Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate 6937470 Sama_1626 succinylglutamic semialdehyde dehydrogenase (RefSeq)
Query= uniprot:Q88CC3 (496 letters) >lcl|FitnessBrowser__SB2B:6937470 Sama_1626 succinylglutamic semialdehyde dehydrogenase (RefSeq) Length = 495 Score = 168 bits (426), Expect = 3e-46 Identities = 130/425 (30%), Positives = 209/425 (49%), Gaps = 19/425 (4%) Query: 47 IDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMI 106 + A+SAF W ++P R ++ FG L EH + L++ E GK E EV M Sbjct: 52 VKAARSAFYNWSAMPLAERLAIIEAFGAQLGEHSEAMARLIAEETGKALWESRTEVAAMT 111 Query: 107 DICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVA 166 ++ + G T+ + PG P GVV V +NFP + + AL+A Sbjct: 112 GKIAISIRAHSERTG-TVENPMPGARAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIA 170 Query: 167 GNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLV 226 GN+V++KPSE TP A L++KA PAG+ L+ G E G+A+ P + + Sbjct: 171 GNTVLFKPSELTPKVAQFTVELWQKA-----GLPAGVINLLQGEVETGKALAGHPGIDGL 225 Query: 227 SATGSTRMGREVGPRVAARFGRSI-LELGGNNAMILAPSADLDLAVRGILFSAVGTAGQR 285 TGS+ G + + A + G+ + LE+GGNN +I+ A+++ AV I+ SA ++GQR Sbjct: 226 FFTGSSNTGHLLHQQYAGQPGKILALEMGGNNPLIVKDVANVNAAVHDIIQSAFISSGQR 285 Query: 286 CTTLRRLIVHRSIK-DEVVARVKAAYGKVRIGDPRKDN--LVGPLIDKQSFDAMQGALAK 342 CT RRL + + D ++A++ A ++R+ +P +N G +I ++ A+ K Sbjct: 286 CTCARRLFIKKDANGDAILAKLIEASRQIRVDEPFAENQPFYGAMISAKA----AAAMVK 341 Query: 343 ARDEGGQVFGGERQLADQYPNAY--YVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEE 400 A+ + Q GG L + P+ +V+P I ++ + E F P+L V YDDF+ Sbjct: 342 AQTD-IQSLGGISLLELKQPDLALGFVTPGIIDVTHVKALPDEEHFGPLLKVYRYDDFDA 400 Query: 401 ALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETG 460 A+ N GLS+ + + + + F + GI N N +GA FGG +G Sbjct: 401 AIDEANNTAFGLSAGLLADNEADYDHFFRRIRA--GIVNWNKPITGASSAAPFGGIGASG 458 Query: 461 GGRES 465 R S Sbjct: 459 NHRAS 463 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: 589 Number of extensions: 33 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: 495 Length adjustment: 34 Effective length of query: 462 Effective length of database: 461 Effective search space: 212982 Effective search space used: 212982 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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