Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_086511983.1 BZY95_RS21775 branched-chain amino acid transaminase
Query= BRENDA::P54691 (305 letters) >NCBI__GCF_002151265.1:WP_086511983.1 Length = 322 Score = 147 bits (371), Expect = 3e-40 Identities = 92/270 (34%), Positives = 151/270 (55%), Gaps = 14/270 (5%) Query: 9 YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68 + + +++P+ DAK + TH LHYG F G+R GT L FR+ H RL SA Sbjct: 12 WLDGEWLPWRDAKTHLLTHTLHYGMGCFEGVRAYAGAH--GTHL-FRVAEHTRRLLDSAH 68 Query: 69 FLHYDISAEKIKEVIVDFVKK---NQPDKSFYIRPLVYSSGLGIAPRLHNLEKDFLVYGL 125 L DI +EV+++ ++ ++ Y++P V+ G+ R L ++ Sbjct: 69 AL--DIPVAFDEEVLIEAQRQCLVRNELRNAYLKPTVFFGAEGLGLRAKGLSVHVMIAAW 126 Query: 126 EMGDYLAAD----GVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAIL 181 ++GDY++++ G+ SSW R R K + Y+ S LA AV++GFDEAI+ Sbjct: 127 DLGDYVSSEAATLGLRALTSSWARHHVNISLCRAKTNGHYVNSILALNTAVKAGFDEAIM 186 Query: 182 MNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAAD-LGIPTCQRPIDK 240 ++ +G V EA+ NVF++R+G + TP L+GITRDS++ +A + LG+ +R I + Sbjct: 187 LDPEGYVAEASAANVFLLRDGALHTP-EVTSCLQGITRDSVIHLAREVLGLEVRERRITR 245 Query: 241 SELMIADEVFLSGTAAKITPVKRIENFTLG 270 EL ADE F++GTAA+I P++ ++ +G Sbjct: 246 DELYTADEAFVTGTAAEILPLRELDGRHIG 275 Lambda K H 0.320 0.138 0.406 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: 215 Number of extensions: 8 Number of successful extensions: 5 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: 305 Length of database: 322 Length adjustment: 27 Effective length of query: 278 Effective length of database: 295 Effective search space: 82010 Effective search space used: 82010 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 10 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