Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_089229754.1 B9O00_RS20310 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15203 (503 letters) >NCBI__GCF_900177295.1:WP_089229754.1 Length = 477 Score = 248 bits (633), Expect = 3e-70 Identities = 152/465 (32%), Positives = 243/465 (52%), Gaps = 18/465 (3%) Query: 24 EVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRARVMFKFLELLNAHKD 83 E +PATG+V +V +A +A V++AVAAA+A F WS R RV+ + E++ A D Sbjct: 15 ETRDPATGEVLAEVQVAGEAAVEAAVAAAEAGFRVWSRMTGTERGRVLRRAAEIVRARND 74 Query: 84 ELAEAITREHGKVFTDAQ-GEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPL 142 EL+E TR+ GK + + A G D +E+ G+ L G++ + +T R+PL Sbjct: 75 ELSEIETRDTGKPIQETLVADAASGADCLEYYGGLAGSLAGEHIDLGHAFA--YTRREPL 132 Query: 143 GVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMADLLKQAGLPDGVFN 202 G+ AGI +N+P+ + W A+A GN+ + KP+ L P ++ +A++ ++AGLPDGVFN Sbjct: 133 GICAGIGAWNYPIQIACWKSAPALACGNAMIFKPAELTPLTAVKLAEIYREAGLPDGVFN 192 Query: 203 VVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGARSGKRIQALGGAKNHMVVMPDA 262 VVQG ++ L HP + +S G + A K + G K+ ++V DA Sbjct: 193 VVQGFAETGRLLTRHPKIAKVSLTGEVGTGRKVMADAAGGLKHVTLELGGKSPILVFEDA 252 Query: 263 NLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERARDLKIKNGLELDAEM 322 +LD+AV + + SAGE C + + V + +L R + + + L+ ++ Sbjct: 253 DLDRAVSGALLGNFFSAGEVCSNGTRVFVQESVRAAFLEKLVARTEAMTVGDPLDPATQV 312 Query: 323 GPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCADGFWMGGTLFDHVTPEM 382 G +++ ++ GYIE G AEGA + G +T CA G+++ T+FD +M Sbjct: 313 GALISEGHMAKVLGYIETGKAEGATALTGG----GRITEGACAKGWFVAPTVFDGCRDDM 368 Query: 383 TIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESGSVAREFGRRIQVGMVGI 442 T+ REEIFGPV+A + D AI+ N +FG FT + A R+Q G I Sbjct: 369 TVVREEIFGPVMAVLSFEDEEEAIRRANATDFGLSAGVFTRDLARAHRTIARLQAGTCWI 428 Query: 443 N----VPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKSI 483 N P+ +P FGG K+S G + G+ + Y++ KS+ Sbjct: 429 NTYNVTPVEMP-----FGGVKQSGLGREN--GKAAIEHYSQLKSV 466 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: 597 Number of extensions: 40 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: 477 Length adjustment: 34 Effective length of query: 469 Effective length of database: 443 Effective search space: 207767 Effective search space used: 207767 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