Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_090445639.1 BLS63_RS14235 aldehyde dehydrogenase family protein
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_900100495.1:WP_090445639.1 Length = 476 Score = 209 bits (532), Expect = 2e-58 Identities = 142/447 (31%), Positives = 225/447 (50%), Gaps = 13/447 (2%) Query: 25 TPIDGSQIASVKLLGKAE-TIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADL 83 +P D + + + A+ T + I A+ A W + P +R + + G + + +L Sbjct: 21 SPSDTNDLVGLYAQASADDTQSAIAAAEHAQPLWAAKPPQQRADALDFIGAEILLRREEL 80 Query: 84 GELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVV 143 G L++ E GK E + EV I F G + ++ G + S RPG + P+GV+ Sbjct: 81 GTLLAREEGKTLPEAIAEVVRAGQIFKFFAGEALRIPGEHLDSVRPGIEVDVLRQPVGVI 140 Query: 144 GVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGL 203 G+I+ +NFP+A+ AW A AL GN+VV+KP++ P +A A + +A P G Sbjct: 141 GIIAPWNFPIAIPAWKIAPALAYGNAVVFKPADLVPGSAWALSEIIHRA-----GLPDGT 195 Query: 204 AQLVIG-GREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILA 262 LV+G G G+ +V+ PRV +S TGS+ GR + ARF + LE+GG N +++ Sbjct: 196 FNLVMGRGSVVGQTLVESPRVKALSFTGSSDTGRRILHSAGARFAKLQLEMGGKNPLVVL 255 Query: 263 PSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP-RKD 321 ADL+ A+ + A + GQRCT R IV + I V+A +++G D Sbjct: 256 NDADLEQAIECAVQGAYFSTGQRCTASSRFIVEKGIYRRFSEGVQARLQALQVGHALHAD 315 Query: 322 NLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAI-AEMPAQSDV 380 +GP+ ++ ++ + EG + G R L + YY+SPA+ + AQ + Sbjct: 316 TQIGPVAEQGQYEQNLAYVDIGLSEGAVLACGGRPL-QRDTQGYYMSPALFVDAEAQMRI 374 Query: 381 VRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANV 440 + E F PI + DD+E AL+L N P GLS+ I TT ++ A F+ S G+ + Sbjct: 375 AQEEIFGPIACAIPADDYEHALQLANASPYGLSAGICTTSLKYAAHFKRHMHS--GMVMI 432 Query: 441 NIGTSGAEIGGAFGGEKETG-GGRESG 466 N T+G + FGG K + G RE G Sbjct: 433 NTPTAGVDYHVPFGGTKGSSYGSREQG 459 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: 555 Number of extensions: 28 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: 476 Length adjustment: 34 Effective length of query: 462 Effective length of database: 442 Effective search space: 204204 Effective search space used: 204204 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