Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 221 bits (562), Expect = 6e-62 Identities = 153/476 (32%), Positives = 235/476 (49%), Gaps = 19/476 (3%) Query: 3 AGLLERLGVAAEAYTQGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPA 62 A L++ V EA + V P DG+ IA+V LG AET ID A A AW + A Sbjct: 13 AALIDGQWVRGEA----SFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAARTA 68 Query: 63 PRRGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGL 122 RG ++R + +++ H DL L++ E GK E GEV D+ +++ YG Sbjct: 69 KERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAYGH 128 Query: 123 TIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTA 182 TI + PG + P+GV I+ +NFP+A+ AL AG +VV KP+ +TPL+A Sbjct: 129 TIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLSA 188 Query: 183 LACQALFEKALKAFGDAPAGLAQLVIGGR--EAGEAMVDDPRVPLVSATGSTRMGREVGP 240 LA L +A PAG+ +V R E G+ + DD RV +S TGST +G+ + Sbjct: 189 LAIARLATEA-----GVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQ 243 Query: 241 RVAARFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKD 300 + A + LELGGN I+ ADL+ AV G + S AGQ C RLIV I D Sbjct: 244 QCAGTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHD 303 Query: 301 EVVARVKAAYGKVRIGDPRKDNL-VGPLIDKQSFDAMQGALAKARDEGGQVF-GGERQLA 358 AR+ +++G + + +GPLI++++ + G ++ A G +V GG+ Sbjct: 304 AFAARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGD---V 360 Query: 359 DQYPNAYYVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFT 418 +Y + + + + E F P+ ++ ++ EA+ L N P GL++ ++ Sbjct: 361 HGLGGHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYS 420 Query: 419 TDIREAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474 D+ R A + G+ +N G E+ FGG KE+G GRE S+ Y+ Sbjct: 421 RDVGRCWRV--AEQIEAGMVGINEGLISTEV-APFGGVKESGLGREGASEGLDEYL 473 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: 548 Number of extensions: 24 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: 485 Length adjustment: 34 Effective length of query: 462 Effective length of database: 451 Effective search space: 208362 Effective search space used: 208362 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