Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >NCBI__GCF_001484605.1:WP_058929223.1 Length = 508 Score = 214 bits (546), Expect = 4e-60 Identities = 134/387 (34%), Positives = 198/387 (51%), Gaps = 9/387 (2%) Query: 39 PLTGADLFGLRAHTPEDVDRAVEAAHTAFLT--WRTTPAPVRGALVKRFGELLTEHKQDL 96 P A + A T EDVDRAV AA AF W T R AL++RF +LLTE+ +L Sbjct: 43 PYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWPQTLPSQRAALLRRFADLLTENADEL 102 Query: 97 ADLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVV 156 A E GK+ E +M + GL+ + GRT+ S P P+GVV Sbjct: 103 ARGQIHENGKLIGEMTWGALQMGQHAHYVAGLAETIQGRTIESNWPNTAAFTFREPIGVV 162 Query: 157 GVISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLN 216 +I+ +N P+ + +W AL G+TVV KPSE TP + A L +AG P G+ Sbjct: 163 AMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEATPTSTLRMAELA----MEAGFPPGVI 218 Query: 217 QVVVGAAD-VGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTP 275 VV G G LVD V ++ TGST GRA+ + A RF R LELGG + ++ Sbjct: 219 NVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGRAINKQAAERFARVTLELGGKSPNIIFS 278 Query: 276 SADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTT 335 AD+D V+ A+ G GQ C R++V + I D V+R+ A + L +GDP T Sbjct: 279 DADIDNAVHGAMAGIFGATGQTCMGGSRVLVQDSIYDDFVDRMARATQALTLGDPLDPTV 338 Query: 336 LVGPLVNEAAFGRMREAVERATAEGGTLCAGGER--QFPDAAPGAYYVRPALVRMPAQTA 393 +GP+ N A F ++ + V+ +EG + AGG R + + G ++ + ++ Sbjct: 339 DMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGARCMTTSELSKGLFFEPTVFANVSNESR 398 Query: 394 VVREETFAPILYVLTYRDLDEAIRLNN 420 + +EE F P+ ++ +RD DEA+++ N Sbjct: 399 LAQEEIFGPVASIIRFRDEDEAVKIAN 425 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: 493 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: 508 Length adjustment: 34 Effective length of query: 462 Effective length of database: 474 Effective search space: 218988 Effective search space used: 218988 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