPRKCQNPSIIVITKPWGKL-Y 122 ++ EI+ + + R AY+ + TRG DPR+ N + P+G + Sbjct: 92 FDRDGVTEILHNCVALSGHRAAYVEMLCTRGASPTFSRDPRQAVN-RFMAFAVPFGSVAN 150 Query: 123 GDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVS 182 + ++GL R ++ P IK+ ++L+ + +A +G + A+ LD NG V+ Sbjct: 151 AEQLQRGLRVAISDKMRIPPASIDPAIKNYHWLDLVRGLYDAYDRGAETALLLDFNGNVA 210 Query: 183 EGSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLYDLYTADEVF 242 EG G N+F VK+G ++TP T L G+TR V ++ G+ T++ + L ADEVF Sbjct: 211 EGPGFNVFCVKDGKLSTPAT-GVLPGVTRRTVFDLCAEEGLAATATDVSVTALREADEVF 269 Query: 243 VTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEF 277 +T TA I P+ IDG I +GK G IT +LM + Sbjct: 270 ITSTAGGIMPVTEIDGAAIANGKVGPITSRLMARY 304 Lambda K H 0.319 0.142 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: 243 Number of extensions: 12 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: 290 Length of database: 321 Length adjustment: 27 Effective length of query: 263 Effective length of database: 294 Effective search space: 77322 Effective search space used: 77322 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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