Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate AZOBR_RS14455 AZOBR_RS14455 D-amino acid aminotransferase
Query= BRENDA::E6TUA8 (302 letters) >FitnessBrowser__azobra:AZOBR_RS14455 Length = 287 Score = 136 bits (343), Expect = 5e-37 Identities = 85/277 (30%), Positives = 145/277 (52%), Gaps = 8/277 (2%) Query: 3 SQWIFSNGKFVTKQEAVISVYDHGFLYGDGVFEGIRVYDGNIFKLTEHLKRLYESAQSIM 62 ++W + NG+++ ++A + V D GF + DGV+E + + DG L H++RL S + Sbjct: 2 ARWAYVNGRYLPHRQAAVHVEDRGFQFADGVYEVVTLLDGRFADLDGHMERLGRSLSELR 61 Query: 63 LEIPYSKEDFQQIIVDTVRKNQLESGYIRVVVSRGPGNLGLD-PSRCSAPHVIVIAEELA 121 ++ P + I + VR+N + +G + + V+RG P+ SA V+ + A Sbjct: 62 MDWPAAPRVVTMIARELVRRNGVRNGSLYIQVTRGVAPRDFKFPASVSATLVMTVKRVTA 121 Query: 122 LFPKELYELGLTVASVAS-RRNRPDVLSPQIKSLNYLNNILVKLEANQAGAHEALMLNDQ 180 E E G+ V +V R R D IK++ L +L K +A ++GA+EA +++ Sbjct: 122 FAKPEQLEKGVAVVTVPDIRWGRCD-----IKTVGLLAPVLAKQQAAESGAYEAWLIDPD 176 Query: 181 GYVTEGSADNIFIV-KNNTIITPPVYLGALEGITRNAIIDLAKECGYEMKETPFTRHDVY 239 G VTEGS+ N +IV ++ ++T L GITR +++ LA E G ++E FT + Sbjct: 177 GTVTEGSSSNAWIVTQDGVLVTRAPSQKILNGITRLSLLRLAGERGIPVEERSFTVEEAL 236 Query: 240 VADEVFLTGTAAEVIAVVEVDKRMISDGKPGKVTNHL 276 A E F++ + V +D + + +GKPG VT L Sbjct: 237 AAREAFVSSAGTFALPVTRIDGKPVGEGKPGPVTRTL 273 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: 217 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: 302 Length of database: 287 Length adjustment: 26 Effective length of query: 276 Effective length of database: 261 Effective search space: 72036 Effective search space used: 72036 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 Jul 25 2024. The underlying query database was built on Jul 25 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