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_012407008.1 NPUN_RS00985 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_000020025.1:WP_012407008.1 Length = 388 Score = 154 bits (390), Expect = 4e-42 Identities = 101/320 (31%), Positives = 158/320 (49%), Gaps = 22/320 (6%) Query: 66 VVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGHPALVKALSCLYGKIYQRQID- 124 V + G PD P+++K KA + +Y G P L +A++ + +D Sbjct: 32 VCSFSAGEPDFDTPAHIKAAAVKA-LDEGKTKYGAAAGEPKLREAIA--HKLKNDNGLDY 88 Query: 125 PNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLRSKPT 184 +E ++V G SL+N I L+D GDEVII P++ Y MV + G V V +P + T Sbjct: 89 KSENVIVTNGGKHSLYNLIVALIDLGDEVIIPAPYWLSYPEMVTLVGGVAVIVP--TDAT 146 Query: 185 DGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKHDTLC 244 G K T P +L + KTK ILN+P NP G VYT E++ +A + V D Sbjct: 147 TGYKIT-------PEQLRKAITPKTKLFILNSPSNPTGMVYTPDEIKALAQVVVDADIFV 199 Query: 245 ISDEVYEWLVYTGHTHVKIATL-PGMWERTITIGSAGKTFSVTGWKLGWSIGPAHLIKHL 303 +SDE+YE ++Y G H+ I +L +++RT+ K +S+TGW++G+ GP +IK Sbjct: 200 VSDEIYEKILYDGAEHISIGSLGKEIFDRTLISNGFAKAYSMTGWRIGYLAGPVEIIKAA 259 Query: 304 QTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLNSV-G 362 T+Q +S T Q A +C + + +R M+ LN++ G Sbjct: 260 STIQGHSTSNVCTFAQYGAIAAL------QSSQDC-VEEMRQAFAKRRQVMLDRLNAIPG 312 Query: 363 LKPIVPDGGYFIIADVSSLG 382 L PDG +++ D+S G Sbjct: 313 LSTAKPDGAFYLFPDISKTG 332 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: 409 Number of extensions: 31 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: 455 Length of database: 388 Length adjustment: 32 Effective length of query: 423 Effective length of database: 356 Effective search space: 150588 Effective search space used: 150588 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: 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