Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate Dsui_3339 Dsui_3339 branched-chain amino acid aminotransferase, group I
Query= BRENDA::P0AB80 (309 letters) >FitnessBrowser__PS:Dsui_3339 Length = 306 Score = 291 bits (745), Expect = 1e-83 Identities = 146/297 (49%), Positives = 199/297 (67%), Gaps = 2/297 (0%) Query: 8 YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKI 67 +IW +G++V W +A H ++H+LHYG +VFEG+R Y + KG +FR ++H QRL SA I Sbjct: 9 FIWQDGKLVPWREATTHALTHSLHYGMAVFEGVRAYQTDKGTAIFRLQDHTQRLARSAHI 68 Query: 68 YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPW 127 ++ + S +EL EA ++VIR NNL S YIRPL F G MGV+ P G VIIAA+PW Sbjct: 69 FQMALPYSQEELNEAQKEVIRANNLESGYIRPLAFYGSEKMGVS-PKGAKVHVIIAAWPW 127 Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187 GAYLG E +++GI SS+ R N AKA GNY++S+L +EA GY E + LD Sbjct: 128 GAYLGEEGMQRGIRIKTSSFTRHHVNITMVRAKASGNYMNSILANNEALTDGYDEAMLLD 187 Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESL 247 GY+ EGAGEN+F VK+G L+TP T S L GITR +I+LA E+GIEV E+ ++R+ + Sbjct: 188 PEGYVCEGAGENIFIVKNGKLYTPDLT-SCLEGITRATVIQLAGEMGIEVVEKRITRDEV 246 Query: 248 YLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWL 304 Y ADE F +GTAAE+TP+R +D Q+G G GPVTK +Q+ +F + G + WL Sbjct: 247 YCADEAFFTGTAAEVTPIRELDNRQIGVGHRGPVTKALQEKYFDVVNGRSAAHADWL 303 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: 293 Number of extensions: 12 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: 309 Length of database: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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