Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate CCNA_01274 CCNA_01274 piperideine-6-carboxylate dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Caulo:CCNA_01274 Length = 507 Score = 646 bits (1666), Expect = 0.0 Identities = 327/493 (66%), Positives = 386/493 (78%), Gaps = 2/493 (0%) Query: 5 LLERLGVAAEAYTQGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPR 64 +L +LG G+ PV PIDG+ + V + A++ A AF WR VPAPR Sbjct: 15 ILAKLGAPPLPADAGE-PVRGPIDGAILGHVVYDDARQIEAKVAAACRAFADWRVVPAPR 73 Query: 65 RGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTI 124 RGELVRLFGE LR KADL LV++EAGKI E GEVQEMIDICDFAVGLSRQL+GLTI Sbjct: 74 RGELVRLFGEELRAAKADLAALVTLEAGKIASEAAGEVQEMIDICDFAVGLSRQLHGLTI 133 Query: 125 ASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALA 184 ASERPGH MRETWHPLG V VISAFNFPVAVWAWN LALV G+ V+WKPSEKTPLTALA Sbjct: 134 ASERPGHAMRETWHPLGPVAVISAFNFPVAVWAWNACLALVCGDPVIWKPSEKTPLTALA 193 Query: 185 CQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAA 244 QA+ E+AL F DAP GL+ +V+G R+AGE + DPR+PLVSATGSTRMGR V P VA Sbjct: 194 TQAILERALARFRDAPQGLSSVVLGARDAGERLARDPRIPLVSATGSTRMGRAVAPMVAE 253 Query: 245 RFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVA 304 RFGRSILELGGNNAMI+ PSADL LA+R I+FSA GTAGQRCT+LRRLIVH S+ D+V Sbjct: 254 RFGRSILELGGNNAMIVTPSADLSLALRAIVFSAAGTAGQRCTSLRRLIVHESLVDKVSD 313 Query: 305 RVKAAYGKVRIGDPR-KDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPN 363 V+AA+ ++ +GDPR L+GPLIDK ++DA A+ + R EGG V GGER L D++P+ Sbjct: 314 AVEAAFQRLSVGDPRDPKTLLGPLIDKAAYDAFIAAMNQVRAEGGSVAGGERVLIDEHPD 373 Query: 364 AYYVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIRE 423 AYYV PA+A +PA + ++ ETFAP+L+V+ Y+ F+ A+ + N+VPQGLSSC+ T D+RE Sbjct: 374 AYYVRPALARLPAPAPCMQRETFAPLLHVVPYNSFDMAIAIQNDVPQGLSSCVMTNDVRE 433 Query: 424 AERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNY 483 AERF +A+GSDCGIANVNIG SGAEIGGAFGGEKETGGGRESGSD+WK YMRRQT TVNY Sbjct: 434 AERFLAAAGSDCGIANVNIGPSGAEIGGAFGGEKETGGGRESGSDSWKQYMRRQTATVNY 493 Query: 484 SRELPLAQGIVFD 496 S LPLAQG+ FD Sbjct: 494 SGALPLAQGVRFD 506 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: 780 Number of extensions: 28 Number of successful extensions: 3 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: 507 Length adjustment: 34 Effective length of query: 462 Effective length of database: 473 Effective search space: 218526 Effective search space used: 218526 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 Sep 17 2021. 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