Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_010529654.1 ON01_RS03650 aldehyde dehydrogenase family protein
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_000224785.1:WP_010529654.1 Length = 498 Score = 338 bits (868), Expect = 2e-97 Identities = 178/471 (37%), Positives = 287/471 (60%), Gaps = 10/471 (2%) Query: 10 KWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILL 69 +W++ S E INPA+ D ++ + L V A+ A EW+ PAP+R +L Sbjct: 18 EWVETS-ESTRVINPANGDTIV-NVPLSDSGAVNNAVEGAKKAQKEWALVPAPQRAEVLF 75 Query: 70 KAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPN 129 K G++M++ + + L+T+E GK L+++ EV ++ + ++ G T P+ PN Sbjct: 76 KVGQMMKERKERLSQLLTMENGKVLEEARGEVQEGIDMAFYMAGEGRRLFGHTTPAELPN 135 Query: 130 TRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLS 189 + + P+GVV +ITPWNFP++I WK PA+ AGN + KPAT+TP+M +L ++L Sbjct: 136 KFSMSQRAPVGVVGIITPWNFPIAIATWKSFPAIVAGNAVIWKPATETPIMAYELAKILE 195 Query: 190 KAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLE 249 +AGLP+G++N+V GKGS+VGD +V +I +SFTGS + G+ I G ++ ++ LE Sbjct: 196 EAGLPKGIMNVVYGKGSQVGDAMVHHADIKVISFTGSNDTGRHIASECG--RQLKKVSLE 253 Query: 250 LGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKK 309 +GGKNA+ V ADL LA E + +G +GQ CTA SR+I+++DV Q ++RLL ++K Sbjct: 254 MGGKNAITVMDDADLDLAVEGILWSAYGTSGQRCTAASRVIVHEDVKEQLEERLLVEIEK 313 Query: 310 WRVGPGTEDVD-MGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII-PGK---GYFLEPT 364 +G G ++ + +GP++++ +K +YI+ GK GA LI GG ++ GK G++ PT Sbjct: 314 LTIGDGLDESNTVGPIINKAGLEKIEKYIQIGKEEGANLIAGGYVLDDGKYTNGHYFAPT 373 Query: 365 IFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVS 424 +F T+DMR+ +EEIFGPV+S+ K +EAI + N V YG ++ I +D + + Sbjct: 374 LFTDCTADMRISQEEIFGPVISLIPVKSFEEAIEVNNGVSYGLSSSIFTTDANRVFKAQR 433 Query: 425 RVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475 ++ G++ VN T G E+ PFGG K +G ++ G AL+ + + K VY Sbjct: 434 DLDTGIVYVNAGTTGAEIHLPFGGTKGTG-NGHRDSGVQALDVFTEWKAVY 483 Lambda K H 0.316 0.135 0.389 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: 687 Number of extensions: 33 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: 478 Length of database: 498 Length adjustment: 34 Effective length of query: 444 Effective length of database: 464 Effective search space: 206016 Effective search space used: 206016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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