Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3961 Length = 512 Score = 220 bits (560), Expect = 1e-61 Identities = 150/454 (33%), Positives = 233/454 (51%), Gaps = 15/454 (3%) Query: 32 IASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGELVSIEA 91 I + + + + + A +AF AW +R +++ G + KA+LG+L++ E Sbjct: 62 IGDYAVASREQALDAVAAAHAAFPAWSLSTPQQRFDILDAVGNEIIARKAELGDLLAREE 121 Query: 92 GKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNF 151 GK E +GEV I F G + + G + S RPG + T PLG +G+I+ +NF Sbjct: 122 GKTLPEAIGEVGRAAAIFKFFAGEALRPGGEVMPSVRPGVGIEITREPLGTIGIITPWNF 181 Query: 152 PVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIG-G 210 P+A+ AW A AL GN VV+KP+E P +A A + +A PAG+ LV+G G Sbjct: 182 PIAIPAWKIAPALAYGNCVVFKPAEVVPGSAWALADILHRA-----GLPAGVFNLVMGRG 236 Query: 211 REAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILAPSADLDLA 270 + G +++D R+ VS TGS G+ V R + LE+GG N ++ ADL++A Sbjct: 237 SDVGAVLLEDERIAGVSFTGSVGTGQRVAAACVPRGAKVQLEMGGKNPFVVLDDADLNVA 296 Query: 271 VRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRKDNL-VGPLID 329 V + S + GQRCT R+IV I D VA + +++ D RK +GP++D Sbjct: 297 VGAAINSGFFSTGQRCTASSRVIVTEGIHDRFVAAMVEKMKTLKVDDARKAGTDIGPVVD 356 Query: 330 KQSFDAMQGALAKARDEGGQV-FGGE--RQLADQYPNAYYVSPAI-AEMPAQSDVVRHET 385 + + + EG ++ +GGE + AD P +Y+ PA+ E + R E Sbjct: 357 DRQLAQDLEYIGIGQQEGAKLAYGGEALEKNADGAP-GFYLRPALFTETTPGMRINREEI 415 Query: 386 FAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANVNIGTS 445 F P++ VL ++EEAL L N+ P GL+S I TT ++ A F+ + G+ VN+ T+ Sbjct: 416 FGPVVSVLRAKNYEEALALANDTPFGLASGIATTSLKHATHFK--RHAQAGMVMVNLPTA 473 Query: 446 GAEIGGAFGGEKETG-GGRESGSDAWKGYMRRQT 478 G + FGG K + G RE G A + Y +T Sbjct: 474 GVDYHVPFGGRKSSSYGPREQGRYAAEFYTTVKT 507 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: 637 Number of extensions: 32 Number of successful extensions: 4 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: 512 Length adjustment: 34 Effective length of query: 462 Effective length of database: 478 Effective search space: 220836 Effective search space used: 220836 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