Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_023431853.1 N177_RS08305 aldehyde dehydrogenase family protein
Query= reanno::Smeli:SMc00781 (498 letters) >NCBI__GCF_000496075.1:WP_023431853.1 Length = 484 Score = 247 bits (631), Expect = 6e-70 Identities = 161/477 (33%), Positives = 248/477 (51%), Gaps = 12/477 (2%) Query: 5 GHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAA-QPKWAATNPQ 63 G FIDG+ A SGR NPATG + V A D+ AV SA+AA + W Sbjct: 11 GLFIDGRFSAPLSGRSFATSNPATGSLITHVGEADAVDVDRAVRSARAAFEGPWGHMRAA 70 Query: 64 RRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKG-DIVRGLEVCEFVIGIPHLQKSE 122 R R+ + +L+ +N++EL ++ S + GK + + D+ L+ + G + Sbjct: 71 ERGRLLSRLAELVGENLDELVDLESLDSGKPVSAIRRQDLPAVLDTLTYYAGWADKINGQ 130 Query: 123 FTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVP 182 + Y++R+P+G+ I P+NFP MI +W APA+ACG +LKP+E Sbjct: 131 VIPARADALT-YTVREPIGVVGAIVPWNFPLMIGVWKLAPALACGCTVVLKPAELTSLTA 189 Query: 183 IRLAELMIEAGLPAGILNVVNG-DKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNG 241 +RL EL +EAG PAG+LNVV G K A A++ HPD+ V+F GS + R + +AA N Sbjct: 190 LRLGELAMEAGFPAGVLNVVPGLGKTAGAALVDHPDVDKVTFTGSPAVGRQILRSAAGNL 249 Query: 242 KRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDK 301 KR G K+ +I PDAD++ AA A + ++G+ C A S V V E+ + ++++ Sbjct: 250 KRVTLELGGKSANVIFPDADVEAAAKAAAAGIFFNSGQVCSAGS-RVLVHEDVHDEVVER 308 Query: 302 LVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYEN 361 LV LR+G D MGP+V++ +R+ ++ G +GA + V G + + Sbjct: 309 LVDRAARLRLGDPLDPATQMGPLVSETQMERVLGYVEIGRREGATVAVGGG----RVGDE 364 Query: 362 GHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGD 421 G F+ + V DM + + EIFGPV+SVVR R+ EEA+ + Y +++ D Sbjct: 365 GCFVAPTVLTGVEHDMRVSQEEIFGPVVSVVRFRDEEEAVRMANGTAYSLAAGVWSSDLG 424 Query: 422 AARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTI 478 A RI G V VN P + +GG + S FG +HG +I+ +T K + Sbjct: 425 RIHRLAKRIRAGTVWVNTFGPTDIRL-PWGGSRDSGFG--REHGEAAIENFTEPKAV 478 Lambda K H 0.319 0.137 0.409 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: 565 Number of extensions: 32 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: 498 Length of database: 484 Length adjustment: 34 Effective length of query: 464 Effective length of database: 450 Effective search space: 208800 Effective search space used: 208800 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 (21.7 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