Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein
Query= metacyc::MONOMER-12387 (496 letters) >MicrobesOnline__882:208821 Length = 464 Score = 163 bits (412), Expect = 1e-44 Identities = 126/356 (35%), Positives = 175/356 (49%), Gaps = 18/356 (5%) Query: 74 PAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLY 133 PA R A+++R L+ H + L E GK ++++ EV+ ID +A QL Sbjct: 45 PAHERLAILERLATLMRTHAEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELAQLG 104 Query: 134 GRTMPS----ERPGHRLMETWHPLGVVGVISAFNFPVAVWAWNAAVALVCGDTVVWKPSE 189 GR +P G P GVV ISAFN PV + A A G V+ KP+ Sbjct: 105 GREVPMGLTPASAGRLAFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPAS 164 Query: 190 LTPLNRAACAALLDLAIADAGAPKGLNQVVVGAADVGERLVDSPRVPLVSATGSTRMGRA 249 TPL+ C +L L + +AG P+ ++ AA E+LV PRV +S GS+R+G Sbjct: 165 ATPLS---CRNVLRL-MHEAGVPEAWATMLPCAAATAEKLVADPRVAFLSFIGSSRVGWH 220 Query: 250 VGPRVAARFGRTI-LELGGNNAAVVTPSADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHE 308 + ++A G T LE GG V+ SADLD + + AGQ C +++R+ Sbjct: 221 LRSKLAP--GATCALEHGGAAPVVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPH 278 Query: 309 DIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFGRMREAVERATAEGGTLCAGGE 368 + A T ERL AA +LP GDP + T VGPL++ R+ E VE A A GGT+ GG Sbjct: 279 ETARTFAERLAAAAAQLPTGDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGG- 337 Query: 369 RQFPDAAPGAYYVRPALVRMPAQ-TAVVREETFAPILYVLTYRDLDEAIRLNNEVP 423 A P +V P Q + R E F P++ V + RD DEAI N+VP Sbjct: 338 -----APLSETLYSPTVVYDPPQGCRLARNEVFGPVVAVFSTRDRDEAIARANDVP 388 Lambda K H 0.320 0.135 0.406 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: 519 Number of extensions: 38 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: 464 Length adjustment: 34 Effective length of query: 462 Effective length of database: 430 Effective search space: 198660 Effective search space used: 198660 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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