Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate RR42_RS26645 RR42_RS26645 succinate-semialdehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Cup4G11:RR42_RS26645 Length = 494 Score = 211 bits (538), Expect = 4e-59 Identities = 150/466 (32%), Positives = 225/466 (48%), Gaps = 15/466 (3%) Query: 15 AYTQGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGE 74 A+T V P + A V + D A +AF AW A R ++++ + Sbjct: 27 AHTGHRLDVTNPATNTVFACVPDSDARDASQATDAAAAAFPAWSRRTARDRAQIIKRWHA 86 Query: 75 VLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMR 134 ++ EH+ DL ++S E GK +E GEV ++ + ++ G +A PG M Sbjct: 87 LILEHQEDLARIISTEQGKPIKEARGEVLYGASYVEWFAEEATRISGEIVAESVPGRKML 146 Query: 135 ETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALK 194 P+GVV I+ +NFP+A+ A A AL AG +VV KP+E TPLTALA L ++A Sbjct: 147 VLKEPVGVVAAITPWNFPLAMIARKIAPALAAGCTVVAKPAEDTPLTALALVYLAQQA-- 204 Query: 195 AFGDAPAGLAQLVIGGREAGEAMVD----DPRVPLVSATGSTRMGREVGPRVAARFGRSI 250 PAG+ +V R A+VD D RV ++ TGST +G+ + A + Sbjct: 205 ---GLPAGVLNIVTASRAKTPAVVDAWLADSRVRKITFTGSTPVGKHLARESAGTLKKLS 261 Query: 251 LELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAY 310 LELGGN I+ AD+D AV G++ S GQ C R+ V + D VAR+ Sbjct: 262 LELGGNAPFIVFDDADIDAAVDGLMASKFRNGGQTCVCPNRVYVQAGVHDYFVARLSQRV 321 Query: 311 GKVRIGDPRKD-NLVGPLIDKQSFDAMQGALAKARDEGGQVF-GGERQLADQYPNAYYVS 368 +++G +D + +GP+I+ ++ + + +A A +G V GGER P+ YY Sbjct: 322 AALQVGPATEDASQIGPMINARAVEKIARHVADAVAKGAVVMTGGERVRLADGPH-YYAP 380 Query: 369 PAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQ 428 + Q + ETF P+ V + D E +R N+ P GL++ ++ D+R R Sbjct: 381 TVLTNATPQMALSCEETFGPVAAVFRFTDEAEVIRDANDTPFGLAAYFYSNDVRRIWRV- 439 Query: 429 SASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474 A + GI VN G +E FGG KE+G GRE YM Sbjct: 440 -AQALETGIVGVNEGAIASE-AAPFGGVKESGYGREGSRHGLDDYM 483 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: 575 Number of extensions: 35 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: 494 Length adjustment: 34 Effective length of query: 462 Effective length of database: 460 Effective search space: 212520 Effective search space used: 212520 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