Align glutamine-pyruvate transaminase (EC 2.6.1.15); kynurenine-oxoglutarate transaminase (EC 2.6.1.7); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_028989557.1 G579_RS0106655 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_000423825.1:WP_028989557.1 Length = 394 Score = 139 bits (349), Expect = 2e-37 Identities = 87/266 (32%), Positives = 142/266 (53%), Gaps = 14/266 (5%) Query: 61 AADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGHPALVKALSCLYGKIYQ 120 AA +V+LG G PD P Y+KE +A D +YT G P L +A+ + + Sbjct: 29 AAGRDIVSLGAGEPDFDTPDYIKEAAIQA-IRDGFTKYTAVDGTPGLKQAIIDKFARDNG 87 Query: 121 RQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLR 180 P E+ILV+VG S+FN Q L++PGDEVI+ P++ Y + +A A PV + Sbjct: 88 FHFAP-EQILVSVGGKQSIFNLCQALLNPGDEVIVPAPYWVSYTDIAILAEARPVIL--- 143 Query: 181 SKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKH 240 GM S + P +L + + +T+ + +N+P NP G YT EL + ++ +H Sbjct: 144 ---ETGM---DSGFKITPEQLAAAITPQTRLLFINSPSNPTGAAYTAAELAALGEVLRRH 197 Query: 241 DTLCI-SDEVYEWLVYTGHTHVKIA-TLPGMWERTITIGSAGKTFSVTGWKLGWSIGPAH 298 + I +D++YE +++T V IA P + RT+ + K +++TGW++G+ GP Sbjct: 198 PRVLIATDDMYEKILFTEAPFVNIANACPDLLPRTVVLNGVSKAYAMTGWRIGYCAGPRE 257 Query: 299 LIKHLQTVQ-QNSFYTCATPLQAALA 323 LI+ + VQ Q++ C+ +AA A Sbjct: 258 LIQAMTNVQSQSTSNPCSIAQKAAEA 283 Lambda K H 0.320 0.136 0.419 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: 368 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 455 Length of database: 394 Length adjustment: 32 Effective length of query: 423 Effective length of database: 362 Effective search space: 153126 Effective search space used: 153126 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 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