Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate 8501665 DvMF_2383 aminotransferase class IV (RefSeq)
Query= curated2:O29329 (290 letters) >FitnessBrowser__Miya:8501665 Length = 313 Score = 132 bits (332), Expect = 1e-35 Identities = 82/267 (30%), Positives = 132/267 (49%), Gaps = 4/267 (1%) Query: 22 DHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIPITKEEFMEIILETLRKN 81 DH GDG+FE ++ + R+++L H++R+ SA + L P T E EII+E + Sbjct: 49 DHLAHRGDGIFESMKYLHRRIYQLDAHLERMRRSAAGLYLAPPCTWERLREIIIEVAKAG 108 Query: 82 NLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYGDLYEKGLTAITVAVRRNS 141 D IR +V RG G G+DP +C PS+ V + ++KGLTA ++ Sbjct: 109 GEADGSIRVLVGRGPGGFGIDPAECPEPSLYVAAYHFTPKPEAWFDKGLTAFRSSIPAK- 167 Query: 142 FDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVSEGSGDNIFVV-KNGAITTP 200 IK+ NYL N+L EA+ +G D D G ++E + N+ +V + G + P Sbjct: 168 -QGYLARIKNANYLPNVLMTREAHERGMDVPFSFDDEGCLAETAIANVALVDQTGTLVVP 226 Query: 201 PTINNLRGITREAVIEIINRLGIPFKETNIGLYDLYTADEVFVTGTAAEIAPIVVIDGRK 260 N L G T +E+ +P + +L+ A E+ V GT+++ +V +GR Sbjct: 227 EFTNALAGTTVLRAVELAQG-EVPVSFRKVREEELHAAREILVLGTSSDCVAVVAYEGRP 285 Query: 261 IGDGKPGEITRKLMEEFSKLTESEGVP 287 + DG+PG ++R+L GVP Sbjct: 286 VADGRPGPVSRRLRALLQADLMEHGVP 312 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: 230 Number of extensions: 14 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: 313 Length adjustment: 27 Effective length of query: 263 Effective length of database: 286 Effective search space: 75218 Effective search space used: 75218 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: 48 (23.1 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