Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate Ac3H11_612 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_612 Length = 483 Score = 232 bits (591), Expect = 3e-65 Identities = 153/451 (33%), Positives = 230/451 (50%), Gaps = 13/451 (2%) Query: 32 IASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGELVSIEA 91 +A + +T + A A W RR +++ + G L K +LG L++ E Sbjct: 37 VAEYARADRNQTELAVRAAADALPTWSQSTPQRRADVLDMIGSELLARKDELGALLAREE 96 Query: 92 GKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNF 151 GK EG+ EV I F G + ++ G +AS R G + T P+GVVG+I+ +NF Sbjct: 97 GKTLPEGVAEVARSGQIFKFFAGEALRIQGELLASVRQGVQVDVTREPVGVVGIIAPWNF 156 Query: 152 PVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIG-G 210 P A+ AW A AL GN+VV+KP+E P A + ++ PAG L++G G Sbjct: 157 PFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAEIISRS-----GLPAGAFNLIMGSG 211 Query: 211 REAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILAPSADLDLA 270 RE G+ +VD P V +S TGS G + + R + LE+GG N +I+ ADLD A Sbjct: 212 REVGQTLVDHPLVNALSFTGSVATGDRILRAASQRRAKVQLEMGGKNPLIVLADADLDQA 271 Query: 271 VRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP-RKDNLVGPLID 329 V L + + GQRCT RLIV + D VAR++ +++G + +GP++D Sbjct: 272 VDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVARLRNRLASLKVGHALERGTEMGPVVD 331 Query: 330 KQSFDAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAIAEMPAQSDVVRHETFAP 388 G + A+ EG + V+GGER ++ +Y+SPA+ + V R E F P Sbjct: 332 DNQLAQNLGYIDIAKSEGAEHVWGGER--LERPTPGHYMSPALFLARPEHRVAREEIFGP 389 Query: 389 ILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANVNIGTSGAE 448 + VL DD++ AL L N+ P GL + I TT ++ A F+ + G+ VN+ T+G + Sbjct: 390 VACVLRADDYDHALALANDTPFGLCAGICTTSLKRAMHFKRHAA--VGMTMVNLPTAGVD 447 Query: 449 IGGAFGGEKETG-GGRESGSDAWKGYMRRQT 478 FGG KE+ G RE G A + Y +T Sbjct: 448 FHVPFGGRKESSYGAREQGRYAAEFYTTVKT 478 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: 570 Number of extensions: 37 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: 483 Length adjustment: 34 Effective length of query: 462 Effective length of database: 449 Effective search space: 207438 Effective search space used: 207438 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