Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_035236424.1 Q366_RS03525 branched chain amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000745975.1:WP_035236424.1 Length = 275 Score = 152 bits (384), Expect = 8e-42 Identities = 99/275 (36%), Positives = 149/275 (54%), Gaps = 10/275 (3%) Query: 1 MLYVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAID 60 M VY+DG+F+P ++A + + D L G V + IR + GR + L EH++RL S I Sbjct: 1 MKTVYVDGKFLPWDKAVIPVDDLAVLRGYAVCDIIRTFGGRPYCLDEHVNRLLSSVTTIG 60 Query: 61 LEIPITKEEFMEIILETLRKN-NLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWG 119 L TKEE I+ L KN ++ +A IR +VT G P +P +IV+ Sbjct: 61 LTPAWTKEEIKTIVFNVLEKNAHMDEANIRILVTGGSSPDFFSP--ADHPRLIVLVTDIP 118 Query: 120 KLYGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNG 179 L Y KG+ IT +R+ P+ K+ NY+ +LA +A A+G EA+++ R+ Sbjct: 119 ALPAHWYTKGVKVITFVQQRSL-----PDAKATNYIPAVLALKKAKAQGAAEALYMTRDK 173 Query: 180 YVSEGSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLYDLYTAD 239 V EG+ N+F + +G + TP L+GITR+ V+ + +L P E +I L L +A Sbjct: 174 MVLEGTTSNLFALVDGTLVTPEK-GVLKGITRKTVLALGKKL-FPVSEQDIALDTLLSAS 231 Query: 240 EVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLM 274 E+F+TGT I P++ +D IG G PG TR LM Sbjct: 232 ELFITGTNKGIVPVIQVDDHVIGTGMPGPGTRALM 266 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: 195 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: 275 Length adjustment: 26 Effective length of query: 264 Effective length of database: 249 Effective search space: 65736 Effective search space used: 65736 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: 47 (22.7 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