Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Smeli:SMa2213 Length = 494 Score = 194 bits (492), Expect = 8e-54 Identities = 143/460 (31%), Positives = 227/460 (49%), Gaps = 24/460 (5%) Query: 39 GKAETIAR-IDQAQSAFEA--WRSVPAPRRGELVRLFGEVLREHKADLGELVSIEAGKIT 95 G AE R + A AF W + RG +++ F ++ EH L ++ + G++ Sbjct: 41 GNAEDADRAVRAAHRAFSQGPWGKMHPTERGRIIQRFAALIEEHADALADIEVRDNGRLL 100 Query: 96 QEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNFPVAV 155 E +++ + + G + ++ G ++P PLGV I +N P+ + Sbjct: 101 AEMTHQIRYIPRWYHYYAGFADKIEGTLHPCDKPALSFSRH-EPLGVCVGIVPWNAPLLL 159 Query: 156 WAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIG-GREAG 214 ++ A AL AGN++V KP+E T TAL L EKA P G+ +V G G E G Sbjct: 160 FSLKAAPALAAGNTLVMKPAEFTSATALKLMELVEKA-----GFPTGVINVVTGYGPEVG 214 Query: 215 EAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILAPSADLDLAVRGI 274 E +V P V TGST+ G + A R LELGG + I+ ADLD AVRG+ Sbjct: 215 EPLVTHPLTRHVGFTGSTKTGAHLYSLAAKDVKRVSLELGGKSPNIVFGDADLDNAVRGV 274 Query: 275 LFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRK-DNLVGPLIDKQSF 333 + G GQ C RL+VHRSI DE + ++ RIGDPRK + +GP+ + F Sbjct: 275 VGGIFGAVGQTCIAGSRLLVHRSIHDEFLEKLAVFTKTARIGDPRKVETQIGPIANSMQF 334 Query: 334 DAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAI-AEMPAQSDVVRHETFAPILY 391 + + G + AR EG + + GG R ++ Y++ P I A + + R E F P+L Sbjct: 335 EKVLGYIDIARREGAELILGGGRPDLEECGTGYFIEPTIFAGVSNDMRIAREEVFGPVLS 394 Query: 392 VLAYDDFEEALRLNNEVPQGLSSCIFTTDIREA----ERFQSASGSDCGIANVNIGTSGA 447 + +D+ EEAL + N+ GL + ++T+D+R A ER ++ S +++ T Sbjct: 395 AIVFDEPEEALAIANDSEFGLGAGVWTSDMRLALKMSERLEAGSVWVNTYRDISYTT--- 451 Query: 448 EIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNYSREL 487 FGG K++G GRE+G Y++ + ++ + E+ Sbjct: 452 ----PFGGYKKSGIGRENGVAGIYEYLQTKAVWLSTAEEI 487 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: 558 Number of extensions: 23 Number of successful extensions: 6 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