Align aryl-acylamidase (EC 3.5.1.13); amidase (EC 3.5.1.4) (characterized)
to candidate SMc02442 SMc02442 hydrolase
Query= BRENDA::A0A088BHP3 (267 letters) >FitnessBrowser__Smeli:SMc02442 Length = 285 Score = 78.2 bits (191), Expect = 2e-19 Identities = 78/257 (30%), Positives = 113/257 (43%), Gaps = 22/257 (8%) Query: 14 DVAANLRELDAACRRARAEGAELLITTELFITGY------DIGDAVRDLARTDLLSPAQE 67 D A N + R A + GA + T E+ TG + ++D ++ A Sbjct: 15 DPAGNAETMAKLVREAASRGATYVQTPEM--TGAVQRDRTGLRSVLKDGENDVVVREASR 72 Query: 68 IAAAHGIALVLGAPE--HDDGACYNSAFFIDPAGAILGRHRKNHLFG-DLDR-------R 117 +A GI L +G+ DG N F P GA + + K H+F DL+ Sbjct: 73 LARELGIYLHVGSTPIARADGKIANRGFLFGPDGAKICDYDKIHMFDVDLENGESWRESA 132 Query: 118 YFTPGDRTAPVIDYAGVRIAMLICYDVEFPENVRAAALAGADLVAVPTA-QMQPYEFIAE 176 + PG+ TA D ++ ICYDV FPE R A+AGA++++VP A Q E E Sbjct: 133 AYHPGN-TARTADLPFGKLGFSICYDVRFPELFRQQAVAGAEIMSVPAAFTRQTGEAHWE 191 Query: 177 HLLRVRAWENQIYIAYVNHDG-DEGSLRYVGRSSIVSPSATVL-DSVEHGNRLLFATVEP 234 LLR RA EN +++ G E G S IV P VL ++ G ++ A ++ Sbjct: 192 ILLRARAIENGLFVIAAAQAGTHEDGRETFGHSMIVDPWGRVLAEAGATGEEIIVAEIDV 251 Query: 235 HTVRTARKANPYLADLR 251 V AR P L + R Sbjct: 252 AAVHAARAKIPNLRNAR 268 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: 169 Number of extensions: 5 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: 285 Length adjustment: 25 Effective length of query: 242 Effective length of database: 260 Effective search space: 62920 Effective search space used: 62920 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