Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_085121241.1 B9O00_RS04475 aldehyde dehydrogenase family protein
Query= BRENDA::Q02252 (535 letters) >NCBI__GCF_900177295.1:WP_085121241.1 Length = 484 Score = 212 bits (540), Expect = 2e-59 Identities = 142/472 (30%), Positives = 230/472 (48%), Gaps = 11/472 (2%) Query: 44 IGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADTSVLSRQQ 103 IGG+ ++S + NP I +V ++ A++ AA+A+ + A P WA T + R Sbjct: 12 IGGEERPAESGRSFANVNPHDGSEICQVARSEAADVSAAVAAARAAQPGWAATPAVQRGH 71 Query: 104 VLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMGETMPSI 163 +L + ++ EIA + E GK L D++G+V + + G TMPS Sbjct: 72 ILHQVMNALEARADEIAAAVAAEAGKRLKDSKGEVGGAILCGRFFAGEGQRLFGRTMPSG 131 Query: 164 TKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATMLLAK 223 T + + R P GV I N PA W A++CGN ++K +E P + L+A+ Sbjct: 132 TPNKYNMTVRTPCGVAGLIIAANTPAPNFAWKVFPALICGNAVVLKSAEDTPVSAWLMAR 191 Query: 224 LLQDSGAPDGTLNIIHG-QHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRHGKRVQA 282 + +++G P G LN++HG EA + DHP + +SF GS G I E R K++ Sbjct: 192 ICEEAGLPKGVLNVVHGLGAEAGQPLVDHPGVDVLSFTGSTAVGRRIAESCGRQLKKLSL 251 Query: 283 NMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEA--KKWLPELVEHA 340 +G KN VV DA+ +N + +A+ AGQRC A + LV E+ + + +LVE Sbjct: 252 ELGGKNPFVVCDDADLDNAVKWACLSAYSNAGQRC-AAGSRFLVFESVYEAFRDKLVEAT 310 Query: 341 KNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENGNFVG 400 + ++ G + DLGP+I + + I+ T +GA +L+ GR+ KG ++ Sbjct: 311 RAQKL--GVEEDCDLGPVINERQLNNMLGAIERATGKGAKVLIGGRRAGDKGC----YLE 364 Query: 401 PTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGATARKY 460 PT++ P+ + E+FGPV + +A+ + N++PYG I T + A + Sbjct: 365 PTVVEGAAPDDEISQTELFGPVASLYRVRDFAQALAMANDHPYGLTACIHTRSLDRALAF 424 Query: 461 AHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTI 512 +H V G VN P F G + S G T G + + Y++LK I Sbjct: 425 SHGVQAGATVVNAGTYGSEPHMPFGGPKQSGNG-TREPGTEALDVYSELKDI 475 Lambda K H 0.318 0.133 0.391 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: 560 Number of extensions: 28 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: 535 Length of database: 484 Length adjustment: 34 Effective length of query: 501 Effective length of database: 450 Effective search space: 225450 Effective search space used: 225450 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 (21.7 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