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 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)
Query= curated2:Q81QR5 (486 letters) >FitnessBrowser__PV4:5211158 Length = 506 Score = 213 bits (541), Expect = 2e-59 Identities = 144/469 (30%), Positives = 231/469 (49%), Gaps = 23/469 (4%) Query: 8 RVKNHINGEWVESTGTEVEAVPNPATGKIIAYVPLSPKEDVEKAVEAAKAAYETWSKVPV 67 R N I G+WV G E +P G++ V S + D+E A++AA AA + W K V Sbjct: 18 RYDNFIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAAKDAWGKTSV 77 Query: 68 PNRSRQLYKYLQLLQENKEELAKIITLENGKTLTDA-TGEVQRGIEAVELATSAPNLMMG 126 RS L K +++N E LA T ENGK + + ++ ++ G Sbjct: 78 TERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEG 137 Query: 127 QALPNIASGIDGSIWRY----PIGVVAGITPFNFPMMIPLWMFPLAIACGNTFVLKTSER 182 A+ ID + Y P+GVV I P+NFP+++ W A+A GN VLK +E+ Sbjct: 138 S-----AADIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQ 192 Query: 183 TPLLAERLVELFYEAGFPKGVLNLVQG-GKDVVNSILENKDIQAVSFVGSEPVARYVYET 241 TP+ +VEL + P GVLN+V G G + ++ +K I ++F GS + ++ + Sbjct: 193 TPVSILVMVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHILKC 251 Query: 242 GTKHGKRVQALAGAKNHAIVMPDC------NLEKTVQGVIGSAFASSGERCMACSVVAVV 295 + G K+ I D L+K V+G++ AF + GE C S V + Sbjct: 252 AAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGML-LAFFNQGEVCTCPSRVLIA 310 Query: 296 DEIADEFIDVLVAETKKLKVGDGFHEDNYVGPLIRESHKERVLGYINSGVADGATLLVDG 355 + I D+FID ++A K +K G+ D VG + +++L Y+ G +GA +L+ G Sbjct: 311 ESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGG 370 Query: 356 R--KIKEEVGEGYFVGATIFDGVNQEMKIWQDEIFAPVLSIVRVKDLEEGIKLTNQSKFA 413 ++ + G+++ TI G N +M+++Q+EIF PV+S+ KD E + + N +++ Sbjct: 371 TSCQLSGDQSSGFYIEPTILKGHN-KMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYG 429 Query: 414 NGAVIYTSNGKHAQTFRDNIDAGMIGVNVNVPAPMAFFAFAGNKASFFG 462 GA ++T + AQ I AG + +N P A AF G K S G Sbjct: 430 LGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYP-AHAAFGGYKKSGIG 477 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: 597 Number of extensions: 31 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: 506 Length adjustment: 34 Effective length of query: 452 Effective length of database: 472 Effective search space: 213344 Effective search space used: 213344 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: 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