Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__HerbieS:HSERO_RS05645 Length = 493 Score = 211 bits (538), Expect = 4e-59 Identities = 149/462 (32%), Positives = 226/462 (48%), Gaps = 21/462 (4%) Query: 23 VHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKAD 82 V P G ASV G A+ A ++ A +AF AWR+ PA +R +++ + ++L H+ D Sbjct: 33 VSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRATPAKQRAGIIKRWNDLLLAHQDD 92 Query: 83 LGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGV 142 LG L+S E GK E GEV ++ + + G I + G M P+GV Sbjct: 93 LGRLISREQGKPLAEAKGEVAYAASYVEWFGEEATRANGDIIPAPVTGRRMMALKEPVGV 152 Query: 143 VGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAG 202 V I+ +NFP A+ A A AL AG +VV KP+E TPLT+LA L ++A P G Sbjct: 153 VAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTPLTSLALVRLAQEA-----GVPVG 207 Query: 203 LAQLVIGGREAGEAMVD----DPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNA 258 + +V RE +VD D RV +S TGST +G+ + A + LELGGN Sbjct: 208 VINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLARHSADTLKKLSLELGGNAP 267 Query: 259 MILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP 318 I+ AD+D A+ G++ + GQ C + R+ V + D V ++ A +++G P Sbjct: 268 FIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYDAFVDKLGARVAALKVG-P 326 Query: 319 RKD--NLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYP----NAYYVSPAIA 372 D + +GP+I+ ++ + + A G +V G ++L Q P + YY +A Sbjct: 327 ATDPASQIGPMINARAIAKIDQHVRDAIARGARVITGGKRL--QGPGFGSDNYYAPTVLA 384 Query: 373 EMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASG 432 ++ ETF P+ + + +E + N P GL++ ++TD+R R A Sbjct: 385 DVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFGLAAYFYSTDVRRIHRVTDALE 444 Query: 433 SDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474 S GI VN G AE FGG KE+G GRE Y+ Sbjct: 445 S--GIVGVNEGALAAE-AAPFGGVKESGYGREGSVHGLDDYL 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: 616 Number of extensions: 34 Number of successful extensions: 4 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: 493 Length adjustment: 34 Effective length of query: 462 Effective length of database: 459 Effective search space: 212058 Effective search space used: 212058 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