Align aryl-acylamidase (EC 3.5.1.13); amidase (EC 3.5.1.4) (characterized)
to candidate BPHYT_RS00250 BPHYT_RS00250 hydratase
Query= BRENDA::A0A088BHP3 (267 letters) >FitnessBrowser__BFirm:BPHYT_RS00250 Length = 283 Score = 114 bits (286), Expect = 2e-30 Identities = 94/274 (34%), Positives = 132/274 (48%), Gaps = 26/274 (9%) Query: 1 MKISGLQTAGTPGDVAANLRELDAACRRARAEGAELLITTELFITGY---------DIGD 51 ++I+ +Q A G+ N+R RA GAEL++ EL TGY + + Sbjct: 8 VQIACVQMAPRIGEKDLNVRRAIDFVTRAADLGAELVVLPELANTGYVFDSRAEAESLAE 67 Query: 52 AVRDLARTDLLSPAQEIAAAHGIALVLGAPEHDDGACYNSAFFIDPAGAILGRHRKNHLF 111 V D + T S E+A+A G+ +V G E DGA YNSA + P G LG +RK HL+ Sbjct: 68 PVPDGSTTAAWS---EVASALGVYIVAGIAEKADGALYNSAVLLGPDG-YLGSYRKTHLW 123 Query: 112 GDLDRRYFTPGDRTAPVIDYAGVRIAMLICYDVEFPENVRAAALAGADLVAVPT------ 165 GD +++ F GDR +P+ D RIA+ ICYD+ FPE R AL GA +V VPT Sbjct: 124 GD-EKKLFASGDRPSPIYDTPLGRIAIAICYDLWFPELFRLYALGGAQIVCVPTNWVPMP 182 Query: 166 AQMQPYEFIAEHLLRVRAWENQIYIAYVNHDGDEGSLRYVGRSSIVSPSATVLDSVEHGN 225 Q +A L A N + +A + G E + G+S +V S + V + Sbjct: 183 NQSADRPAMANTLAMAAAHTNGLVVACADRVGVERGQPFEGQSLVVDQSGWPVGDV--AS 240 Query: 226 RLLFATVEPHTVRTARKA----NPYLADLRPDLF 255 R L V AR + N LAD R D++ Sbjct: 241 RSLEEIVSASITLDARTSVGTHNDVLADRRADIY 274 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: 170 Number of extensions: 12 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: 267 Length of database: 283 Length adjustment: 25 Effective length of query: 242 Effective length of database: 258 Effective search space: 62436 Effective search space used: 62436 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