Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate WP_086510442.1 BZY95_RS13490 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q16773 (422 letters) >NCBI__GCF_002151265.1:WP_086510442.1 Length = 386 Score = 159 bits (402), Expect = 1e-43 Identities = 107/328 (32%), Positives = 160/328 (48%), Gaps = 28/328 (8%) Query: 25 ASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELL 84 A+ HDV++L G PDF P+ V A Q A++ L +Y+ G P L + +A +GE Sbjct: 27 AAGHDVIHLEVGEPDFATPEPVVAAGQAALAAG--LTRYSPAAGLPALREAIAGHYGEHF 84 Query: 85 GQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSL 144 G ++DP R VLVT G GAL A Q LV GD V++ +P + C +AG Sbjct: 85 GADVDP-RRVLVTPGASGALLLASQLLVGPGDRVLMADPNYPCNRHFMALAGAE------ 137 Query: 145 KPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQ 204 + +G S WQLD +A + T+ +L TP+NP G + +L+ VA Sbjct: 138 ----VDTVPIGPQSGWQLDANLVARHWQDATRLAMLATPSNPTGHMLDAAQLKAVADTVA 193 Query: 205 QHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDH 264 + DE+YQ + YD I+ S+ + + S K F TGW++GW+L P Sbjct: 194 ARGGHLLVDEIYQGLSYD----IAPLSVASLTADAFVVNSFSKYFGMTGWRLGWLLAPQA 249 Query: 265 IMKHLRTVHQNSVFHCPTQSQAAVAESF--EREQLLFRQPSSYFVQFPQAMQRCRDHMIR 322 ++ L + QN PT +Q A +F E LL + S + R RD ++ Sbjct: 250 AVEPLTRLAQNVFLAAPTPAQHAALAAFTPECRALLEARRSE--------LGRRRDALLA 301 Query: 323 SLQSVGLKPII-PQGSYFLITDISDFKR 349 L +GL P + PQG+++L DIS + R Sbjct: 302 GLARLGLAPSLPPQGAFYLWLDISRYSR 329 Lambda K H 0.323 0.139 0.435 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: 369 Number of extensions: 14 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: 422 Length of database: 386 Length adjustment: 31 Effective length of query: 391 Effective length of database: 355 Effective search space: 138805 Effective search space used: 138805 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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