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_012568785.1 RC1_RS17510 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_000016185.1:WP_012568785.1 Length = 387 Score = 265 bits (676), Expect = 3e-75 Identities = 150/400 (37%), Positives = 219/400 (54%), Gaps = 29/400 (7%) Query: 51 SNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGHPALVKA 110 + ++ ++LA + VNLGQGFPD P V E + + NQY G PAL +A Sbjct: 13 TTIFEVMSRLAEEHRAVNLGQGFPDGGGPPEVVAEAQRY-LAEGWNQYPPMMGLPALRQA 71 Query: 111 LSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMA 170 ++ + Y ++D +E++V GA +L + GL++PGDE ++ P YD Y P++R A Sbjct: 72 VAAHAARFYGLEVDWRQEVMVTSGATEALAACLFGLLEPGDEAVLFEPLYDSYVPIIRRA 131 Query: 171 GAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKVYTRQEL 230 GAVP F+PLR+ DWTF +L + F +TK ++LN P NP KV++ +EL Sbjct: 132 GAVPRFVPLRAP----------DWTFSREDLAAAFGPRTKLVVLNNPLNPAAKVWSAEEL 181 Query: 231 QVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFSVTGWKL 290 V+A++ V HD + + DEVYE LV+ G H+ + LPGM ERT+ IGSAGKTFS+TGWK+ Sbjct: 182 AVLAEMLVAHDAVAVCDEVYEHLVFDGRRHLPLMALPGMRERTLRIGSAGKTFSLTGWKV 241 Query: 291 GWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLPKELEVK 350 G+ L++ + Q +T LQ A+A + P+ YF+ L E++ + Sbjct: 242 GYVTAAPALLQPVAKAHQFLTFTTPPDLQHAVACG-------LGGPDTYFDGLAAEMQRR 294 Query: 351 RDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTKHKKLTA 410 RDR+ L + G + G YF+ AD+ L D D F + MT + A Sbjct: 295 RDRLSAGLAACGFGVLPAQGTYFVTADIRPLAGDEDDA--------AFCRRMTVEAGVAA 346 Query: 411 IPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFRAW 450 IPVSAF + H L+RFCF K+D+ LD A R W Sbjct: 347 IPVSAFFEQAPPRH---LIRFCFCKRDAVLDEAVARLRGW 383 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: 436 Number of extensions: 21 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: 387 Length adjustment: 32 Effective length of query: 423 Effective length of database: 355 Effective search space: 150165 Effective search space used: 150165 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