Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_077244617.1 B1A74_RS10545 D-amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_001995255.1:WP_077244617.1 Length = 299 Score = 147 bits (372), Expect = 2e-40 Identities = 95/282 (33%), Positives = 148/282 (52%), Gaps = 14/282 (4%) Query: 1 MLYVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAID 60 M +GEF+P E ++S D GFL+GD V+E I +Y GR F L H+DRL S AI Sbjct: 1 MSIALFNGEFLPLEEVRISPLDRGFLFGDSVYEVIPSYAGRFFLLDAHLDRLARSLAAIR 60 Query: 61 LEIPITKEEFMEIILETLRKNNLR--------DAYIRPIVTRGIGDLGLDPRKCQNPSII 112 L P +E++ + + LR N D + VTRG+ P+++ Sbjct: 61 LPNPFGREQWERHLGDLLRHNGAEPTDGSTPPDLGLYLQVTRGVAPRDHAFPDVSEPTVL 120 Query: 113 VITKPWGKLYGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEA 172 + P L + E G++A+T R +IK+ L N+LA+ EA EA Sbjct: 121 GMVSPIRPLGPAVREAGVSAVTRTDERWG----RCDIKATTLLANVLARQEAVESDAVEA 176 Query: 173 IFLDRNGYVSEGSGDNIFVVKNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIG 231 + L RNG ++EG+ N FVV++G + TPP + L G+TR+ V+ + G+P +E + Sbjct: 177 LLL-RNGRLTEGAASNAFVVRDGTLVTPPLDSGMLAGVTRDFVLGLARGEGVPVEERGVT 235 Query: 232 LYDLYTADEVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKL 273 +L TADEV+++ + E+ P+ IDG +G G+PG + +L Sbjct: 236 AAELRTADEVWLSSSTRELLPVTRIDGEPVGTGRPGPLWTRL 277 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: 250 Number of extensions: 13 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: 299 Length adjustment: 26 Effective length of query: 264 Effective length of database: 273 Effective search space: 72072 Effective search space used: 72072 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 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