Align aryl-acylamidase (EC 3.5.1.13); amidase (EC 3.5.1.4) (characterized)
to candidate PfGW456L13_4783 Aliphatic amidase AmiE (EC 3.5.1.4)
Query= BRENDA::A0A088BHP3 (267 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4783 Length = 273 Score = 127 bits (318), Expect = 3e-34 Identities = 89/255 (34%), Positives = 132/255 (51%), Gaps = 8/255 (3%) Query: 1 MKISGLQTAGTPGDVAANLRELDAACRRARAEGAELLITTELFITGYDIGDAVRDLART- 59 MK+ Q AG D A NL E A A A ++L++ E + G+ ++V ++A Sbjct: 1 MKVELAQLAGRDNDTAYNL-ERTLAAMAACAADSQLILFPEGHLMGFPSAESVAEVAEPL 59 Query: 60 DLLSPAQEIAAA--HGIALVLGAPEHDDGACYNSAFFIDPAGAILGRHRKNHLFGDLDRR 117 D S + IAAA H I++ +G E+D+G YN+ I P G L ++RK HL+ DR Sbjct: 60 DGPSVSAVIAAARQHNISVAIGMAENDNGRFYNTTLLITPEGIAL-KYRKTHLWAS-DRG 117 Query: 118 YFTPGDRTAPVIDYAGVRIAMLICYDVEFPENVRAAALAGADLVAVPTAQMQPYEFIAEH 177 + GDR A + + GVR+ +LICYD+EFPE+ RA A GA+L+ V M PY Sbjct: 118 VYEAGDRYATCL-WNGVRVGLLICYDIEFPESARALAQLGAELLIVTNGNMDPYGPTHRT 176 Query: 178 LLRVRAWENQIYIAYVNH-DGDEGSLRYVGRSSIVSPSATVLDSVEHGNRLLFATVEPHT 236 + RA ENQ + VN + +G L + G S++V P T+L ++ + Sbjct: 177 AIMARAQENQAFALMVNRVEEGDGGLLFAGGSALVDPLGTLLFEAGREEGQFAVELDLNQ 236 Query: 237 VRTARKANPYLADLR 251 + AR+ YL D R Sbjct: 237 LTVARQDYRYLDDQR 251 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: 186 Number of extensions: 6 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: 273 Length adjustment: 25 Effective length of query: 242 Effective length of database: 248 Effective search space: 60016 Effective search space used: 60016 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