Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 288 bits (736), Expect = 4e-82 Identities = 178/485 (36%), Positives = 263/485 (54%), Gaps = 17/485 (3%) Query: 15 AYTQGDYPVHTPIDGSQIASVKLLGKAETIAR-IDQAQSAFEAWRSVPAPRRGELVRLFG 73 A T+ H P + S+I + +A+ R + A+ A+ +WR VPAP R E + G Sbjct: 18 AATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKVPAPARAEYIFRVG 77 Query: 74 EVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHM 133 E+L +HK +L +L+S E GK E G+VQE +D ++ G R+L+G T SE P Sbjct: 78 ELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEGRRLFGQTTPSEMPNKFA 137 Query: 134 RETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKAL 193 P+GV +I+ +NFPVA+ W ALV GN+V+ KP+E TP A +F Sbjct: 138 MTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACATKLIEIF---- 193 Query: 194 KAFGDAPAGLAQLVIG-GREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILE 252 A P G+ LV G G EAG+A+V+ P + LVS TGS+ G VG R LE Sbjct: 194 -AAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCGRTHKRVCLE 252 Query: 253 LGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGK 312 +GG NA ++ ADL+LA+ G L+ A GT GQRCT RLI+HR IK++ ++ + Sbjct: 253 MGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFTTMLRERTSQ 312 Query: 313 VRIG---DPRKDNLVGPLIDKQSFDAMQGALAKARDEGGQV-FGGERQLADQYPNAYYVS 368 +R+G +P D +GP+I+ + + + AR+EG ++ GGE Q Y+ Sbjct: 313 LRLGAGTEPETD--IGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEGQLKQGYFFQ 370 Query: 369 PAIAE-MPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERF 427 P I + + Q V R E F P++ ++ FEEA+ + N+ GLSS ++T DI A F Sbjct: 371 PTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINRA--F 428 Query: 428 QSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGG-RESGSDAWKGYMRRQTNTVNYSRE 486 + + GI +N T GAE+ FGG K+TG G RE+G+ A + ++ V++S Sbjct: 429 VAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKSVYVDFSGS 488 Query: 487 LPLAQ 491 L AQ Sbjct: 489 LQRAQ 493 Lambda K H 0.318 0.135 0.396 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: 586 Number of extensions: 26 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: 496 Length of database: 498 Length adjustment: 34 Effective length of query: 462 Effective length of database: 464 Effective search space: 214368 Effective search space used: 214368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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