Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_090218033.1 CV091_RS10640 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_002796795.1:WP_090218033.1 Length = 483 Score = 246 bits (629), Expect = 1e-69 Identities = 143/469 (30%), Positives = 235/469 (50%), Gaps = 4/469 (0%) Query: 9 NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68 N I G W D+ E+ +++ ++ + +D A A W+ + R+ Sbjct: 7 NLIAGSWTVG-VDEIENRNPSDLSDLVGMFAQASSDQLDATLDQAKIAQAEWAAYGIERK 65 Query: 69 ARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLA 128 +L + EEL L++ E GK E GEV R + + A +G++ Sbjct: 66 YNVLMAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAETLRQIGENAD 125 Query: 129 SIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKL 188 S+ +E R +G V I+P+NFP W A+ GN + KP+ TP L Sbjct: 126 SVREGIEIDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANATPASAVAL 185 Query: 189 VELFEKAGLPKGVFNVVYGA-HDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRV 247 E+ E+ +PKG+F++V GA ++ ++E ++ AISF GS PVG+ + +NL +V Sbjct: 186 TEIIERQDIPKGLFSLVMGAGREIGQRLVESSKVDAISFTGSVPVGKGIASAAIQNLTKV 245 Query: 248 QSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEK 307 Q G+KN V++DA+++ V+ +G AFG G++C A + + V + DEF++KL Sbjct: 246 QMEMGSKNALAVMDDADIDLAVSLALGGAFGGTGQKCTASSRLVVHSAVHDEFVSKLVAG 305 Query: 308 VADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYFVGP 366 +K+G+ L+ G +GPV+ E L+Y++ G EGA L+C G R + GY++ P Sbjct: 306 AKAMKVGHALEAGTQIGPVVTEQQLNENLAYVDLGKSEGAELLCGGQRLEMPHQGYYMNP 365 Query: 367 TIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFR 426 IF T +M I ++E+FAP+ +VI+V EA+ + N + F + + T + +FR Sbjct: 366 GIFIGTTNDMRINREEMFAPLAAVIKVSGYDEALSVVNDTNFGLTSGIVTKSLARANHFR 425 Query: 427 ENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475 N G + +NL PF G S +G GK + +FYT K Sbjct: 426 RNAQTGCVMVNLPTAGTDYHVPFGGRGDSSYGP-REQGKAAAEFYTTVK 473 Lambda K H 0.318 0.136 0.396 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: 527 Number of extensions: 21 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: 487 Length of database: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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 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