Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate GFF3096 HP15_3039 N-succinylglutamate 5-semialdehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Marino:GFF3096 Length = 491 Score = 176 bits (446), Expect = 2e-48 Identities = 148/479 (30%), Positives = 221/479 (46%), Gaps = 22/479 (4%) Query: 26 PIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGE 85 P+ G + + + A + +A++AF W+ R +V FGE+L HK +L Sbjct: 27 PVTGETLWDGESANLEDVDAAVREARNAFVKWQRKSFAERQAVVEAFGELLEAHKEELAH 86 Query: 86 LVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGV 145 + +E GK E EV MI +V G T S+ G H P GVV V Sbjct: 87 QIGLETGKPLWESRTEVAAMIGKIGISVKAYNDRTG-TSESDVAGGHAVLRHRPHGVVAV 145 Query: 146 ISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDA--PAGL 203 +NFP + + AL+AGN+VV+KPSE TP A E +K +G A P G+ Sbjct: 146 FGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPGVA-------ELTVKLWGKAGIPDGV 198 Query: 204 AQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSI-LELGGNNAMILA 262 LV G G+++ P + + TGS+ +G + + + + + LE+GGNN +I+ Sbjct: 199 INLVQGASATGKSLAGHPLIDGLFFTGSSTVGHLLHKQFGGQPEKIVALEMGGNNPLIVQ 258 Query: 263 PSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIK-DEVVARVKAAYGKVRIG--DPR 319 AD+D AV L SA +AGQRCT RRL+V + K D + R+ ++++G D Sbjct: 259 DVADVDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDAFIDRLVEVSARIKVGEFDAD 318 Query: 320 KDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAIAEMPAQSD 379 +G +I ++ + + A A ++GG+ + L +SP I + D Sbjct: 319 PQPFMGSVISSEAAEKLLAAQASLLEKGGKSLLEMKSLKS---GTGLLSPGIVDATG-LD 374 Query: 380 VVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIAN 439 V E F P+L V Y F++AL L N+ GLS+ I T D + ER GI N Sbjct: 375 VTDEEFFGPLLKVYRYKSFDDALALANDTHYGLSAGILTDDRKLYERL--VEEVRAGIVN 432 Query: 440 VNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNYSRELP--LAQGIVFD 496 N +GA FGG +G R S A + E+P LA G+ FD Sbjct: 433 WNRPLTGASSAAPFGGVGASGNHRPSAYYAADYCAWPMASLEAGKSEMPESLAPGLNFD 491 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: 591 Number of extensions: 41 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: 491 Length adjustment: 34 Effective length of query: 462 Effective length of database: 457 Effective search space: 211134 Effective search space used: 211134 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