Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_086511983.1 BZY95_RS21775 branched-chain amino acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_002151265.1:WP_086511983.1 Length = 322 Score = 232 bits (592), Expect = 8e-66 Identities = 128/303 (42%), Positives = 184/303 (60%), Gaps = 13/303 (4%) Query: 8 YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKI 67 +IW +GE + W DAK H+++H LHYG FEG+R Y G +FR EH +RL DSA Sbjct: 10 WIWLDGEWLPWRDAKTHLLTHTLHYGMGCFEGVRAYAGAHGTHLFRVAEHTRRLLDSAHA 69 Query: 68 YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPW 127 PV+ + L+EA R + +N L +AY++P +F G G+G+ G S V+IAA+ Sbjct: 70 LDIPVAFDEEVLIEAQRQCLVRNELRNAYLKPTVFFGAEGLGLR-AKGLSVHVMIAAWDL 128 Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187 G Y+ +EA G+ A+ SSW R N AK G+Y++S+L + A + G+ E I LD Sbjct: 129 GDYVSSEAATLGLRALTSSWARHHVNISLCRAKTNGHYVNSILALNTAVKAGFDEAIMLD 188 Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKE-LGIEVREQVLSRES 246 GY++E + N+F ++DG L TP T S L GITRD++I LA+E LG+EVRE+ ++R+ Sbjct: 189 PEGYVAEASAANVFLLRDGALHTPEVT-SCLQGITRDSVIHLAREVLGLEVRERRITRDE 247 Query: 247 LYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGP----------VTKRIQQAFFGLFTGE 296 LY ADE F++GTAAEI P+R +DG +G P VT ++QQ + + GE Sbjct: 248 LYTADEAFVTGTAAEILPLRELDGRHIGARAGAPLPGQPIDANSVTAQLQQLYRQVTRGE 307 Query: 297 TED 299 ED Sbjct: 308 LED 310 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: 268 Number of extensions: 9 Number of successful extensions: 4 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: 322 Length adjustment: 27 Effective length of query: 282 Effective length of database: 295 Effective search space: 83190 Effective search space used: 83190 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 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