Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_086511458.1 BZY95_RS19015 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_002151265.1:WP_086511458.1 Length = 515 Score = 140 bits (352), Expect = 1e-37 Identities = 111/350 (31%), Positives = 165/350 (47%), Gaps = 16/350 (4%) Query: 41 LAGGLPSPKTFPVSAFAAASAAVLANDGPAALQYAASEGYAPLRQAIADFLPWDVDA--- 97 LA G+P+ FP + L Y A G LR+A+AD+L Sbjct: 157 LAPGVPALDRFPHGPWQRLVRRHQQRMPREWLAYQAQGGVPTLREALADYLQLSRSVRCR 216 Query: 98 -DQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEPSVVAVASDDEGVL 156 +QILI G+QQ +LIA++L D +V +E P Y GA F + AV DDEG Sbjct: 217 PEQILIVQGAQQGFELIARLLSDPGDKVWIEEPGYPGAQACFAAAGLDLQAVPVDDEG-- 274 Query: 157 IDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPYGDL 216 L A+ R +YV P+ Q P+G TM+ +RR AL++AA +VED+ + Sbjct: 275 ---LSVAAAANAESPRLIYVTPSHQYPSGVTMSLSRRLALLEAAERHGAWIVEDDYDSEF 331 Query: 217 WFDNPPPAPLTAR-NPEGCIYMGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAADLHTP 275 + P A L + IY+G+FSKV+ PGLRLG+VV P+ + +A A LH Sbjct: 332 RYGQRPIAALQGLVDDSRVIYVGTFSKVMYPGLRLGYVVLPEPLVEPFRRAN--ARLHRE 389 Query: 276 GYN--QRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVEWNRPDGGMFL 333 G Q +AE + G RH+ +R Y+++ +A+L G+ + GM L Sbjct: 390 GQYPVQAALAEFIVGGQFSRHIRRMRDCYRRR-QALLRKALAPAVARGLRLSDGQAGMHL 448 Query: 334 WVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVTSTVE 383 L E ELL + + ++ P +++Y + L L + TVE Sbjct: 449 VAWLDEAEQERELLRRGAAQGLSLSPLSSYYLETPARPGLVLGY-AGTVE 497 Lambda K H 0.318 0.134 0.392 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: 480 Number of extensions: 28 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: 401 Length of database: 515 Length adjustment: 33 Effective length of query: 368 Effective length of database: 482 Effective search space: 177376 Effective search space used: 177376 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: 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