Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_073035875.1 BUB04_RS00400 hypothetical protein
Query= curated2:Q58414 (288 letters) >NCBI__GCF_900129305.1:WP_073035875.1 Length = 293 Score = 103 bits (258), Expect = 3e-27 Identities = 83/262 (31%), Positives = 126/262 (48%), Gaps = 13/262 (4%) Query: 3 IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCID- 61 ++LNG FV E DA+VS D G LYGD +FE +RA DG + +H+ RL D + L +D Sbjct: 9 LWLNGSFVAEDDARVSPLDRGFLYGDALFETLRAQDGQPLYVADHLKRLRDGCRQLRLDW 68 Query: 62 ------IPLTKEEMIDVVLETLRVNNLRD--AYIRLVVTRGVGDLGLDPRKCGKPTIFCI 113 +P D + E L N L + A IR+ +TRG + GL PT+ + Sbjct: 69 AGTPRFLPEDARLWRDQLEELLGRNGLTEGTARIRIQITRGRAE-GLGLPAPHAPTLLAM 127 Query: 114 AIPMPPLLGEDGIRAITVS-VRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLD 172 A P P D + + V + L+P K+ NYL + A A AG DEA L D Sbjct: 128 AAPYHPPSERDYEQGRRLHLVEGIFTPPLSP-FKTCNYLAYLQAGQAARDAGFDEALLKD 186 Query: 173 DKGFVVEGTGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDL 232 G + E + ++ +K G T L G + + ++G +V+ P+T D+ Sbjct: 187 KDGTLAETSTGSLLFLKEGTC-TLSASPFRLPGTAEQRIACMLHDDGWQVIRAPVTEKDI 245 Query: 233 YTADELFITGTAAEIVPVFEID 254 + + L+IT + I+PV +D Sbjct: 246 PSYEALWITNSLMGILPVRAVD 267 Lambda K H 0.321 0.143 0.411 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: 223 Number of extensions: 14 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: 288 Length of database: 293 Length adjustment: 26 Effective length of query: 262 Effective length of database: 267 Effective search space: 69954 Effective search space used: 69954 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 (21.8 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