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_026127539.1 D471_RS0108560 putative succinyldiaminopimelate transaminase DapC
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_000341125.1:WP_026127539.1 Length = 393 Score = 264 bits (675), Expect = 3e-75 Identities = 150/406 (36%), Positives = 221/406 (54%), Gaps = 25/406 (6%) Query: 45 RIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGH 104 R+ V+ E T+LA + VNLGQGFPD P + E + +D +NQY G G Sbjct: 8 RMRSYGETVFAEMTRLAVETESVNLGQGFPDTDGPRSLLEAAT-GHILDGVNQYPPGSGR 66 Query: 105 PALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYE 164 P L +A+S + Y ++DP+ E+ V VGA + S+ LV+ GDEV++ P YD Y Sbjct: 67 PELRRAVSRYRARHYGIELDPDSEVYVTVGATAGIAASLLALVERGDEVVVFEPMYDSYA 126 Query: 165 PMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKV 224 M+ +AG V + LR P G +TFDP EL + +T+ II+NTPHNP G V Sbjct: 127 AMISLAGGVRRPVALRPDPERGA------FTFDPDELRAAVGPRTRVIIVNTPHNPTGTV 180 Query: 225 YTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFS 284 +T +EL+ IA +C +HD L ++DEVYE+L + G HV +ATLPGM ERT+++ S GK F+ Sbjct: 181 FTAEELETIAQVCREHDLLALTDEVYEFLTFDGLPHVPLATLPGMRERTLSVSSVGKMFA 240 Query: 285 VTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLP 344 VT WK GW +GP L++ ++TV Q ++ LQ A+A+A +D + S Sbjct: 241 VTAWKTGWVMGPEPLVRAVRTVNQFLTFSANGALQLAIADA-------IDHEGAWIESQR 293 Query: 345 KELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTK 404 L+ KRDR+ L G +G YF++AD+ LG + D + + + Sbjct: 294 ASLQAKRDRLAAGLVRAGFDVYPCEGTYFLMADIRPLG------HGD---GLTVARALPR 344 Query: 405 HKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFRAW 450 + A+P F D + + L+RF F K+D LD A + +W Sbjct: 345 EAGVAAVPAQVFYDHEEEG--SHLLRFAFCKRDEVLDEAVDRLTSW 388 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: 437 Number of extensions: 15 Number of successful extensions: 5 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: 393 Length adjustment: 32 Effective length of query: 423 Effective length of database: 361 Effective search space: 152703 Effective search space used: 152703 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