Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_005455497.1 SACCYDRAFT_RS08780 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000244975.1:WP_005455497.1 Length = 497 Score = 140 bits (352), Expect = 1e-37 Identities = 123/357 (34%), Positives = 168/357 (47%), Gaps = 26/357 (7%) Query: 53 VSAFAAASAAVLANDGPAALQYAA--SEGYAPLRQAIADFLPWD---VDADQILITTGSQ 107 V A A AV +D L+ A G LR+A+A +Q+L+TTG+ Sbjct: 134 VPEVAEALRAVADHDITELLRDAGYHPRGLPALREAVAHHYTTQGLPTSPEQVLVTTGAH 193 Query: 108 QALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTG 167 QAL L+A+V + S V VE P++ L F +V V DDEGV + L A+ TG Sbjct: 194 QALVLLAEVYLRGASAVAVEVPSWAPCLDIFRQHGVRLVPVGLDDEGVDVHAL-AEALTG 252 Query: 168 ADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPYG--DLWFDNPP-PA 224 A LYV+P F NPTGR M+ ARR + + AA + +VED+ Y L D PA Sbjct: 253 TTPA-LLYVMPTFHNPTGRLMSAARRRQVAELAARHGVAVVEDHAYAGHSLTVDETALPA 311 Query: 225 PLTARNPE-GCIYMGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVA 283 PL A PE G + K + GLR+G+V P + + + K ADL +P Q + A Sbjct: 312 PLAAYAPESGEVLTVESLKGIWAGLRVGWVRGPAGIIERCARRKAMADLGSPLIEQAVAA 371 Query: 284 EVMKGNFLDRHVPTIRALYKQQC---EAMLAALTQEMAGLGVE--WNRPDGGMFLWVRLP 338 R VP + L + +C LA L + E W PDGG LWVRLP Sbjct: 372 ---------RLVPRLAELSRARCVVQRRQLAELEHLLRQRLPEWTWTTPDGGSSLWVRLP 422 Query: 339 EGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVTSTVEQIATGIAALAAA 395 G SA A+ V VPG+ R+ FV +E++A ++ LA+A Sbjct: 423 GGHSADVYAQLALRHGVEVVPGSTMDPTGQHDGYFRIPFV-RPLEELAELVSRLASA 478 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: 454 Number of extensions: 27 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: 497 Length adjustment: 33 Effective length of query: 368 Effective length of database: 464 Effective search space: 170752 Effective search space used: 170752 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