Align Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)
to candidate WP_012674904.1 SULAZ_RS00135 aldehyde dehydrogenase
Query= curated2:Q81QR5 (486 letters) >NCBI__GCF_000021545.1:WP_012674904.1 Length = 474 Score = 230 bits (587), Expect = 7e-65 Identities = 151/441 (34%), Positives = 235/441 (53%), Gaps = 16/441 (3%) Query: 46 EDVEKAVEAAKAAYETWSKVPVPNRSRQLYKYLQLLQENKEELAKIITLENGKTLTDATG 105 EDVEKAVE AK + ++ + + L K QLL+E K+E AK+ITLE GKT+ ++ Sbjct: 39 EDVEKAVEKAKVGLKKLKQLTAYEKYKILLKVAQLLEERKDEFAKVITLETGKTIKESRV 98 Query: 106 EVQRGIEAVELATSAPNLMMGQALPNIAS----GIDGSIWRYPIGVVAGITPFNFPMMIP 161 EV+R I + + + G+ + AS G G +R P G+VA ITPFNFP+ + Sbjct: 99 EVERAINTITFSAEEAKRIGGEVVHFDASPNGRGKRGYYFRVPAGIVAAITPFNFPVNLT 158 Query: 162 LWMFPLAIACGNTFVLKTSERTPLLAERLVELFYEAGFPKGVLNLVQGGKDVVNSILENK 221 AIA G F+LK SE+TPL L +LF EAG PK ++++ G DV ++ + Sbjct: 159 AHKIAPAIAAGCPFILKPSEKTPLSPTMLCQLFLEAGVPKEAVSIIPGFADVGQAMTTHP 218 Query: 222 DIQAVSFVGSEPVARYVYETGTKHGKRVQALAGAKNHAIVMPDCNLEKTVQGVIGSAFAS 281 D++ VSF GS V + + K++ G+ + IV D NLE + + FA Sbjct: 219 DVRVVSFTGSLKVGEIIAKQAGL--KKIVMELGSNSAVIVDKDANLELAAKKSVLGGFAL 276 Query: 282 SGERCMACSVVAVVDEIADEFIDVLVAETKKLKVGDGFHEDNYVGPLIRESHKERVLGYI 341 +G+ C++ V V E+ADEF ++L E KLK GD ED VGP+I + +R+ +I Sbjct: 277 AGQVCISVQRVLVHKEVADEFENLLKKEASKLKYGDPMEEDTDVGPVISINEVDRIQTWI 336 Query: 342 NSGVADGATLLVDGRKIKEEVGEGYFVGATIFDGVNQEMKIWQDEIFAPVLSIVRVKDLE 401 + V GA + + G+ E TI V ++ K++ +E FAPV+++ R + +E Sbjct: 337 SEAVMKGAKVSLGGQ------AEKTLFKPTIVSEVPEDSKLFYEEAFAPVVAVKRFETIE 390 Query: 402 EGIKLTNQSKFANGAVIYTSNGKHAQTFRDNIDAGMIGVNVNVPAPMA-FFAFAGNKASF 460 E I++ N++ + I+T+N K+A + ++ G + VN ++P A + G K S Sbjct: 391 EAIEMVNKTNYGLQVGIFTNNLKNAWKVIEEVEVGGVMVN-DIPTFRADNMPYGGVKGSG 449 Query: 461 FGDLGTNGTDGVQFYTRKKVV 481 G G ++ YT KVV Sbjct: 450 IGREGPK--FAIEDYTEIKVV 468 Lambda K H 0.317 0.135 0.392 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: 544 Number of extensions: 27 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: 486 Length of database: 474 Length adjustment: 34 Effective length of query: 452 Effective length of database: 440 Effective search space: 198880 Effective search space used: 198880 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 (21.6 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