Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_090272859.1 BLU11_RS08070 NAD-dependent succinate-semialdehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_900105005.1:WP_090272859.1 Length = 486 Score = 206 bits (524), Expect = 1e-57 Identities = 143/445 (32%), Positives = 213/445 (47%), Gaps = 14/445 (3%) Query: 23 VHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKAD 82 V P +G + V +L AE A +D A SA WR A R + + + +++ EHK D Sbjct: 33 VDNPANGDVLGHVPVLSAAEVGAAVDAASSALRQWRKRTAQERADCLLAWHDLMLEHKED 92 Query: 83 LGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGV 142 L L+++E GK E GE+ + +R++YG TI R G H+ T P+GV Sbjct: 93 LATLMTLEQGKPLVESQGEIDYAASFIRWFAEEARRMYGETIPGARIGQHIVVTRQPVGV 152 Query: 143 VGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAG 202 I+ +NFP A+ AL AG +++ KP+ TP +ALA L E+A P G Sbjct: 153 CAAITPWNFPAAMITRKAGAALAAGCTIIVKPASATPFSALALAVLAEEA-----GIPHG 207 Query: 203 LAQLVIG-GREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMIL 261 + +V G E E + P V +S TGST +GR + + + + LELGGN I+ Sbjct: 208 VFNVVTGKAGEISEVLTRSPVVRKLSFTGSTDVGRRLMAQCSEHIQKVSLELGGNAPFIV 267 Query: 262 APSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRKD 321 AD+ AV G + GQ C R +V + D+ VA + A GK+RIGD + Sbjct: 268 FDDADISRAVEGAMVCKFRNTGQTCVCANRFLVQSGVHDKFVAALAEAMGKLRIGDGFEP 327 Query: 322 NLV-GPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPA-IAEMPAQSD 379 + LI+ + + + A +G + G AD+ YV P + ++ Sbjct: 328 GVTQSALINGDAVEKVIEHFDDAMAKGAKRVCGPAPDADR---GNYVQPVLLTDINTNMT 384 Query: 380 VVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIAN 439 + ETF P+ VL +D EEA+ L N P GL++ ++ DI R A + GI Sbjct: 385 LCHEETFGPLAAVLRFDTEEEAIELANATPFGLAAYFYSRDIHRVWRV--ADALEAGIIG 442 Query: 440 VNIGTSGAEIGGAFGGEKETGGGRE 464 +N G + FGG KE+G GRE Sbjct: 443 INEGLISNPM-APFGGVKESGLGRE 466 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: 533 Number of extensions: 27 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: 486 Length adjustment: 34 Effective length of query: 462 Effective length of database: 452 Effective search space: 208824 Effective search space used: 208824 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 24 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