Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_012505142.1 PAES_RS02730 branched-chain amino acid transaminase
Query= BRENDA::P54691 (305 letters) >NCBI__GCF_000020625.1:WP_012505142.1 Length = 303 Score = 171 bits (433), Expect = 2e-47 Identities = 108/293 (36%), Positives = 168/293 (57%), Gaps = 13/293 (4%) Query: 9 YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68 + + V + DAKI + +H +HYG++ F G+R D G+ +LF D H RL +S+K Sbjct: 8 WMNGELVNWHDAKIHILSHVIHYGSSTFEGIRCYDT--DKGSAILF-FDEHIKRLYQSSK 64 Query: 69 FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLVY- 123 +I S +++K+ I+ +K N K+ YIRPLV LG+ P L ++E + Sbjct: 65 IYRMEIPYSEQELKDAIIATIKANG-HKACYIRPLVKRGQGALGVNPALASIEVAIATWE 123 Query: 124 -GLEMGDYLAADGVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAILM 182 G +G+ + +GV +SSW R + P K Y+ S L K EA+ + E I + Sbjct: 124 WGSYLGEEVLENGVDVCVSSWARLAPNTLPTWAKAGGNYLNSQLIKMEALMDNYAEGIGL 183 Query: 183 NSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDKSE 242 + G V E +G N+F++R+G I TP + Q IL GITR++++ IA +LG + I + Sbjct: 184 DVHGYVAEGSGENIFVIRDGIIYTPMSGQSILPGITRNAVIHIARELGYEVQETLIPREA 243 Query: 243 LMIADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRS-VLTAVTENREP 292 L IADEVFL+GTAA+ITPV+ I+ + +G ++ PITE L+S L V + +P Sbjct: 244 LYIADEVFLTGTAAEITPVRSIDKYAVGDEKRGPITELLQSKYLDIVKKGTDP 296 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: 222 Number of extensions: 13 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: 305 Length of database: 303 Length adjustment: 27 Effective length of query: 278 Effective length of database: 276 Effective search space: 76728 Effective search space used: 76728 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