Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate H281DRAFT_06351 H281DRAFT_06351 succinate semialdehyde dehydrogenase (EC 1.2.1.16)
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Burk376:H281DRAFT_06351 Length = 491 Score = 218 bits (555), Expect = 4e-61 Identities = 151/461 (32%), Positives = 231/461 (50%), Gaps = 18/461 (3%) Query: 21 YPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHK 80 +PV P G I V A+ A D A SA AWR R E++R + ++ E+ Sbjct: 30 FPVTNPATGDTIVEVANSSAADARAATDAAASALPAWRGKLPRERAEILRRWHALIVENT 89 Query: 81 ADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPL 140 DL +L+S E GK E GEV + + ++YG I ++ G M + Sbjct: 90 EDLAKLMSTEQGKPLAESRGEVAYGASYVAWFADEATRIYGDIIPQQQRGKRMSAVKEAI 149 Query: 141 GVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAP 200 G+V I+ +NFP+A+ A A AL AG +VV KP+E TPLTALA AL ++A P Sbjct: 150 GIVAAITPWNFPLAMIARKIAPALAAGCTVVAKPAEDTPLTALALAALAQEA-----GVP 204 Query: 201 AGLAQLVIGGREAG-EAMVD---DPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGN 256 G+ ++ R+ G EA+ D D RV ++ TGST +G+ + AA + LELGGN Sbjct: 205 DGVLNMLSASRDQGIEAVADWLADARVRKITFTGSTPVGKHLARESAATLKKLSLELGGN 264 Query: 257 NAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKD---EVVARVKAAYGKV 313 I+ ADLD AV G++ + GQ C R+ V + + +++A+ AA Sbjct: 265 APFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVYVQAGVYERFADLLAKRVAALKVA 324 Query: 314 RIGDPRKDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAIAE 373 DP +GP+I++++ D + + A +G +V G ++L + PN YY + + Sbjct: 325 PATDPSAQ--IGPMINERAIDKIARHVEDAVKQGAKVLTGGKRLTELGPN-YYAPTVLTD 381 Query: 374 MPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGS 433 V ETF P+ + + D EA+RL N+ P GL++ FT D+R +R A+ Sbjct: 382 ANDGMLVCCEETFGPVAPLFRFSDEAEAVRLANDTPFGLAAYFFTQDVRRIDRV--ATRL 439 Query: 434 DCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474 + G+ +N G +E+ FGG KE+G GRE Y+ Sbjct: 440 EAGVIGINEGAVSSEV-APFGGVKESGYGREGSKYGLDDYL 479 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: 584 Number of extensions: 38 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: 491 Length adjustment: 34 Effective length of query: 462 Effective length of database: 457 Effective search space: 211134 Effective search space used: 211134 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