Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_018947475.1 B1A74_RS06385 branched-chain amino acid transaminase
Query= BRENDA::P54691 (305 letters) >NCBI__GCF_001995255.1:WP_018947475.1 Length = 306 Score = 177 bits (450), Expect = 2e-49 Identities = 105/300 (35%), Positives = 166/300 (55%), Gaps = 13/300 (4%) Query: 7 IAYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKS 66 + + + + VP+ DAK V TH LHYG F G+R P P +FRL+ H RL S Sbjct: 9 VIWLDGEMVPWRDAKTHVLTHTLHYGMGVFEGVRAYPTDHGPA---IFRLEDHTRRLFNS 65 Query: 67 AKFLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVYSSGLGIAPRLHNLEKDFLVYG 124 AK L + +AE++ + +N + S Y+RP+ + G+ R NLE +V Sbjct: 66 AKILGMTLPFTAERLNRAQQAAITENNLE-SAYLRPMAFFGSEGMGLRADNLEVHVMVAA 124 Query: 125 LEMGDYLAADGVS----CRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAI 180 G YL DG+ R SS+ R + K + Y+ S +A EA G+DEA+ Sbjct: 125 WSWGSYLGDDGIENGIRIRTSSFSRHHVNVTMCKAKANGNYMNSMMALQEATRCGYDEAM 184 Query: 181 LMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDK 240 L++++G V E +G N+F++ G I TP + L+GITR +++ +AA+ G ++ I + Sbjct: 185 LLDTEGYVAEGSGENIFIISGGVIYTP-DLTSALDGITRRTVIELAAEEGFRVVEKRITR 243 Query: 241 SELMIADEVFLSGTAAKITPVKRIENFTLG-GDR-PITEKLRSVLTAVTENREPKYQDWV 298 E+ IADE F +GTAA++TP++ +++ +G G R PITE L+S V R+ ++QDW+ Sbjct: 244 DEVYIADEAFFTGTAAEVTPIREVDDRPIGTGSRGPITELLQSRYFDVVHGRDSRHQDWL 303 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: 238 Number of extensions: 16 Number of successful extensions: 6 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: 306 Length adjustment: 27 Effective length of query: 278 Effective length of database: 279 Effective search space: 77562 Effective search space used: 77562 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