Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_041702288.1 PAES_RS06865 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q6YP21 (454 letters) >NCBI__GCF_000020625.1:WP_041702288.1 Length = 402 Score = 150 bits (379), Expect = 7e-41 Identities = 106/352 (30%), Positives = 173/352 (49%), Gaps = 29/352 (8%) Query: 29 FSTSAKMSLKFTNAKRIEGLDSNVWIEFTKLAADPSVVNLGQGFPDISPPTYVKEELSKI 88 + T ++++ + RI GL + E +V+L G PD P +V + + I Sbjct: 11 YLTRRVLNMQESQTMRITGLAKKMKAE------GKDIVSLSAGEPDFPTPLFVSQ--AGI 62 Query: 89 AAIDSLNQYTRGFGHPSLVKALSYLYEKLYQ-KQID-SNKEILVTVGAYGSLFNTIQALI 146 AIDS +TR + + + S + KL + Q+D + E++V+ G +L N I AL Sbjct: 63 EAIDS--GFTRYTANSGIAELKSAVIAKLKRDNQLDYTPDEVIVSNGGKQTLINAILALC 120 Query: 147 DEGDEVILIVPFYDCYEPMVRMAGATPVFIPLRSKPVYGKRWSSSDWTLDPQELESKFNS 206 EGDEVI+ P++ + MVR+AGA+PV +P + Y + P++LE+ Sbjct: 121 QEGDEVIIPAPYWVSFPEMVRLAGASPVTVPTSIENGY---------KMTPEDLENAITD 171 Query: 207 KTKAIILNTPHNPLGKVYNREELQVIADLCIKYDTLCISDEVYEWLVYSGNKHLKIATFP 266 KTK ILN+P NP G VYN +E+ + + ISDE+Y+ +VY K A Sbjct: 172 KTKLFILNSPSNPSGAVYNEQEVTALMQVLEGRGIFVISDEMYDKIVYGDVKPYSPARIE 231 Query: 267 GMWERTITIGSAGKTFSVTGWKLGWSIGPNHLIKHLQTVQQNTIYTCATPLQEALAQAFW 326 M + + KT+++TGW++G+ GP +IK +Q T + Q+A A A Sbjct: 232 AMRDWVLVSNGVSKTYAMTGWRIGYLAGPKWIIKACDKIQSQTTSNPNSIAQKAAAAALN 291 Query: 327 IDIKRMDDPECYFNSLPKELEVKRDRMVRLLESV-GLKPIVPDGGYFIIADV 377 D + ++D E E +RD M + L + G+ +P+G ++I V Sbjct: 292 GDQQVVEDRRL-------EFEKRRDYMYKALNEIPGITASLPEGAFYIFPSV 336 Lambda K H 0.319 0.135 0.407 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: 398 Number of extensions: 17 Number of successful extensions: 2 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: 454 Length of database: 402 Length adjustment: 32 Effective length of query: 422 Effective length of database: 370 Effective search space: 156140 Effective search space used: 156140 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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