Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 174 bits (442), Expect = 5e-48 Identities = 121/373 (32%), Positives = 181/373 (48%), Gaps = 6/373 (1%) Query: 52 TPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEA 111 T +VD AV AA AF TWR TP R + ++ +L+ E+ +LA ++ E GK +A Sbjct: 43 TTSEVDDAVAAAKEAFKTWRKTPIGTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDA 102 Query: 112 LGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVGVISAFNFPVAVWAW 171 G+V +++ + A + G + G PLGV I+ FNFP + W Sbjct: 103 EGDVFRGLEVVEHAAAIGNLQLGELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLW 162 Query: 172 NAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVGAADVGERLVD 231 +A+ G+T V KPSE P+ L++LA+ +AG PKG+ VV G +V + D Sbjct: 163 MFPMAIATGNTFVLKPSEQDPM---VTMRLVELAL-EAGIPKGVLNVVHGGEEVVNAICD 218 Query: 232 SPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTPSADLDLTVNAAVFAAA 291 P + VS GSTR+G V R + R +G N AVV P A+ + T+NA V AA Sbjct: 219 HPDIKAVSFVGSTRVGTHVYNRASLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAF 278 Query: 292 GTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFGRMRE 351 G AGQRC L++ + A + V L A + L + T VGP+++ +A R+ Sbjct: 279 GAAGQRCMAASTLVLVGE-ARSWVPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEG 337 Query: 352 AVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVR-MPAQTAVVREETFAPILYVLTYR 410 + +G TL G D +V P + + + +EE F P+L +L Sbjct: 338 LIASGLEQGATLDLDGRNPQVDGFEKGNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAE 397 Query: 411 DLDEAIRLNNEVP 423 L++AI L N P Sbjct: 398 TLEDAIALVNSNP 410 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: 465 Number of extensions: 27 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: 501 Length adjustment: 34 Effective length of query: 462 Effective length of database: 467 Effective search space: 215754 Effective search space used: 215754 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 Apr 09 2024. 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