Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_074200966.1 BUQ81_RS03220 D-amino acid aminotransferase
Query= BRENDA::E6TUA8 (302 letters) >NCBI__GCF_900141795.1:WP_074200966.1 Length = 291 Score = 157 bits (397), Expect = 3e-43 Identities = 94/285 (32%), Positives = 159/285 (55%), Gaps = 10/285 (3%) Query: 1 MSSQWIFSNGKFVTKQEAVISVYDHGFLYGDGVFEGIRVYDGNIFKLTEHLKRLYESAQS 60 MS+Q + NG++ + A +S D GFL+GDGV+E I VY+ +F HL+RL S ++ Sbjct: 1 MSTQTAWLNGEWQPLEAARVSPLDRGFLFGDGVYEVIPVYERRVFAFKPHLQRLKHSLEA 60 Query: 61 IMLEIPYSKEDFQQIIVDTVRKNQLESGYIRVVVSRG--PGNLGLDPSRCSAPHVIVIAE 118 + P++ E+++ + V ++ Y+ + V+RG P L P C P V Sbjct: 61 TGIPNPHTDEEWEALCNSLVERHPWTDQYLYIQVTRGVQPKRDHL-PQNCLVPTVFAYTS 119 Query: 119 ELALFPKELYELGLTVASVASRR-NRPDVLSPQIKSLNYLNNILVKLEANQAGAHEALML 177 EL + + + G+ + R R D IK++ L N+++KLEA +AGA +A+++ Sbjct: 120 ELKPMDEAVLQRGVRCITTQDIRWQRCD-----IKAITLLANVMMKLEAQRAGADDAILI 174 Query: 178 NDQGYVTEGSADNIFIVKNNTIITPPVYLGALEGITRNAIIDLAKECGYEMKETPFTRHD 237 + G V+EG+A N+ IV+ +++TPP+ L GITR +++ A G E P + Sbjct: 175 RN-GMVSEGTASNVMIVEGQSLVTPPLDHHLLGGITRQILLNCAPAIGLLPVEEPISIQR 233 Query: 238 VYVADEVFLTGTAAEVIAVVEVDKRMISDGKPGKVTNHLLSEFRK 282 +Y ADE++LT + E + VVE+D+R + DG PG V + S +++ Sbjct: 234 LYQADEIWLTSSTKEALPVVELDERSVGDGTPGPVWQAMRSHYQQ 278 Lambda K H 0.318 0.136 0.385 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: 171 Number of extensions: 8 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: 302 Length of database: 291 Length adjustment: 26 Effective length of query: 276 Effective length of database: 265 Effective search space: 73140 Effective search space used: 73140 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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