Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_000745975.1:WP_035239838.1 Length = 484 Score = 199 bits (505), Expect = 2e-55 Identities = 134/454 (29%), Positives = 221/454 (48%), Gaps = 12/454 (2%) Query: 23 VHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKAD 82 V P G + +V G ET I+ A + +AWRS A R ++R + ++L E++ D Sbjct: 31 VTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERSAILRKWYDLLMENQED 90 Query: 83 LGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGV 142 L +++ E GK E GE+ ++ ++++YG I + P+GV Sbjct: 91 LAVIMTAEQGKPLAESRGEIAYAAAFFEWFAEEAKRVYGDVIPQTVASQRLVVIKQPVGV 150 Query: 143 VGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAG 202 V I+ +NFP A+ AL AG ++V KP+ TP +ALA L ++A P G Sbjct: 151 VAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPFSALAIAKLGQQA-----GVPKG 205 Query: 203 LAQLVIGGREA-GEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMIL 261 + +V G A G + +P V ++ TGST++G+++ A R +ELGGN I+ Sbjct: 206 VFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAGTMKRLSMELGGNAPFIV 265 Query: 262 APSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRKD 321 AD+D AV G + +GQ C R+ V + DE ++ AA ++++G+ D Sbjct: 266 FDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVYDEFCRKLTAAVQELKVGNGFDD 325 Query: 322 NL-VGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAIAEMPAQSDV 380 + GPLID + + ++ + A D+GG+V G + A ++ IA++ V Sbjct: 326 GVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTRHA--LGRTFFAPTIIADVTDDMRV 383 Query: 381 VRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANV 440 R ETF P+ V +D EE +R N+ GL++ +T D+ A ++ + G+ + Sbjct: 384 AREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDM--ARSWRIGEKLEYGLVGI 441 Query: 441 NIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474 N G + FGG KE+G GRE Y+ Sbjct: 442 NSGIISNPV-APFGGVKESGNGREGSKYGLDDYL 474 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: 523 Number of extensions: 32 Number of successful extensions: 4 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: 484 Length adjustment: 34 Effective length of query: 462 Effective length of database: 450 Effective search space: 207900 Effective search space used: 207900 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