Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_086510928.1 BZY95_RS16190 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Query= metacyc::MONOMER-15203 (503 letters) >NCBI__GCF_002151265.1:WP_086510928.1 Length = 503 Score = 909 bits (2350), Expect = 0.0 Identities = 445/503 (88%), Positives = 478/503 (95%) Query: 1 MTIKRIEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWS 60 MT I HYI G T+G + HQ V NPATGQVTGQVALAS+ADV +AVAAA+AAFPAW+ Sbjct: 1 MTQNTIAHYIAGQMTSGESGRHQSVYNPATGQVTGQVALASRADVATAVAAAKAAFPAWA 60 Query: 61 DTPPIRRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQL 120 DTPPIRRARV+FKFLELLNA+KDELA AIT EHGKVFTDAQGEVARGIDIVEFACGIPQL Sbjct: 61 DTPPIRRARVLFKFLELLNANKDELARAITLEHGKVFTDAQGEVARGIDIVEFACGIPQL 120 Query: 121 LKGDYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLD 180 LKGD+TEQVS GIDNWT RQPLGVVAGITPFNFP MVPMWMFP+AIAAGN+F+LKPSP D Sbjct: 121 LKGDFTEQVSNGIDNWTVRQPLGVVAGITPFNFPAMVPMWMFPVAIAAGNTFILKPSPTD 180 Query: 181 PSASLMMADLLKQAGLPDGVFNVVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGA 240 PSASL++A+LLKQAGLPDGVFNVVQGDK+SV+ALI+HPDV+ALSFVGSTPIANLIYE GA Sbjct: 181 PSASLLIAELLKQAGLPDGVFNVVQGDKESVDALIEHPDVQALSFVGSTPIANLIYENGA 240 Query: 241 RSGKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIV 300 R GKR+QALGGAKNHMVVMPDA+LDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIV Sbjct: 241 RHGKRVQALGGAKNHMVVMPDADLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIV 300 Query: 301 PRLAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVT 360 PRLAERAR LK+KNGLELDAEMGPIVT+QAHQRITGYIEKGVAEGAE+VVDGR+FD++ T Sbjct: 301 PRLAERARALKVKNGLELDAEMGPIVTAQAHQRITGYIEKGVAEGAELVVDGREFDAATT 360 Query: 361 GEGCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSC 420 G+GC +GFWMGG+LFDHVTPEMTIY+EEIFGPVLACVRVPDVATAIQLINDHEFGNGVSC Sbjct: 361 GDGCGEGFWMGGSLFDHVTPEMTIYKEEIFGPVLACVRVPDVATAIQLINDHEFGNGVSC 420 Query: 421 FTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQ 480 FTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRS+FGDTHAYGEEGVRFYTKQ Sbjct: 421 FTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSLFGDTHAYGEEGVRFYTKQ 480 Query: 481 KSIMQRWSDSIDAGAEFAMPTAK 503 KSIMQRWSDSI+AGAEFAMPT K Sbjct: 481 KSIMQRWSDSINAGAEFAMPTHK 503 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: 951 Number of extensions: 16 Number of successful extensions: 1 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: 503 Length adjustment: 34 Effective length of query: 469 Effective length of database: 469 Effective search space: 219961 Effective search space used: 219961 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 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