Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_022949157.1 H035_RS0111665 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000421465.1:WP_022949157.1 Length = 473 Score = 172 bits (435), Expect = 2e-47 Identities = 114/366 (31%), Positives = 177/366 (48%), Gaps = 13/366 (3%) Query: 17 GASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEG 76 G + + L++ + + +PDP F P + RA + NSG A Y G Sbjct: 94 GQALVLRLIQATNERDFVQLGAAVPDPGFLPVRPLQRALSAAAR-NSGEHLAT-YQFPPG 151 Query: 77 FTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQ 136 LR I + G + DE++VTSG Q+AL + + PG+ I + P + LQ Sbjct: 152 NPELRRQIARRMADSGCRIPPDEIVVTSGCQEALILALRAVARPGDVIAIESPCFYVLLQ 211 Query: 137 AFSPYEPQYLSVPGD-AEGPDLAAVEAALEQKP-KFFYLVPDFQNPNGTTISLARREALL 194 A Q L +P G L A+ ALEQ P K L +F NP G + +++AL+ Sbjct: 212 AIESLGLQALEIPTHPTTGISLEALTLALEQWPVKACALTANFSNPLGYCMPAEKKQALV 271 Query: 195 DLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRV 254 L A+HG P++ED Y +L ++G+ P++ A D + V++C SFSKT+ P L V Sbjct: 272 ALLARHGTPLIEDDIYGDLGFDGDRPPAVRAFDEEGS------VIYCSSFSKTLSPGLGV 325 Query: 255 GWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQN-FDSHIRRLRAGYKERRDAML 313 GWI P + +K +L T T Q + D + +D H+R++R Y M+ Sbjct: 326 GWII-PGRWREAVAFLKCVTNLATPTWPQFAIADFLRHGGYDHHLRQVREEYSRHVALMI 384 Query: 314 TALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGK 373 A+ + P G T+P GG +W+ELP+ D V L A++ ++ PG F A Sbjct: 385 RAVGRYFPEGTRVTQPRGGFVIWVELPQSVDAVTLCQEALQ-RRISIAPGPIFSAAGKYA 443 Query: 374 NTLRLS 379 + +RL+ Sbjct: 444 HFIRLN 449 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: 494 Number of extensions: 28 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: 404 Length of database: 473 Length adjustment: 32 Effective length of query: 372 Effective length of database: 441 Effective search space: 164052 Effective search space used: 164052 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