Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_026596677.1 H035_RS0115230 D-amino acid aminotransferase
Query= curated2:Q58414 (288 letters) >NCBI__GCF_000421465.1:WP_026596677.1 Length = 281 Score = 143 bits (361), Expect = 4e-39 Identities = 95/275 (34%), Positives = 147/275 (53%), Gaps = 11/275 (4%) Query: 3 IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDI 62 +YLNG F+ AKVSV D G L+GDGV+E I AY G +F L+EH+ RL S + + +D Sbjct: 6 VYLNGDFLPLSQAKVSVLDRGFLFGDGVYEVIPAYGGKLFRLEEHLQRLEYSLRGIRLDS 65 Query: 63 PLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLG--LDPRKCGKPTIFCIAIPMPPL 120 PL ++ E +R + D I L +TRG + P +PT+F +A P+ Sbjct: 66 PLEALRWRHILGELVRDDG--DQSIYLQITRGTAPKRDHVFPEHI-RPTVFAMATPIQTT 122 Query: 121 LGEDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEG 180 + +A+T R + L K++ L +VL + A G E+ L+ D G V EG Sbjct: 123 KPQPA-KAVTCEDIRWQLCHL----KTITLLANVLLRQDAVDHGCQESILVRD-GTVTEG 176 Query: 181 TGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFI 240 N+F V G + TPP +L G+TRD++++LA+ GI E + L + A+E++ Sbjct: 177 AASNLFAVMEGTVVTPPKGPHLLPGVTRDLILELAETHGIPAAERAIPLAEFRRAEEIWY 236 Query: 241 TGTAAEIVPVFEIDGRVINNKQVGEITKKLKEKFK 275 T + E+VPV E+D R + G I +++ E F+ Sbjct: 237 TSSTRELVPVVELDNRPVGKGTPGPIWRQMYELFQ 271 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: 215 Number of extensions: 12 Number of successful extensions: 2 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: 281 Length adjustment: 26 Effective length of query: 262 Effective length of database: 255 Effective search space: 66810 Effective search space used: 66810 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: 47 (22.7 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