Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011606633.1 FRAAL_RS24185 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000058485.1:WP_011606633.1 Length = 484 Score = 140 bits (353), Expect = 8e-38 Identities = 110/361 (30%), Positives = 164/361 (45%), Gaps = 6/361 (1%) Query: 37 GIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAALQYAASEGYAPLRQAIADFLPWDVD 96 G++ LA P PV AAA+A P A G LR IA + Sbjct: 126 GVLDLASAYLDPAAQPVGLLAAAAARAARR--PGAWDRTPVAGLPDLRGLIAGLVSPSHT 183 Query: 97 ADQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEPSVVAVASDDEGVL 156 A +L+T+G Q AL L+ + L + VE TY GAL A V V +D GV Sbjct: 184 ASDVLVTSGGQAALALVFRALGRPGEALAVEHTTYPGALAAARAAGLVPVPVPADGAGVR 243 Query: 157 IDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPYGDL 216 DDL +G AR +Y+ P NPTG + RR A++ A + VED+ L Sbjct: 244 PDDLADVLGRSG--ARLVYLQPRHANPTGAVLAPDRRPAVLAALRDHRAFCVEDDWVAPL 301 Query: 217 WFDNPPPAPLTARNPEG-CIYMGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAADLHTP 275 P PL A +P+G +++ S SK ++PGLR+ V A V +L +A+ DL Sbjct: 302 DLTAVSPPPLAAADPDGHVVHVLSLSKSVSPGLRIAAVTARGPVAARLARARITDDLFVA 361 Query: 276 GYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVEWNRPDGGMFLWV 335 Q+ E++ RH+ ++R + + A+LAA+ + + LG P GG+ +W+ Sbjct: 362 PVLQQTAVELLSTPGWRRHLASLRRVLLARRAALLAAIARALPTLGPP-QPPSGGVHVWL 420 Query: 336 RLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVTSTVEQIATGIAALAAA 395 LP G + A VA PG+A+ LRL++ + E + + LAA Sbjct: 421 PLPPGADDRLVTAAARRAGVAVGPGSAYTVGEVVAPHLRLTYSRTPGEGLVAAVDRLAAV 480 Query: 396 I 396 + Sbjct: 481 L 481 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: 542 Number of extensions: 29 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: 484 Length adjustment: 32 Effective length of query: 369 Effective length of database: 452 Effective search space: 166788 Effective search space used: 166788 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