Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_019744147.1 BA79_RS03900 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >NCBI__GCF_000691145.1:WP_019744147.1 Length = 486 Score = 211 bits (538), Expect = 4e-59 Identities = 130/385 (33%), Positives = 202/385 (52%), Gaps = 6/385 (1%) Query: 38 HPLTGADLFGLRAHTPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLA 97 +P TG + + T DV+ AV+AA AF TW T P R ++ ++ +LL E +LA Sbjct: 30 NPATGEVIAEVPLSTKTDVEHAVQAAQEAFTTWSKTAVPRRARILFKYQQLLVEKWDELA 89 Query: 98 DLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVG 157 +LVT+E GK +EA GEVQ I+ +FA G + G+ +P G +P+GV+G Sbjct: 90 ELVTLENGKSVTEAKGEVQRGIECVEFAAGAPTLMMGKQLPDIATGLESGMYRYPIGVIG 149 Query: 158 VISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQ 217 I+ FNFP+ V W +A+ CG+T V KPSE TP+ A A L + +AG PKG+ Sbjct: 150 GITPFNFPMMVPCWMFPLAIACGNTFVLKPSERTPILAARLAELFE----EAGLPKGVLN 205 Query: 218 VVVGAADVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTPSA 277 +V GA DV L++ +V +S GS + V + A R G N ++V A Sbjct: 206 IVNGAHDVVNGLLEHEKVKAISFVGSQPVAEYVYKKGTAHGKRVQALAGAKNHSIVLKDA 265 Query: 278 DLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLV 337 DL+ + AA G+AG+RC + V ED+AD ++++L +L IG+ + Sbjct: 266 DLESATKQIIGAAFGSAGERCMAAAVVAVEEDVADDLIQQLVDESNQLVIGNGINKDVFL 325 Query: 338 GPLVNEAAFGRMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALV-RMPAQTAVVR 396 GP++ + R + ++ EG +L G RQ + Y+V P + + Q + + Sbjct: 326 GPVIRKEHKERTLQYIQSGIEEGASLIRDG-RQDNETNGEGYFVGPTIFDHVTNQMKIWQ 384 Query: 397 EETFAPILYVLTYRDLDEAIRLNNE 421 +E FAP+L ++ L EAI L+N+ Sbjct: 385 DEIFAPVLSIVRVSSLAEAIDLSNQ 409 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: 379 Number of extensions: 10 Number of successful extensions: 2 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: 486 Length adjustment: 34 Effective length of query: 462 Effective length of database: 452 Effective search space: 208824 Effective search space used: 208824 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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