Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate N515DRAFT_2015 N515DRAFT_2015 branched-chain amino acid aminotransferase
Query= BRENDA::P0AB80 (309 letters) >FitnessBrowser__Dyella79:N515DRAFT_2015 Length = 305 Score = 345 bits (884), Expect = 1e-99 Identities = 175/307 (57%), Positives = 221/307 (71%), Gaps = 2/307 (0%) Query: 1 MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR 60 M + ++IW NG++ W +A HVMSHALHYG+SVFEGIR Y + G +FR +H++R Sbjct: 1 MAQQYPEWIWQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKR 60 Query: 61 LHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120 L+ SAKIY + S D++ ACRDVI++N L +AY+RP+ + G G G++ A DV Sbjct: 61 LYQSAKIYDMVLPYSQDQIAAACRDVIKQNGLGAAYLRPVAYRGLGGFGLS--AETPIDV 118 Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180 +AA+P G YLG EALE GIDA VSSW R APNTIP AKAGGNYLS L+ EARR G+ Sbjct: 119 AVAAWPMGPYLGPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGF 178 Query: 181 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ 240 EGIAL G +SEGAGENLF V DGVL T P ++S L GITR +I LA+E GIEV E+ Sbjct: 179 GEGIALANTGLLSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIER 238 Query: 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDK 300 + RE LYL DE+ M GTAAEITP+RSVDG ++G G+ G VT+R+Q+ FFGLF G+T D+ Sbjct: 239 DIPREYLYLCDELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQ 298 Query: 301 WGWLDQV 307 WGWL+ V Sbjct: 299 WGWLEPV 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: 315 Number of extensions: 8 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: 309 Length of database: 305 Length adjustment: 27 Effective length of query: 282 Effective length of database: 278 Effective search space: 78396 Effective search space used: 78396 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