Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate AO353_28230 AO353_28230 succinate-semialdehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28230 Length = 485 Score = 199 bits (506), Expect = 2e-55 Identities = 141/452 (31%), Positives = 221/452 (48%), Gaps = 15/452 (3%) Query: 26 PIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGE 85 P +G +A V + ET ID A+ A+ AWR+ PA R L+ + + + ++ DL Sbjct: 36 PANGQLLARVPAMQGTETRRAIDAAEKAWPAWRARPAAERAALLERWYQAMIDNLDDLAL 95 Query: 86 LVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGV 145 +++ E GK E GE++ + +R++YG TI + + P+GV Sbjct: 96 IMTCEQGKPLNEAKGEIRYGAGFVKWFAEEARRVYGETIPAPSGDRRLLTLKQPVGVCAA 155 Query: 146 ISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQ 205 I+ +NFP A+ A AL AG ++ KPS+ TPL+ALA L E+ PAG+ Sbjct: 156 ITPWNFPNAMITRKCAPALAAGCPIIVKPSDLTPLSALALAVLAERV-----GIPAGVFN 210 Query: 206 LVIG-GREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILAPS 264 ++ G GE + +P V +S TGST +GR + + A R LELGGN I+ Sbjct: 211 VLTGMPAGIGEELTGNPSVRKISFTGSTAVGRLLMRQSAEHIKRLSLELGGNAPFIVFDD 270 Query: 265 ADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP-RKDNL 323 ADL+ AV GI+ S AGQ C R++V I + R+ GK+++G+ D Sbjct: 271 ADLEQAVAGIMLSKFRNAGQTCVCANRILVQDGIYERFAQRLVEEVGKLKVGNGLDADVT 330 Query: 324 VGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAI-AEMPAQSDVVR 382 +GPLI+ + + + A +G ++ G D + +V P + + A + Sbjct: 331 IGPLINPAAVSKVARHIDDALSQGARLLCGGIPEGD----SQFVQPTVLGDAHAGMLLAN 386 Query: 383 HETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANVNI 442 ETF P+ ++ + + EAL L N P GL + FT D+R + RF A + G+ +N Sbjct: 387 EETFGPVAPLMRFTEEAEALALANATPYGLGAYYFTQDLRRSWRFGEA--LEFGMVGLNT 444 Query: 443 GTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474 G E+ FGG K++G GRE Y+ Sbjct: 445 GIISMEV-APFGGIKQSGLGREGSKYGLDEYL 475 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: 566 Number of extensions: 24 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: 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