Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_028582888.1 G494_RS0100225 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000429965.1:WP_028582888.1 Length = 393 Score = 308 bits (789), Expect = 2e-88 Identities = 161/397 (40%), Positives = 239/397 (60%), Gaps = 6/397 (1%) Query: 19 EKYFSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQ 78 + FS + + S +RE+LK+ +IS AGGLP + FPV+ + + V + Sbjct: 2 DSLFSDRITDVPQSFIREILKVTLDPSIISFAGGLPNRQLFPVQALQQAADTVFSQAGMD 61 Query: 79 ALQYGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVV 138 ALQY ++G+ PLR +A+ R++ + ++ I+IT+GSQQ LDL+G+ IN GD V++ Sbjct: 62 ALQYANSEGYLPLREFIAQRYRQKQQLEVAPEHILITTGSQQGLDLLGKTLINSGDPVMI 121 Query: 139 EAPTYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNP 198 EAP YL A+QAF Y P+F I +D+ GM + LE+ L KL+YT+P FQNP Sbjct: 122 EAPGYLGAIQAFSMYRPQFETIAVDEAGMDIPALEQVLDRCSP-----KLLYTVPNFQNP 176 Query: 199 AGVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSK 258 +G++ S R + E ++++D+PYGELR+SG P + + E V+ LG+FSK Sbjct: 177 SGISYSSDNRAAVAARIRESHCILIQDDPYGELRFSGHPRENFLSLIPEQTVL-LGSFSK 235 Query: 259 ILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFY 318 +AP RIGW+ A P L+ KL IAKQ+ DL T+ +Q I +Y+ LD H+ II+ Y Sbjct: 236 TVAPALRIGWLVAPPQLMEKLLIAKQASDLHTDYLAQRILHQYLRDNDLDLHVNRIIQAY 295 Query: 319 KPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAF 378 +++AM+ A+ P GV T PEGGMF+WVTLP I + A+ + VA+VPG F Sbjct: 296 GRQKEAMVAAIGRHFPAGVHCTNPEGGMFLWVTLPAAISAMELFHTAIREKVAFVPGTPF 355 Query: 379 FAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEM 415 + +R NT+RLNF+ + E I GI+RL + I+ M Sbjct: 356 YVNRQDCNTLRLNFSCMDSETIERGIERLGQAIQGMM 392 Lambda K H 0.318 0.137 0.398 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: 395 Number of extensions: 21 Number of successful extensions: 3 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: 417 Length of database: 393 Length adjustment: 31 Effective length of query: 386 Effective length of database: 362 Effective search space: 139732 Effective search space used: 139732 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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