Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate HSERO_RS22910 HSERO_RS22910 benzaldehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__HerbieS:HSERO_RS22910 Length = 487 Score = 209 bits (531), Expect = 2e-58 Identities = 146/464 (31%), Positives = 213/464 (45%), Gaps = 21/464 (4%) Query: 39 PLTGADLFGLRAHTPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLAD 98 P TG L + +P+DV +VE A A W P R + +R L +H +LA Sbjct: 33 PATGRPLTQVGLASPDDVSASVELAIAAQAAWVAMPPRERADIFRRAAGLFHQHFDELAR 92 Query: 99 LVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVGV 158 +V E G + + EV+E I +C A G+ Q G+ +PS PG + PLGV+GV Sbjct: 93 MVARETGGVLFKGEHEVREAITLCHLAAGMPLQAQGQLLPST-PGRLSIARRAPLGVIGV 151 Query: 159 ISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQV 218 IS FNFP+ + A AL G+ VV KP TP++ A + AG P GL V Sbjct: 152 ISPFNFPLILTLRTVAPALAAGNAVVVKPDLRTPVSGGFMLARI---FEQAGLPAGLLHV 208 Query: 219 VVGAADVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTPSAD 278 + G A+ GE LV +P VP+++ TGS +GR +G + LELGG NA V+ AD Sbjct: 209 LPGGAETGEALVTAPGVPMIAFTGSPAVGRRIGELAGRHLKKLSLELGGANALVILEDAD 268 Query: 279 LDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVG 338 LD+ + A + A GQ C R++VH + + +++RL LP+GD +G Sbjct: 269 LDVAASHAAWGAWLHQGQICMAANRILVHASLEEGLLQRLADKARHLPVGDGASGQVALG 328 Query: 339 PLVNEAAFGRMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQTAVVREE 398 P+++E R+ V+ + A G L AGG + +Y L + V EE Sbjct: 329 PMIDERQLQRVHALVQESVAAGAQLVAGGRYE------QLFYQPTVLGGVRPGMRVFEEE 382 Query: 399 TFAPILYVLTYRDLDEAIRLNNEVPQACRQGSRTDG-APADDPRCRARRRAGGANCPAV- 456 F P+ V+ + + ++AI L N G + A R R+ N V Sbjct: 383 IFGPVASVIRFDNDEDAIALANRHAGGLAAGVLSPSVGRAMAVAARLRQGMVHVNDQTVN 442 Query: 457 ---------PGRSGTGAGAGGTADRVRTGGTSHRLVRHRRVPDP 491 PG +G GA GG AD +R + +P P Sbjct: 443 DECVNPFGGPGIAGNGASVGGPADWEEYTQWRWTTIRQQAMPYP 486 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: 487 Number of extensions: 24 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: 487 Length adjustment: 34 Effective length of query: 462 Effective length of database: 453 Effective search space: 209286 Effective search space used: 209286 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 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