Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_037570893.1 BS73_RS08760 aminodeoxychorismate lyase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000744815.1:WP_037570893.1 Length = 274 Score = 125 bits (315), Expect = 8e-34 Identities = 89/288 (30%), Positives = 146/288 (50%), Gaps = 19/288 (6%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 ++++GE ++ A VS DHG GDGVFE ++A +GR F L H+ RL SA+ + L Sbjct: 3 IWINGELREQDSASVSALDHGLTVGDGVFETVKAEDGRPFALTRHLHRLERSARGLGLPA 62 Query: 64 PITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYG 123 P + E L N L +R T G+ LG D R P+++V G Sbjct: 63 P-DLDRVREACAAVLEANPLPLGRLRITYTGGLSPLGSD-RGDSAPTLVV-------ALG 113 Query: 124 DLYEK--GLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181 + + ITV RN A+ +K+ +Y N++A A+ +G EA+F + G + Sbjct: 114 EAAHRPDSTAVITVPWTRNEHSAI-AGLKTTSYAENVVALARAHEQGASEALFANTAGRL 172 Query: 182 SEGSGDNIFVVKNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTADE 240 EG+G N+FVV G + TP + L GITR V+E + +E ++ L A+E Sbjct: 173 CEGTGTNVFVVLGGRLLTPALASGCLAGITRGLVVEWLGA-----EEADLPFDVLGQAEE 227 Query: 241 VFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTESEGVPI 288 VF+T + ++ P+ +D R++ G G + K +E F++ + ++ P+ Sbjct: 228 VFLTSSLRDVQPVHRLDERRL-PGTAGAMAVKAVEVFAERSSADRDPV 274 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: 181 Number of extensions: 11 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: 274 Length adjustment: 26 Effective length of query: 264 Effective length of database: 248 Effective search space: 65472 Effective search space used: 65472 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 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