Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate WP_089302294.1 CHB84_RS15310 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q16773 (422 letters) >NCBI__GCF_900188115.1:WP_089302294.1 Length = 414 Score = 157 bits (398), Expect = 4e-43 Identities = 90/239 (37%), Positives = 136/239 (56%), Gaps = 13/239 (5%) Query: 30 VVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEID 89 V+ G G PDFP PD+ + A + AV + + YT G P L + +A+ G EI+ Sbjct: 48 VIGFGAGQPDFPTPDYILAAAEDAVH-QRVNHGYTAAAGLPELREAIATKTERDSGVEIE 106 Query: 90 PLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPGPI 149 P + VLVT GG A+++A L D GDEV++ P++ Y +AGG PV V+ Sbjct: 107 PSQ-VLVTNGGKQAVYSAMATLCDPGDEVLLPAPYWTTYPESIKLAGGVPVQVTAD---- 161 Query: 150 QNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVV 209 S+ +++ +L T RTKAL+ N+P+NP G V+ REE+E + +H + Sbjct: 162 ------ESTGYRVTVEQLEAARTERTKALLFNSPSNPTGAVYPREEVEAIGRWALEHGIW 215 Query: 210 CITDEVYQWMVYDGHQHISI-ASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMK 267 ITDE+Y+ +VYDG + SI A +P + + TL + KT+S TGW+VGW+ GP ++K Sbjct: 216 VITDEIYEHLVYDGARAHSISAVVPELADTTLVLNGVAKTYSMTGWRVGWIAGPQDVIK 274 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: 437 Number of extensions: 23 Number of successful extensions: 3 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: 414 Length adjustment: 32 Effective length of query: 390 Effective length of database: 382 Effective search space: 148980 Effective search space used: 148980 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