Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_093428336.1 BM272_RS08380 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_900112605.1:WP_093428336.1 Length = 482 Score = 182 bits (461), Expect = 2e-50 Identities = 122/391 (31%), Positives = 190/391 (48%), Gaps = 13/391 (3%) Query: 17 GASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEG 76 G + + +++ PE++ +P DF P + RA+ + G L Y G Sbjct: 102 GQALVLRVVQAASEPEVVQMGAAVPHADFLPARGLRRAFAGV--PARWGGRELAYAFPPG 159 Query: 77 FTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQ 136 LR+ I + G Q +EV+VT+G+Q+AL + + PG+ + + PT+ G LQ Sbjct: 160 PAELRQAIARRMADAGCQISPEEVVVTNGAQEALVLSLRAVTEPGDVVAIESPTFYGILQ 219 Query: 137 AFSPYEPQYLSVPGDA-EGPDLAAVEAALEQKP-KFFYLVPDFQNPNGTTISLARREALL 194 A + L +P D EG A+ AL+Q P K L+P+F NP G R+ AL+ Sbjct: 220 AIEGLGLRALEIPTDPDEGIAPEALALALDQWPVKAALLMPNFGNPLGHCAGDERKRALV 279 Query: 195 DLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRV 254 +L GVP++ED Y +L +E P P R G VL+CGSFSKT+ P LRV Sbjct: 280 ELLEDRGVPLIEDDVYGDLPFE-PPRPWAAKAFETRGG-----VLYCGSFSKTLSPGLRV 333 Query: 255 GWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQ-NFDSHIRRLRAGYKERRDAML 313 GW P +RL +K A T + + D + + +D ++RR R Y D + Sbjct: 334 GWA-VPGRFRDRLEYLKYATSSSTPAWPGLAVADFLERGGYDRYLRRARGDYARAVDRVS 392 Query: 314 TALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGK 373 A+ P G T+P GG +W+ELPE D + L RA+++ ++ PG F + Sbjct: 393 RAVVRHFPPGTRQTRPAGGFVLWLELPEAVDALALYRRALEE-GISVAPGPMFSPTGKFR 451 Query: 374 NTLRLSFSNNNPERIREGIRRLCGLLQTVAA 404 N LRL+ + R+ + RL +++ + A Sbjct: 452 NHLRLNCAQPWDARLERALARLGEVVRGMVA 482 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: 585 Number of extensions: 42 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: 482 Length adjustment: 32 Effective length of query: 372 Effective length of database: 450 Effective search space: 167400 Effective search space used: 167400 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 Jul 25 2024. The underlying query database was built on Jul 25 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