Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= reanno::Smeli:SMc00781 (498 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 206 bits (524), Expect = 2e-57 Identities = 154/478 (32%), Positives = 244/478 (51%), Gaps = 11/478 (2%) Query: 6 HFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQRR 65 H I GK V G V + NPATGE+ GT A + D+ AV SAKAAQ WA + + R Sbjct: 20 HLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKDWAKQSARAR 79 Query: 66 ARVFMKFVQLLNDNMNELAEMLSREHGKTI-DDAKGDIVRGLEVCEFVIGIPHLQKSEFT 124 ++ + ++L+ ++ EL +++ E GK + +++ + ++ F G+ K E T Sbjct: 80 GKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELKGE-T 138 Query: 125 EGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPIR 184 P + ++R+PVG+ I P+N P ++ A A+ GN+ ++K +E P +R Sbjct: 139 IPFNPDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPLTVLR 198 Query: 185 LAELMIEAGLPAGILNVVNGDKGAVDA-ILTHPDIAAVSFVGSTPIARYVYGTAAMNGKR 243 +AE+M LP G+ N+++G A ++ HPD+ V+F GS R VY AA Sbjct: 199 VAEIM-NTVLPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEKLIP 257 Query: 244 AQCFGGAKNHMIIMPDADLDQA-ANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKL 302 G K+ MI+ DAD+DQA A AL G + G+ C A S + V E + + K+ Sbjct: 258 VTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTA-SSRLFVHESIHDEFVAKV 316 Query: 303 VPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIE-QGAKLVVDGRDFKLQGYEN 361 V+++ +G DEK D+G +V+ +R+RS I G E +GA V Sbjct: 317 KAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTDPKLAK 376 Query: 362 GHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGD 421 G F+ +F + + + EIFGPV +V++ +YE+ L+ EYG +I+TRD Sbjct: 377 GRFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRDFK 436 Query: 422 AARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDS-IKFWTRTKTI 478 A D R+ G V VN + V S+GG K+S G + +S ++ +T KTI Sbjct: 437 LAMDATKRLEAGFVQVNQNLVVQPGL-SYGGVKTSGIG--KEASLESMLEHFTHKKTI 491 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: 557 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: 498 Length of database: 496 Length adjustment: 34 Effective length of query: 464 Effective length of database: 462 Effective search space: 214368 Effective search space used: 214368 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 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