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_012542465.1 KVAR_RS18515 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_000025465.1:WP_012542465.1 Length = 386 Score = 208 bits (529), Expect = 3e-58 Identities = 129/399 (32%), Positives = 204/399 (51%), Gaps = 30/399 (7%) Query: 45 RIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGH 104 ++ L + ++ + + LA +NL QGFPD P Y++E L+ NQY G Sbjct: 11 KLPALGTTIFTQMSALAQQHQAINLSQGFPDFDGPRYLQERLAYHV-AQGANQYAPMTGV 69 Query: 105 PALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYE 164 PAL +A++ ++Y D N +I V GA +L+ +I LV GDEV+ P YD Y Sbjct: 70 PALREAIAGKTAELYGYLPDVNSDITVTAGATEALYAAITALVRRGDEVVCFDPSYDSYA 129 Query: 165 PMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKV 224 P V +AG I L+ P + W ++ + S KT+ +ILNTPHNP V Sbjct: 130 PAVALAGGELRRIALQP-PHFRVDW---------QQFAAALSDKTRLVILNTPHNPSATV 179 Query: 225 YTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFS 284 + R++ + + + +SDEVYE + + H + P + ER + + S GKTF Sbjct: 180 WQREDFAALWQAIAEREIYVLSDEVYEHICFAEGGHASVLAHPQLRERAVAVSSFGKTFH 239 Query: 285 VTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLP 344 +TGWK+G+ + PA + L+ V Q ++ TP Q A+A+ + PE ++ LP Sbjct: 240 MTGWKVGYCVAPAAISAELRKVHQYLTFSVNTPAQLAIADML------REAPE-HYRELP 292 Query: 345 KELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTK 404 +RD + L L+ + +G YF++AD S++ +DL D++ F +W+T Sbjct: 293 AFYRERRDLFIEALRPSRLELLPCEGTYFLLADYSAI-SDLDDVS--------FCRWLTT 343 Query: 405 HKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAA 443 + AIP+S FC + P KL+R CF K+ +TL AA Sbjct: 344 EVGVAAIPLSVFC---ADPFPHKLIRLCFAKQPATLLAA 379 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: 427 Number of extensions: 24 Number of successful extensions: 6 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: 386 Length adjustment: 32 Effective length of query: 423 Effective length of database: 354 Effective search space: 149742 Effective search space used: 149742 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