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) >FitnessBrowser__SB2B:6937470 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:
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