Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012335186.1 M446_RS26500 branched-chain amino acid aminotransferase
Query= BRENDA::F2L0W0 (295 letters) >NCBI__GCF_000019365.1:WP_012335186.1 Length = 288 Score = 110 bits (275), Expect = 4e-29 Identities = 79/251 (31%), Positives = 122/251 (48%), Gaps = 6/251 (2%) Query: 27 GFGVFEGIRAYWNGENLYVFRLRDHMERLLRSAKIIGLDVPYTAEELSKAVVETVRANGF 86 G VF+G R++ L H+ R+ RSA +GL E V E + Sbjct: 36 GSTVFDGARSFEG----VTPDLDLHLARVNRSATAMGLKPVVAVETWRDLVREGLARFDA 91 Query: 87 KEDLYIRPVAYISKPQISLDVRGLQASVAIAAIPFGKYLKVEGVRAAVVS-WRRVHTSMM 145 + LYIRP+ Y ++ + VR S + + V G + +S +RR Sbjct: 92 RTPLYIRPM-YWAESGFAGGVRFDPESTNWCLCLYEAPMPVPGRLSVTLSPFRRPTAETA 150 Query: 146 PVMAKATGIYLNSIMAAVEARARGYDEAIMLNAEGKVVEGSGENIFIVRRGVLMTPPLED 205 PV AKA +Y N A EA++RG+ ++ +A G + E + N F+VR GV+ TP Sbjct: 151 PVEAKAGCLYPNGARALAEAQSRGFGNCLVRDALGNIAEFANANAFLVRDGVVATPAANG 210 Query: 206 GILEGITRETVISIAGDLGIPLLEKSITREELYAADEAFFVGTAAEITPIIEIDGRVLQR 265 L G+TR VI + + G+ + E ++T + AADE F G +++ P+ IDGR L+ Sbjct: 211 TYLAGVTRNRVIGLLREAGVTVAETTLTHADFAAADEIFSTGNFSKVMPVTGIDGRELEP 270 Query: 266 GPITQKIAETY 276 GPI Q+ + Y Sbjct: 271 GPIYQRARDLY 281 Lambda K H 0.320 0.138 0.396 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: 203 Number of extensions: 11 Number of successful extensions: 2 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: 295 Length of database: 288 Length adjustment: 26 Effective length of query: 269 Effective length of database: 262 Effective search space: 70478 Effective search space used: 70478 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