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_057506846.1 ABB28_RS01035 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_001431535.1:WP_057506846.1 Length = 382 Score = 234 bits (596), Expect = 5e-66 Identities = 143/401 (35%), Positives = 215/401 (53%), Gaps = 29/401 (7%) Query: 45 RIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGH 104 ++ + + ++ ++LAA+ VNLGQGFPD S P + + + AA D +NQY G Sbjct: 6 KLPKVGTTIFTVMSQLAAEHGAVNLGQGFPDFSAPQRLIDATT-AAMADGLNQYPPMTGV 64 Query: 105 PALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYE 164 L +A++ +Y Q+DP+ EI V GA ++FN+I +V G+EVI++ P YDCYE Sbjct: 65 APLRQAIAQKSLDLYGAQVDPDTEITVTSGATEAIFNAIHAVVRAGEEVIVLDPAYDCYE 124 Query: 165 PMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKV 224 P + +AGA V +PL + + DW + + + +T+ +++NTPHNP G + Sbjct: 125 PAIDLAGARAVHVPLDPQTF------AVDWD----RVRAAITPRTRLLMVNTPHNPSGAM 174 Query: 225 YTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFS 284 +LQ +ADL D ISDEVYE ++Y G H P + R I S GKT+ Sbjct: 175 LAEADLQALADLLRGTDIYLISDEVYEHIIYDGRRHESALRHPELRARAFVISSFGKTYH 234 Query: 285 VTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLP 344 TGWK+G++I P L + V Q + +T P Q A D+P+ + L Sbjct: 235 CTGWKIGYAIAPPALSAEFRKVHQYNTFTSFGPAQYGFAAMI------RDEPQHHL-ELG 287 Query: 345 KELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTK 404 + KRDR L L P+ GGYF + D S++ SD P D++FVKW+T Sbjct: 288 AFYQAKRDRFREQLAQTRLVPLAVPGGYFQLVDYSAI--------SDLP-DHEFVKWLTI 338 Query: 405 HKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEE 445 K + AIP+S F + + P +++VR CF K ++TLDAA E Sbjct: 339 EKGVAAIPLSPFYE--APPVGQRIVRLCFAKNEATLDAAIE 377 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: 441 Number of extensions: 20 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: 382 Length adjustment: 31 Effective length of query: 424 Effective length of database: 351 Effective search space: 148824 Effective search space used: 148824 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