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_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= curated2:Q5L025 (488 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 327 bits (837), Expect = 8e-94 Identities = 179/475 (37%), Positives = 268/475 (56%), Gaps = 5/475 (1%) Query: 12 KNYIGGQWVASSGTETLEVPNPAT-GEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVP 70 +NYI GQW+ ++ TL NPA E++A P S +D D+AV AA++A+ +W+ VP P Sbjct: 8 QNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKVPAP 67 Query: 71 KRARIMFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMGES 130 RA +F LL QH EELA+L+ +E GK EA G++Q G++C ++AG L G++ Sbjct: 68 ARAEYIFRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEGRRLFGQT 127 Query: 131 LSNIAEEIDSEMFRYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILAN 190 + + R P+GV A ITP+NFP+ +P W A+VCGNT +LKP+E TP A Sbjct: 128 TPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACAT 187 Query: 191 KLAELFTEAGAPPGVLNVVHG-AHEVVNALIDHEDIRAISFVGSQPVAKYVYERTAAQGK 249 KL E+F AG PPGV+N+VHG E AL++H +I +SF GS YV E K Sbjct: 188 KLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCGRTHK 247 Query: 250 RVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGE-NETFVRRLK 308 RV G KN +VM DAD+E A+ + AFG+ GQRC A S +++ + E F L+ Sbjct: 248 RVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFTTMLR 307 Query: 309 QKADELIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMDDR-PEGN 367 ++ +L +G G +PE + P+I ++V Y+ EEGA +L G + + +G Sbjct: 308 ERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEGQLKQGY 367 Query: 368 FLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTKDAKAV 427 F PTI D VTP M +A+EEIF PV++L+ + +EA++ + ++YG +++YT+D Sbjct: 368 FFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINRA 427 Query: 428 RKFREEADAGMLGINVGVPATMAFFPFSGWKDSFYGDLHVNGKDGVNFYTRKKMI 482 + + G+ IN PF G K + G G ++ +T K + Sbjct: 428 FVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREA-GTTALDVFTEWKSV 481 Lambda K H 0.319 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: 601 Number of extensions: 28 Number of successful extensions: 6 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: 488 Length of database: 498 Length adjustment: 34 Effective length of query: 454 Effective length of database: 464 Effective search space: 210656 Effective search space used: 210656 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 Apr 09 2024. 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