Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_011187330.1 DP_RS00415 D-alanine aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000025945.1:WP_011187330.1 Length = 283 Score = 152 bits (383), Expect = 1e-41 Identities = 95/281 (33%), Positives = 146/281 (51%), Gaps = 18/281 (6%) Query: 6 MDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIPI 65 +DG F+ E +A +S+ D L G GVF+ +R+YNG F+L+ HIDRL SA+ + L +P+ Sbjct: 11 LDGNFIAEEKATISVHDLSLLRGYGVFDFLRSYNGHPFQLQAHIDRLARSAQLVGLSLPV 70 Query: 66 TKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYGDL 125 + EE + +ET+ NN ++ IR ++T G G P + +I++ P L Sbjct: 71 SCEEIFRLTMETIAHNNHQEYQIRLVITGGESLGGFLPER-GAARLIIMVSPLHPLPEQW 129 Query: 126 YEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVSEGS 185 Y G+ T R P K+ NY+ ILA EA A+G E+I+LD G++ EG+ Sbjct: 130 YSNGVKVTTCRTSR-----FLPGAKTTNYIPAILAMQEATARGAVESIYLDAGGFLQEGT 184 Query: 186 GDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLYDLY-----TADE 240 N F + TPP+ L GITREAV+++ E NI + ++ DE Sbjct: 185 TSNFFAFFGSTLVTPPSSRILPGITREAVLDLAQ------GEFNIEIRPIHQDEIRLMDE 238 Query: 241 VFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLT 281 +T + EI P+ I+ +I K G ++KLM+ F T Sbjct: 239 AVITASNKEILPVCAINSEQISQ-KVGLHSKKLMQLFKSFT 278 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: 172 Number of extensions: 6 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: 290 Length of database: 283 Length adjustment: 26 Effective length of query: 264 Effective length of database: 257 Effective search space: 67848 Effective search space used: 67848 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