Align aryl-acylamidase (EC 3.5.1.13); amidase (EC 3.5.1.4) (characterized)
to candidate 7026499 Shewana3_3642 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (RefSeq)
Query= BRENDA::A0A088BHP3 (267 letters) >FitnessBrowser__ANA3:7026499 Length = 264 Score = 77.0 bits (188), Expect = 4e-19 Identities = 63/199 (31%), Positives = 98/199 (49%), Gaps = 15/199 (7%) Query: 61 LLSPAQEIAAAHGIALVLGAPEH--DDGACYNSAFFIDPAGAILGRHRKNHLF----GDL 114 L S +AA + + +V G +DG Y+ + D G LG++ K HLF D Sbjct: 53 LKSALSALAARYCVYMVAGTIPALAEDGRVYSRCYLFDDKGDTLGQYDKLHLFDVDVADG 112 Query: 115 DRRY-----FTPGDRTAPVIDYAGVRIAMLICYDVEFPENVRAAALAGADLVAVPTAQMQ 169 ++Y F PG+ + VID +I + ICYD+ FP+ RA LAGA+++ VP+A + Sbjct: 113 TKQYRESETFCPGNHIS-VIDTPFGKIGLTICYDLRFPDLFRALRLAGAEVITVPSAFTK 171 Query: 170 -PYEFIAEHLLRVRAWENQIYIAYVNHDG--DEGSLRYVGRSSIVSPSATVLDSVEHGNR 226 E + LL+ RA E Q +I G +EGS G+S ++SP V+ + G Sbjct: 172 VTGEAHWQVLLQARAIETQCFILAAAQWGAHNEGSRETWGQSMVISPWGEVIAEQKTGIG 231 Query: 227 LLFATVEPHTVRTARKANP 245 + A ++ V + R P Sbjct: 232 WVHADIDVAEVHSIRSKMP 250 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: 168 Number of extensions: 6 Number of successful extensions: 3 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: 264 Length adjustment: 25 Effective length of query: 242 Effective length of database: 239 Effective search space: 57838 Effective search space used: 57838 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