Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012335934.1 M446_RS30435 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000019365.1:WP_012335934.1 Length = 467 Score = 164 bits (416), Expect = 4e-45 Identities = 111/345 (32%), Positives = 170/345 (49%), Gaps = 18/345 (5%) Query: 38 GGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPLREWICAYLGRRGIQAGL 97 G +P P + P A+ RA + + A L Y G PLR + L RGI AG Sbjct: 114 GWLP-PSWLPDEALRRALRGLARGE--AADLLAYDEPLGHAPLRRALARRLHDRGIPAGP 170 Query: 98 DEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSPYEPQYLSVPGDAEGPDL 157 + +++T + QAL+ V +LL+ PG+ +LV P Y + + + VP GPDL Sbjct: 171 ERIVLTDSATQALDLVARLLLEPGDPVLVDDPCYFNFRSLLQAHRARLVGVPWTPAGPDL 230 Query: 158 AAVEAALE-QKPKFFYLVPDFQNPNGTTISLARREALLDLCAKHGVPIVEDAAYTELRYE 216 A AAL +P+ + FQNP G T+S LL L H V +VEDA + +L + Sbjct: 231 DAFAAALRAHRPRLYVTNSAFQNPTGATMSAGIAHRLLRLAEAHDVLVVEDALFEDL--D 288 Query: 217 GEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDL 276 +P P + LD + V+ GSFSKT+ A+R G+ + ++R+V +K A Sbjct: 289 PDPAPRLATLDG------LDRVIAIGSFSKTLSAAVRCGYAAMRPDWVDRVVDLKLAASF 342 Query: 277 HTSTINQIVLHDVVSQNFDSHIRRLRAGYKER-RDAMLTALSEFAPAGVT-WTKPEGGMF 334 + + ++H ++ D RR G + R DAM A AG+T W +P GG++ Sbjct: 343 GSGRLAAGLVHRFLA---DGSYRRALDGLRARLADAMGATRRRLAAAGLTPWLEPRGGLY 399 Query: 335 VWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKNTLRLS 379 +W+ LPEG D + RA+ + V PG+ F +S + LR + Sbjct: 400 LWVSLPEGLDAAGIARRALAE-GVVLAPGNVFSLSQSAGSFLRFN 443 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: 483 Number of extensions: 28 Number of successful extensions: 4 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