Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_012992059.1 THAL_RS05205 aldehyde dehydrogenase
Query= reanno::Smeli:SMc00781 (498 letters) >NCBI__GCF_000025605.1:WP_012992059.1 Length = 477 Score = 232 bits (592), Expect = 2e-65 Identities = 153/450 (34%), Positives = 230/450 (51%), Gaps = 14/450 (3%) Query: 16 TSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQRRARVFMKFVQL 75 ++G+ ++ P TGEV G +LAS+ D+ AVE A + A+ P R R+ MK QL Sbjct: 14 STGKWLDVVYPYTGEVIGRASLASEEDVHTAVERAIEGHKQMASLTPYERYRILMKAAQL 73 Query: 76 LNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFV------IGIPHLQKSEFTEGAGP 129 L + A L E GKTI +A+ ++ R L+ F IG + G G Sbjct: 74 LEERAEVFARTLVLEVGKTIREARTEVQRALQTLIFSAEEAKRIGGEVIPLDAHPNGKGK 133 Query: 130 GIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPIRLAELM 189 + Y IR+PVGI ITPFNFP + M APA+A GNA ILKPSER P PI L EL+ Sbjct: 134 -VGFY-IREPVGIVGAITPFNFPLNLSMHKVAPALAAGNAVILKPSERTPLTPIMLGELL 191 Query: 190 IEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGKRAQCFGG 249 +EAG+P ++V+ G AI THP I +SF GS + + A + K+ G Sbjct: 192 LEAGVPPMAISVLPGFGDVGKAISTHPQIRVISFTGSRKVGDIITRQAGI--KKVVLELG 249 Query: 250 AKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKLVPMVESL 309 + + +++ D D+ +A +I GY AG+ C+++ V V EE + + +L VE L Sbjct: 250 SNSAVVVHKDGDITKAVQKVIAGGYAIAGQVCISVQ-RVFVHEEVYEKFLMELTSQVEKL 308 Query: 310 RIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENGHFIGGCL 369 ++G DE D+GP+++ +RI+S ID + GA+LV G G + + + Sbjct: 309 KVGDPMDESTDVGPMISVSEVERIQSWIDEAVSMGAQLVTGGVSC---GDKVASILTPTV 365 Query: 370 FDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDAARDFASR 429 V + +++ E F PV+ V R +EA+S+ +YG V ++TRD A +F Sbjct: 366 VSLVPSNAKLFREEAFAPVVVVNPYREVDEAISMVNDSDYGLQVGVFTRDIKVAWEFIRG 425 Query: 430 INIGMVGVNVPIPVPLAYHSFGGWKSSSFG 459 + G V +N + +GG K S G Sbjct: 426 VQAGGVLINEGPNFRADHMPYGGVKQSGIG 455 Lambda K H 0.319 0.137 0.409 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: 530 Number of extensions: 27 Number of successful extensions: 5 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: 498 Length of database: 477 Length adjustment: 34 Effective length of query: 464 Effective length of database: 443 Effective search space: 205552 Effective search space used: 205552 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 (21.7 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