Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_011425015.1 RHE_RS08800 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15203 (503 letters) >NCBI__GCF_000092045.1:WP_011425015.1 Length = 506 Score = 251 bits (640), Expect = 6e-71 Identities = 149/459 (32%), Positives = 246/459 (53%), Gaps = 13/459 (2%) Query: 28 PATGQVTGQVALASQADVDSAVAAAQAAFPA--WSDTPPIRRARVMFKFLELLNAHKDEL 85 P+ G + S D + A+AAA+ AF W R+ ++ K +L+ A +EL Sbjct: 39 PSHGVTVSRFPAGSATDAERAIAAARKAFDEGPWPRMTASERSAILLKAADLIAARAEEL 98 Query: 86 AEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPLGVV 145 A E GK T +GE+A +DI +A + + L G+ + G R+ +GVV Sbjct: 99 AFLDAIEAGKPITQVRGEIAGSVDIWRYAAALARDLHGESYNTLGDGTVGVVLREAIGVV 158 Query: 146 AGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMADLLKQAGLPDGVFNVVQ 205 + ITP+NFP ++ P A+AAG + V+KPS L ++L++ ++L+QAG+PDGV N+V Sbjct: 159 SIITPWNFPFLIVGQKLPFALAAGCTTVVKPSELTSGSTLVLGEILQQAGVPDGVVNIVT 218 Query: 206 GDKDSVEALI-DHPDVKALSFVGSTPIANLIYERGARSGKRIQALGGAKNHMVVMPDANL 264 G V A++ HPDV +SF GST + L + A++ K++ G KN +V PDA+L Sbjct: 219 GTGPEVGAVMTSHPDVDMISFTGSTGVGKLTMKNAAQTLKKVSLELGGKNPQIVFPDADL 278 Query: 265 DKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERARDLKIKNGLELDAEMGP 324 D +DA + AY +AGE C A S +L +A +V R+AE ++ +K+ + L+ ++G Sbjct: 279 DAFIDAAVFGAYFNAGECCNAGSRLILHKSIASDVVRRVAELSKGVKVGDPLDPQTQVGA 338 Query: 325 IVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCADGFWMGGTLFDHVTPEMTI 384 I+T Q ++I+GY+ + GA + G D + G +M T+ + VTP+M + Sbjct: 339 IITPQHLEKISGYVAGARSNGARVTHGGETLDLGM-------GQFMSPTILEAVTPDMAV 391 Query: 385 YREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESGSVAREFGRRIQVGMVGINV 444 REE+FGPVL+ + A A+++ N ++G ++ GR ++ G + +N Sbjct: 392 AREEVFGPVLSVLTFETTAEAVRIANSIDYGLSAGVWSRDFDTCLTIGRSVRAGTIWMNT 451 Query: 445 PIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKSI 483 + + FGG+K+S G G V YT+ K++ Sbjct: 452 FMD-GASELPFGGYKQSGLG--RELGRHAVEDYTETKTL 487 Lambda K H 0.319 0.136 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: 645 Number of extensions: 29 Number of successful extensions: 3 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: 503 Length of database: 506 Length adjustment: 34 Effective length of query: 469 Effective length of database: 472 Effective search space: 221368 Effective search space used: 221368 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