Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 5207770 Shew_0291 branched-chain amino acid aminotransferase (RefSeq)
Query= BRENDA::P0AB80 (309 letters) >FitnessBrowser__PV4:5207770 Length = 307 Score = 429 bits (1102), Expect = e-125 Identities = 202/305 (66%), Positives = 246/305 (80%) Query: 1 MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR 60 M K A+ IWFNGE++ W DAKVHVMSHALHYGTSVFEGIR YD+ +GP FR +H+QR Sbjct: 1 MAAKTAELIWFNGEIMPWGDAKVHVMSHALHYGTSVFEGIRVYDTPQGPAGFRLTDHVQR 60 Query: 61 LHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120 L+DSAKIYR PV S DE M+ACRD+++ N L +AYIRPL+F GDVGMG+ PP D+ Sbjct: 61 LYDSAKIYRMPVPYSFDETMQACRDIVKSNKLDAAYIRPLVFFGDVGMGITPPKDAKCDL 120 Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180 ++AAFPWGAYLG ++E+G+D V+SWNR APNTIPT AKAGGNYLSSL + +EA+R+G+ Sbjct: 121 MVAAFPWGAYLGEGSMERGVDVAVTSWNRLAPNTIPTGAKAGGNYLSSLQISTEAKRNGF 180 Query: 181 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ 240 EGIALDVNG +SEGAG NLF VK L+TPP T++ L GITRD II LA++LG EV E+ Sbjct: 181 DEGIALDVNGLVSEGAGANLFVVKKNKLYTPPATAAILLGITRDTIITLARDLGYEVVEE 240 Query: 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDK 300 +SRE LYLADE+FM+GTAAEI PVRSVD I+VG G GPVT+ +Q +FFGLF GET+DK Sbjct: 241 PMSREFLYLADEIFMTGTAAEIVPVRSVDRIEVGAGGRGPVTQALQASFFGLFNGETQDK 300 Query: 301 WGWLD 305 WGWL+ Sbjct: 301 WGWLE 305 Lambda K H 0.319 0.136 0.413 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: 366 Number of extensions: 9 Number of successful extensions: 1 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: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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