Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_012674904.1 SULAZ_RS00135 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000021545.1:WP_012674904.1 Length = 474 Score = 224 bits (570), Expect = 7e-63 Identities = 150/477 (31%), Positives = 246/477 (51%), Gaps = 16/477 (3%) Query: 6 KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65 +L I GE E D+ DV+ P ++ + + + ED++ A + A K ++ Sbjct: 3 RLPMLIGGE--EVFKDEVIDVIYPYNQQKVGEAVKGSVEDVEKAVEKAKVGLKKLKQLTA 60 Query: 66 PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGD 125 + +IL QLL + K+E A +IT+E GK KE+ EV R I + F+A + G+ Sbjct: 61 YEKYKILLKVAQLLEERKDEFAKVITLETGKTIKESRVEVERAINTITFSAEEAKRIGGE 120 Query: 126 SLASIATDVEAAN----YRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERT 181 + A+ +R P G+V I PFNFP+ + AIA G FILKPSE+T Sbjct: 121 VVHFDASPNGRGKRGYYFRVPAGIVAAITPFNFPVNLTAHKIAPAIAAGCPFILKPSEKT 180 Query: 182 PLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGS 241 PL L +LF +AG+PK +++ G DV + HP+++ +SF GS VGE + K+ Sbjct: 181 PLSPTMLCQLFLEAGVPKEAVSIIPGFADVGQAMTTHPDVRVVSFTGSLKVGEIIAKQA- 239 Query: 242 ENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFM 301 LK++ G+ + IV DANLE V F AG+ C++ V V + +ADEF Sbjct: 240 -GLKKIVMELGSNSAVIVDKDANLELAAKKSVLGGFALAGQVCISVQRVLVHKEVADEFE 298 Query: 302 AKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDG 361 L+++ + +K G+ +++ +GPVI + R ++I + + +GA++ G+ + Sbjct: 299 NLLKKEASKLKYGDPMEEDTDVGPVISINEVDRIQTWISEAVMKGAKVSLGGQAEKT--- 355 Query: 362 YFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNA 421 PTI V + ++ +E FAPV++V R + ++EAIE+ NK+ + +FT+N Sbjct: 356 -LFKPTIVSEVPEDSKLFYEEAFAPVVAVKRFETIEEAIEMVNKTNYGLQVGIFTNNLKN 414 Query: 422 IRYFRENIDAGMLGINLGVPAPMA-FFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477 E ++ G + +N +P A P+ G K S G K +++ YT KVV Sbjct: 415 AWKVIEEVEVGGVMVN-DIPTFRADNMPYGGVKGSGIG--REGPKFAIEDYTEIKVV 468 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: 546 Number of extensions: 24 Number of successful extensions: 4 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: 474 Length adjustment: 34 Effective length of query: 453 Effective length of database: 440 Effective search space: 199320 Effective search space used: 199320 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: 51 (24.3 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