Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate GFF2711 HP15_2655 methylmalonate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15203 (503 letters) >FitnessBrowser__Marino:GFF2711 Length = 503 Score = 911 bits (2355), Expect = 0.0 Identities = 444/503 (88%), Positives = 477/503 (94%) Query: 1 MTIKRIEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWS 60 MT I+HYING + G + Q+V NPATGQVTG+VALA + DVD+AVAAA AAFPAW+ Sbjct: 1 MTNATIQHYINGEISLGTSSQSQDVFNPATGQVTGRVALAGREDVDAAVAAADAAFPAWA 60 Query: 61 DTPPIRRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQL 120 DTPPIRRARVMFKFLELLN HKD+LA AIT EHGKVFTDAQGEVARGIDIVEFACGIPQL Sbjct: 61 DTPPIRRARVMFKFLELLNTHKDDLARAITAEHGKVFTDAQGEVARGIDIVEFACGIPQL 120 Query: 121 LKGDYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLD 180 LKGDYTEQVSTGIDNWTTRQPLGVVAG+TPFNFP MVPMWMFP+AIAAGN+FVLKPSPLD Sbjct: 121 LKGDYTEQVSTGIDNWTTRQPLGVVAGVTPFNFPAMVPMWMFPVAIAAGNTFVLKPSPLD 180 Query: 181 PSASLMMADLLKQAGLPDGVFNVVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGA 240 PSASLM+ADLLKQAGLPDGVFNVVQGDKD+V ALI+HPDV+ALSFVGSTPIANL+YE+GA Sbjct: 181 PSASLMIADLLKQAGLPDGVFNVVQGDKDAVNALIEHPDVQALSFVGSTPIANLLYEKGA 240 Query: 241 RSGKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIV 300 + GKRIQALGGAKNHMVVMPDA+LDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIV Sbjct: 241 KHGKRIQALGGAKNHMVVMPDADLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIV 300 Query: 301 PRLAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVT 360 PRLAERAR LK+KNG +LDAEMGPIVT+ AHQRITGYI+KGVAEGAE+VVDGR FD+S T Sbjct: 301 PRLAERARSLKVKNGEQLDAEMGPIVTAAAHQRITGYIDKGVAEGAELVVDGRGFDASNT 360 Query: 361 GEGCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSC 420 G+GCADGFWMGG+LFDHVTP+MTIYREEIFGPVLACVRVPD+ATAI+LINDHEFGNGVSC Sbjct: 361 GDGCADGFWMGGSLFDHVTPDMTIYREEIFGPVLACVRVPDIATAIRLINDHEFGNGVSC 420 Query: 421 FTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQ 480 FTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGV+FYT+Q Sbjct: 421 FTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVKFYTRQ 480 Query: 481 KSIMQRWSDSIDAGAEFAMPTAK 503 KSIMQRWSDSIDAGAEF MPTAK Sbjct: 481 KSIMQRWSDSIDAGAEFVMPTAK 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 17 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