Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 186 bits (472), Expect = 2e-51 Identities = 137/385 (35%), Positives = 183/385 (47%), Gaps = 11/385 (2%) Query: 38 HPLTGADLFGLRAHTPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLA 97 +P T + + T D DRA AA AF W RGA +++ + L + +L Sbjct: 26 NPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGAERGAFLQKIADGLKARQDELG 85 Query: 98 DLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVG 157 L+ E G + + VQ I FA ++ ER G L+ P G V Sbjct: 86 RLIASEVG-MPVKLATRVQAGNPIFTFAA--CARIAAEGFAEERIGQSLVLKV-PTGPVA 141 Query: 158 VISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQ 217 I+ +NFP+ A AL G TVV KPSE+ PLN A LL I AG P G+ Sbjct: 142 CITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLN----AFLLAEVIEAAGLPAGVFN 197 Query: 218 VVVGAADV-GERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTPS 276 +V G V GE L P + VS TGST G+ V AA R LELGG +A+VV P Sbjct: 198 LVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVSLELGGKSASVVLPD 257 Query: 277 ADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTL 336 ADL V V +GQ C+ L RL+V ++ A +GDP + + Sbjct: 258 ADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAAAAYTLGDPLAEGSR 317 Query: 337 VGPLVNEAAFGRMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALV-RMPAQTAVV 395 +GPLV+ R+R +E+A A+G L GG P+ P YYVRP + R+ A+ Sbjct: 318 LGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAA-PEGLPTGYYVRPTVFGRVRPDAALA 376 Query: 396 REETFAPILYVLTYRDLDEAIRLNN 420 REE F P+L +LTYRD EA + N Sbjct: 377 REEVFGPVLAILTYRDEAEAEAIAN 401 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: 482 Number of extensions: 20 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: 476 Length adjustment: 34 Effective length of query: 462 Effective length of database: 442 Effective search space: 204204 Effective search space used: 204204 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