Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_090218033.1 CV091_RS10640 aldehyde dehydrogenase family protein
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_002796795.1:WP_090218033.1 Length = 483 Score = 314 bits (805), Expect = 4e-90 Identities = 171/472 (36%), Positives = 262/472 (55%), Gaps = 7/472 (1%) Query: 7 LADKWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGS 66 +A W G +E + NP+D ++ + D + +++A EW+ ++ + Sbjct: 9 IAGSWTVGV-DEIENRNPSDLSDLVGMFAQASSDQLDATLDQAKIAQAEWAAYGIERKYN 67 Query: 67 ILLKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSA 126 +L+ G M A+E L++ EEGK L + EV R+ +Y A + G+ S Sbjct: 68 VLMAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAETLRQIGENADSV 127 Query: 127 DPNTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVE 186 I +E +G VA+I+PWNFP + WK+APAL GN V KPA TP L E Sbjct: 128 REGIEIDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANATPASAVALTE 187 Query: 187 VLSKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRI 246 ++ + +P+G+ +LV+G G E+G +V + A+SFTGS VGK I +T++ Sbjct: 188 IIERQDIPKGLFSLVMGAGREIGQRLVESSKVDAISFTGSVPVGKGIASAA--IQNLTKV 245 Query: 247 QLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLER 306 Q+E+G KNAL V AD+ LA LA+ G FG TGQ CTA+SRL+++ V+ +F +L+ Sbjct: 246 QMEMGSKNALAVMDDADIDLAVSLALGGAFGGTGQKCTASSRLVVHSAVHDEFVSKLVAG 305 Query: 307 VKKWRVGPGTE-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYFLEP 363 K +VG E +GPVV E Q ++L Y++ GK+ GA+L+ GG + P +GY++ P Sbjct: 306 AKAMKVGHALEAGTQIGPVVTEQQLNENLAYVDLGKSEGAELLCGGQRLEMPHQGYYMNP 365 Query: 364 TIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFV 423 IF G T+DMR+ +EE+F P+ +V + DEA+ +VN ++G T+GIV + N F Sbjct: 366 GIFIGTTNDMRINREEMFAPLAAVIKVSGYDEALSVVNDTNFGLTSGIVTKSLARANHFR 425 Query: 424 SRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475 + G + VN PT G + PFGG + + +E G+ A EFY KT Y Sbjct: 426 RNAQTGCVMVNLPTAGTDYHVPFGG-RGDSSYGPREQGKAAAEFYTTVKTAY 476 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: 591 Number of extensions: 41 Number of successful extensions: 5 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: 483 Length adjustment: 34 Effective length of query: 444 Effective length of database: 449 Effective search space: 199356 Effective search space used: 199356 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: 51 (24.3 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