Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013088825.1 BC1002_RS04170 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000092885.1:WP_013088825.1 Length = 398 Score = 400 bits (1027), Expect = e-116 Identities = 209/391 (53%), Positives = 272/391 (69%), Gaps = 7/391 (1%) Query: 11 TWTLARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPA 70 TW L+ RA ++ S IREILKVTE+P +IS AGGLPSP TFP AS +L + A Sbjct: 10 TWQLSERARKLTSSAIREILKVTERPEVISFAGGLPSPATFPAERMREASDRILRDTPAA 69 Query: 71 ALQYAASEGYAPLRQAIADFLPWD---VDADQILITTGSQQALDLIAKVLIDENSRVLVE 127 ALQY+A+EGY PLR+ +A + + Q+LITTGSQQALDL+ KVL+ +S VLVE Sbjct: 70 ALQYSATEGYLPLREWVAQRYSINGAQIRPSQVLITTGSQQALDLLGKVLVCVDSPVLVE 129 Query: 128 TPTYLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRT 187 TPTYLGALQ+F+ EP V V +DD G++ + L+ ++ GA R LY PNFQNPTGR Sbjct: 130 TPTYLGALQSFSMYEPHYVQVPTDDHGLIPEGLEPELTKGA---RLLYTQPNFQNPTGRR 186 Query: 188 MTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKVLAPG 247 + RR AL + A + P++ED+PYG L + P + + P+ +Y+GSFSKVLAPG Sbjct: 187 LPVERRRALAEFAKKAPFPVIEDDPYGALDYAGEPLPTMLSMAPDHIVYLGSFSKVLAPG 246 Query: 248 LRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCE 307 LR+GF++AP+ + KL+QAKQA DLHTP + QR+V EV+K FLD HVPTIR LY+ QC+ Sbjct: 247 LRVGFIIAPEELIFKLVQAKQATDLHTPSFTQRIVHEVVKDGFLDTHVPTIRELYRNQCD 306 Query: 308 AMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADN 367 AML AL + M GV WNRP+GGMF+WV+LP G+ ++LL +AV +NVAFVPGA F+A Sbjct: 307 AMLTALERYMPE-GVSWNRPEGGMFIWVKLPAGIDTMKLLEEAVAQNVAFVPGAPFFASE 365 Query: 368 ADPRTLRLSFVTSTVEQIATGIAALAAAIRS 398 A TLRLSFVT +I G+A L A +R+ Sbjct: 366 AQHNTLRLSFVTVPPAKIDEGVARLGALVRA 396 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: 468 Number of extensions: 16 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: 398 Length adjustment: 31 Effective length of query: 370 Effective length of database: 367 Effective search space: 135790 Effective search space used: 135790 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