Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_028310814.1 H566_RS0106550 branched-chain amino acid transaminase
Query= BRENDA::P54691 (305 letters) >NCBI__GCF_000482785.1:WP_028310814.1 Length = 308 Score = 185 bits (469), Expect = 1e-51 Identities = 112/305 (36%), Positives = 169/305 (55%), Gaps = 15/305 (4%) Query: 7 IAYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKS 66 + + + K V + DAKI V TH LHYG F G+R + G+ +FRL H RL S Sbjct: 9 VIWMDGKMVDWRDAKIHVLTHTLHYGMGVFEGVRAYQQAD--GSTAVFRLKEHTRRLFNS 66 Query: 67 AKFLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLV 122 A+ ++ + E+I E V++N+ + S YIRP+ + S LGI R + + V Sbjct: 67 ARIFQMNLPFTEEQISEATKAVVRENKLE-SCYIRPIAWIGSDKLGIGARTNTIH--VAV 123 Query: 123 YGLEMGDYLAADG----VSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDE 178 G YL A+G + + SS+ + K Y S L+ EA G+DE Sbjct: 124 AAWPWGAYLGAEGMERGIRVKTSSFTHHHPNVTMCKAKAVGNYPVSILSNQEATNEGYDE 183 Query: 179 AILMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPI 238 A+LM+ QG VC+ +G NVF+V++G++ TP L+GITR+SI T+AA+ GI +R I Sbjct: 184 AMLMDPQGFVCQGSGENVFLVKDGELHTPDLAGGALDGITRNSIFTLAAEHGIKVVERRI 243 Query: 239 DKSELMIADEVFLSGTAAKITPVKRIENFTLG-GDR-PITEKLRSVLTAVTENREPKYQD 296 + E I DE F +GTAA++TP++ ++ T+G G R P+T KL++ V R PKY + Sbjct: 244 TRDEFYIGDEAFFTGTAAEVTPIRELDGRTIGAGSRGPVTTKLQAAFFDVVNGRNPKYAE 303 Query: 297 WVFKI 301 W+ K+ Sbjct: 304 WLAKV 308 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: 224 Number of extensions: 8 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: 305 Length of database: 308 Length adjustment: 27 Effective length of query: 278 Effective length of database: 281 Effective search space: 78118 Effective search space used: 78118 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