Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_019556825.1 F612_RS0105860 D-amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000381085.1:WP_019556825.1 Length = 295 Score = 171 bits (434), Expect = 1e-47 Identities = 94/273 (34%), Positives = 159/273 (58%), Gaps = 8/273 (2%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 VY++G+++P E+K+S D GFL+GDGV+E I Y+ ++F EH+ RL +S A ++ Sbjct: 11 VYLNGQYMPMLESKISTQDRGFLFGDGVYEVIPVYDRKLFAFPEHLQRLKNSLHATSIQN 70 Query: 64 PITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLD--PRKCQNPSIIVITKPWGKL 121 P+T E++E++ + K+ D YI +TRGI + D P P+I + P + Sbjct: 71 PLTDAEWLELLSTLIEKHPWSDQYIYLQITRGI-QIQRDHLPEDGLIPTIYAYSNPLKAV 129 Query: 122 YGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181 D+ E G++AIT+ L +IK++ L NI+ K+ A A+ D+AI + R G++ Sbjct: 130 SDDIIENGISAITL----EDIRWLNCDIKAITLLPNIMMKLTAKARHADDAILVSREGFI 185 Query: 182 SEGSGDNIFVVKNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTADE 240 +EG+ N F+VKNG + TPP ++ L G+TR + + IP E I L DL +ADE Sbjct: 186 TEGTSSNCFIVKNGTLITPPNGHSLLPGVTRMVIERVAIAHNIPMLEQQITLTDLESADE 245 Query: 241 VFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKL 273 ++++ + + P+ ++ +G GKPG + +K+ Sbjct: 246 IWLSSSTKDALPVTRLNDSAVGTGKPGAVWQKM 278 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: 240 Number of extensions: 11 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: 290 Length of database: 295 Length adjustment: 26 Effective length of query: 264 Effective length of database: 269 Effective search space: 71016 Effective search space used: 71016 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