Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011766198.1 AZO_RS12450 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000061505.1:WP_011766198.1 Length = 467 Score = 175 bits (444), Expect = 2e-48 Identities = 120/378 (31%), Positives = 184/378 (48%), Gaps = 13/378 (3%) Query: 21 IRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPL 80 I E+L ++ P ++ P FP +AR + A + G L Sbjct: 95 IFEILDAVKDPAVVPLGSSFASPALFPLDKLARCLAAAARHMDPR--ATVTDLPPGNDEL 152 Query: 81 REWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSP 140 R I G E++VTSG+ +AL + PG+ + + PT+ LQ Sbjct: 153 RRQIALRYLAAGATVSPGEIVVTSGAMEALNLSLEATTQPGDLVAIESPTFHAILQMIER 212 Query: 141 YEPQYLSVPGDA-EGPDLAAVEAALEQKP-KFFYLVPDFQNPNGTTISLARREALLDLCA 198 + + +P +G DL A+EAAL +P K L+ +FQ+P G + A R ALLDL Sbjct: 213 RGLKVIELPTHPRDGVDLPALEAALATQPVKACMLMLNFQHPTGACVPDASRPALLDLLR 272 Query: 199 KHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWIN 258 +H VP++ED Y EL ++ +P ALD + G + +V FSK++ P R+GW+ Sbjct: 273 RHQVPLIEDDTYAELHFDRQPPLPTKALD---DDGLVLHV---SGFSKSLAPGYRLGWV- 325 Query: 259 GPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQN-FDSHIRRLRAGYKERRDAMLTALS 317 ++ +K + L T+ QI + D + Q FD+H+RRLR+ + + A+ A+ Sbjct: 326 AAGRYAQKVQRLKLSASLATTIPVQIAIADFLRQGAFDAHLRRLRSALEIQEAALAAAVE 385 Query: 318 EFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKNTLR 377 PAG T+P GG F W+ELP GTD + L RA+ D ++ PG F A R N +R Sbjct: 386 RHFPAGTRLTRPRGGYFSWVELPAGTDALALHRRAL-DEGISIAPGPIFSAGREYANFIR 444 Query: 378 LSFSNNNPERIREGIRRL 395 L+F + I +RRL Sbjct: 445 LNFGHPWSGEIERAMRRL 462 Lambda K H 0.320 0.138 0.410 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: 485 Number of extensions: 26 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: 404 Length of database: 467 Length adjustment: 32 Effective length of query: 372 Effective length of database: 435 Effective search space: 161820 Effective search space used: 161820 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: 51 (24.3 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