Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_011975269.1 SMED_RS05470 D-amino-acid transaminase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000017145.1:WP_011975269.1 Length = 287 Score = 149 bits (377), Expect = 5e-41 Identities = 92/288 (31%), Positives = 156/288 (54%), Gaps = 12/288 (4%) Query: 5 YMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIP 64 Y++G +V EA + + D G+ + DGV+E + + L H+DRL S + + P Sbjct: 6 YVNGTYVRHAEAAIHVEDRGYQFADGVYEVCEVRHRFIIDLNRHLDRLGRSLHELAIGWP 65 Query: 65 ITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLG-LDPRKCQNPSIIVITKPWGKLYG 123 +++ + +I E LR+N +R+ VTRG+ + P PSI+V K G Sbjct: 66 MSRAALVHVIREVLRRNRVRNGLFYLQVTRGVARRDHVFPAADTPPSIVVTAKRTDP--G 123 Query: 124 DLYEK---GLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGY 180 + K G++AITV N +D + +IKS+ L N+LA+ +A G EAIF+D +G Sbjct: 124 AIARKNTEGISAITVP--ENRWDRV--DIKSIGLLPNVLARQQAKEAGAQEAIFVDADGM 179 Query: 181 VSEGSGDNIFVV-KNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTA 238 V EG+ N+++V + G + T P + LRGITR ++++ LG+ +E+ + ++ A Sbjct: 180 VKEGAATNVWIVDREGTLRTRPAESGILRGITRTTLMDVAGPLGLTVEESAFSVEEMLAA 239 Query: 239 DEVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTESEGV 286 EVF+T + P++ +DG+ IG+G PG I + + E F + E + Sbjct: 240 REVFITAATSICFPVISVDGKTIGNGHPGSIAQNIREAFFDIAEKTSI 287 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: 218 Number of extensions: 10 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: 287 Length adjustment: 26 Effective length of query: 264 Effective length of database: 261 Effective search space: 68904 Effective search space used: 68904 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