Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_004312947.1 C665_RS12800 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000310185.1:WP_004312947.1 Length = 494 Score = 131 bits (329), Expect = 5e-35 Identities = 104/319 (32%), Positives = 149/319 (46%), Gaps = 20/319 (6%) Query: 44 GLPSPKTFPVSAFAAASAAVLANDGPAALQYAASEGYAPLRQAIADFLP----WDVDADQ 99 G+P FP A+ A + G L YAA G LR A+A L VDA Q Sbjct: 126 GVPDFGAFPFRAWRACLERAWRDAGWRQLGYAAHGGDPSLRAALAAHLGSVRGLAVDAAQ 185 Query: 100 ILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEPSVVAVASDDEGVLIDD 159 +LIT+G+Q LDL A++L D V VE P YL A AF V V DDEG+ Sbjct: 186 LLITSGTQAGLDLCARLLADHGDTVWVENPGYLAARVAFGLAGLQVHDVMVDDEGL---- 241 Query: 160 LKAKVGTGADK-----ARFLYVLPNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPYG 214 GA+ R + P+ Q P+GR M+ RR AL++ A +VED+ Sbjct: 242 -----APGAEDWLRHPPRLIMTTPSHQYPSGRVMSLPRRFALIERARAAGTWIVEDDYDS 296 Query: 215 DLWFDNPPPAPLTARNPEGCI-YMGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAADLH 273 + P P L P + Y G+FSK L PGLRLG++V P+ + + A A Sbjct: 297 EFRRAGPAPPALFGLQPGATVVYAGTFSKTLYPGLRLGYLVLPRTIAADFIHAAARATRA 356 Query: 274 TPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVEWNRPDGGMFL 333 G QR +A+ + H+ +RA Y + A+ AAL Q G G+ + + G+ L Sbjct: 357 GQGIEQRALADFIGRGHYITHLRRMRARYNARQAALRAALRQAF-GPGLLLSGGEAGLHL 415 Query: 334 WVRLPEGMSAIELLPQAVE 352 + LP+ + + + +A + Sbjct: 416 VMWLPDELPDVAVAQRAAQ 434 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: 489 Number of extensions: 26 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: 401 Length of database: 494 Length adjustment: 32 Effective length of query: 369 Effective length of database: 462 Effective search space: 170478 Effective search space used: 170478 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