Align aryl-acylamidase (EC 3.5.1.13); amidase (EC 3.5.1.4) (characterized)
to candidate 3610125 Dshi_3506 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (RefSeq)
Query= BRENDA::A0A088BHP3 (267 letters) >FitnessBrowser__Dino:3610125 Length = 277 Score = 75.1 bits (183), Expect = 2e-18 Identities = 78/257 (30%), Positives = 112/257 (43%), Gaps = 25/257 (9%) Query: 14 DVAANLRELDAACRRARAEGAELLITTEL---FITGYDIGDAV-RDLARTDLLSPAQEIA 69 D ANL +L +A AEGA +++ E+ T AV R A +L+ +E A Sbjct: 13 DPEANLAQLQGLAAQAVAEGAGFVLSPEVSNCLSTSRTRQRAVLRREADDPMLAAMREFA 72 Query: 70 AAHGIALVLGA----PEHDDGACYNSAFFIDPAGAILGRHRKNHLFGDL--------DRR 117 A G+ ++LG+ E +G N + ID G I R+ K H+F + Sbjct: 73 ARRGVWVLLGSLAVTTEDAEGRFANRSILIDAGGGIAARYDKIHMFDVAVSEAETYRESD 132 Query: 118 YFTPGDRTAPVIDYAGVRIAMLICYDVEFPENVRAAALAGADLVAVPTAQMQPYEFIA-- 175 + PGDR A + D +I M +CYD+ FP R A AGA+++ VP+A P A Sbjct: 133 GYRPGDR-AVLADTPFGKIGMTVCYDLRFPHLFRDLARAGAEILTVPSA-FSPVTGAAHW 190 Query: 176 EHLLRVRAWENQIYIAYV----NHDGDEGSLRYV-GRSSIVSPSATVLDSVEHGNRLLFA 230 E LLR RA E ++ H G R G S V P VL + F Sbjct: 191 EPLLRARAIECGAWVLAPAQTGTHPATRGKARSTHGHSLAVDPWGRVLADGGTAPGVCFV 250 Query: 231 TVEPHTVRTARKANPYL 247 ++ + AR+ P L Sbjct: 251 DLDRTEIAAARRKIPSL 267 Lambda K H 0.321 0.137 0.407 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: 174 Number of extensions: 8 Number of successful extensions: 2 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: 267 Length of database: 277 Length adjustment: 25 Effective length of query: 242 Effective length of database: 252 Effective search space: 60984 Effective search space used: 60984 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 (21.9 bits) S2: 47 (22.7 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