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_046010388.1 OLEAN_RS18035 betaine-aldehyde dehydrogenase
Query= curated2:Q5L025 (488 letters) >NCBI__GCF_000967895.1:WP_046010388.1 Length = 491 Score = 266 bits (680), Expect = 1e-75 Identities = 164/480 (34%), Positives = 263/480 (54%), Gaps = 15/480 (3%) Query: 10 VLKNYIGGQWVASSGTETLEVPNPATGEVLARVPISTKEDVDQAVQAAKKAFATWKDVPV 69 +LKN+I G+++ ++ +T +V NPATG + +V ++ ++ A++++++ F TW + Sbjct: 9 ILKNFINGEYLDNASGKTFDVINPATGVLAYQVEVADEKIRSAAIKSSQQGFETWSAMTG 68 Query: 70 PKRARIMFSFHHLLNQHHEELAELVVQENGKAYKEA-YGEIQRGIECVEFAAGAPTLLMG 128 +R RI+ LL + ++ELA++ V + GK ++EA ++ G + +E+ A + Sbjct: 69 FERNRILLKAVELLRERNDELAKIEVIDTGKPWQEASVVDVVTGTDSIEYFAA-----LA 123 Query: 129 ESLSNIAEEIDSEMF---RYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERT 185 S+ +++ + + R PLGV AGI +N+P+ + W A+ CGN+ + KPSE T Sbjct: 124 LSIEGTQQDLGGDFYYTRREPLGVCAGIGAWNYPLQIACWKAAPALACGNSMIFKPSEET 183 Query: 186 PILANKLAELFTEAGAPPGVLNVVHGAHEVVNALIDHEDIRAISFVGSQPVAKYVYERTA 245 P A KLAE+F EAG P GV NVV G EV L H DI +SF G K V A Sbjct: 184 PHGALKLAEIFFEAGVPAGVFNVVQGDGEVGAWLTTHNDIAKVSFTGEVGTGKKVMAAAA 243 Query: 246 AQGKRVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGE-NETFV 304 K V G K+ IV DAD++ AV + F + G+ C + + + + F+ Sbjct: 244 TNLKDVTMELGGKSPLIVFSDADIDDAVSAAMLGNFYTQGEVCTNATRIFVQKDIYPKFI 303 Query: 305 RRLKQKADE-LIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMDDR 363 +LK++ ++ +I G+ MDPE +I ++H++ VL YI+KGI+EGA LL G+ Sbjct: 304 TQLKERTEKNIIAGDPMDPETNFGALISKNHQQLVLSYIEKGIQEGAFLLTGGQALQPPG 363 Query: 364 PEGN-FLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTK 422 EG F+ PTIF T DMTI KEEIF PV+S+L +E + + +G A ++T Sbjct: 364 VEGGYFVAPTIFTDCTDDMTIVKEEIFGPVMSVLTFESEEEVIKRANGTEFGLAAGVFTN 423 Query: 423 DAKAVRKFREEADAGMLGINVGVPATMAFFPFSGWKDSFYGDLHVNGKDGVNFYTRKKMI 482 D + + ++ +AG+ IN A+ A P G+K S G NG +N YT+ K + Sbjct: 424 DIRRAHRVVKQLEAGICWIN-AYGASPAEMPVGGYKLSGIG--RENGSSTMNQYTQIKSV 480 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: 563 Number of extensions: 33 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: 488 Length of database: 491 Length adjustment: 34 Effective length of query: 454 Effective length of database: 457 Effective search space: 207478 Effective search space used: 207478 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 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