Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_013093062.1 BC1002_RS26415 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1015 (396 letters) >NCBI__GCF_000092885.1:WP_013093062.1 Length = 402 Score = 323 bits (827), Expect = 7e-93 Identities = 175/388 (45%), Positives = 247/388 (63%), Gaps = 10/388 (2%) Query: 13 SAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIRAASNAALAEEPGAALQYGATEGYNPL 72 S IRELFK L +PG+ISFAGG+P S +FD EG+ AA+ A + +P LQYG T+G L Sbjct: 14 SPIRELFKYLAQPGMISFAGGYPASDLFDREGLDAAA-ARASHQPTLCLQYGPTDGIAIL 72 Query: 73 REQLAAFMTSKGAKDVAADNLIVTTGSQQALDLLGKTLISPGDKVIVEGPTFLATIQCFR 132 +EQL+ M +GA+ D L+VTTGSQQ DLL + +++PGD V+VE P + AT+Q + Sbjct: 73 KEQLSQLMARRGARCAPTD-LLVTTGSQQGFDLLLRVMVAPGDVVLVEQPAYPATLQALK 131 Query: 133 LYGAELISAPIDGNGVKTDELEKLIA----EHKPKFVYLIPTFGNPSGAMLSLERRKAVL 188 L A++++ P+D +GV +L L+ PK +Y +PTF NP+GA LSLERR A+L Sbjct: 132 LQQADVVTVPVDQHGVDVAKLAALLETGALRRAPKLLYTVPTFANPTGATLSLERRIALL 191 Query: 189 EMAVKHNTLIVEDDPYGDLYFGDAPPPSLLNLSATVPGSRELLVHCGSLSKVLSPGLRVG 248 ++A ++ +IVEDDPYGDL F PSL LS VP SR+ +VH SLSK+++PGLRVG Sbjct: 192 KLAARYRFVIVEDDPYGDLRFDGTAVPSLFALSEQVPDSRDWVVHFSSLSKIVAPGLRVG 251 Query: 249 WMIAPAELLGKATMCKQFSDAHTSTFAQATAAQYLKAGRMPGTLANVRKVYAERAQAMGD 308 WM+A A+++ + + KQ D ++ + Q AA+YL +G + L + YA + + + D Sbjct: 252 WMVAHADIVRRCVIAKQTVDLCSAPWTQVMAAEYLASGALERHLPRIIDAYAVKCRTLCD 311 Query: 309 ALRKELGDAIEFVQPQGGLFVWARLTGAGGKVADGNVLAKRAIEKGVAFVPGTPFFCANP 368 AL L I F +P GG+FVWARL AG D + + IE+ V FVPG F+ Sbjct: 312 ALDTHLAQHIAFHRPAGGMFVWARLNAAG----DASDYLRMCIEQNVVFVPGVAFYNDAV 367 Query: 369 DHATFRLSFATADVDKIREGVARLGQAV 396 D A RLSFA + V++I GV R+ +A+ Sbjct: 368 DRAALRLSFAASGVEEIETGVHRMKRAL 395 Lambda K H 0.319 0.136 0.394 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: 435 Number of extensions: 18 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: 396 Length of database: 402 Length adjustment: 31 Effective length of query: 365 Effective length of database: 371 Effective search space: 135415 Effective search space used: 135415 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 (21.7 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