Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate GFF3711 HP15_3653 acylamide amidohydrolase
Query= reanno::pseudo1_N1B4:Pf1N1B4_2504 (264 letters) >FitnessBrowser__Marino:GFF3711 Length = 348 Score = 78.2 bits (191), Expect = 2e-19 Identities = 74/241 (30%), Positives = 108/241 (44%), Gaps = 12/241 (4%) Query: 13 LDVAGNL-QRLHQLALEAKGADLLVLPEMFLTGYNI-GIDAVSVLAEVHNGESA--QQIA 68 LD A N+ + + + G DL+V PE G + + A V E+A Sbjct: 32 LDNARNIADMIKGMKVGLPGMDLVVFPEYSTMGIMYDNEEMMETAATVPGDETAIFSAAC 91 Query: 69 RIAKTTGIAILYGYPERTEDGQI---YNAVQLIDANGERLCNYRKTHLFGDLDHSMFSPG 125 R A T G+ L G ER ED YN + LI+ GE + YRK + ++ + PG Sbjct: 92 REANTWGVFSLTG--ERHEDHPNKAPYNTLVLINNEGEVVQKYRKCIPWCPIEG--WYPG 147 Query: 126 PDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPYDFIADVTVRAR 185 + G K+ +IC D +PE R A+ GAELI+ M P + ++ Sbjct: 148 DTTYVTEGPKGMKISLIICDDGNYPEIWRDCAMKGAELIVRCQGYMYPAKEQQVMMAKSM 207 Query: 186 AFENQCYVAYANYCGHEGEIQYCGQSSIAAPDGSRIAQAG-LDEALIVGELDRQLMIDSR 244 A+ N CYVA AN G +G Y G S+I DG + + G D + +L + D+R Sbjct: 208 AWANNCYVAVANAAGFDGVYSYFGHSAIIGFDGRTLGECGEEDMGIQYAQLSVSQIRDAR 267 Query: 245 A 245 A Sbjct: 268 A 268 Lambda K H 0.322 0.140 0.420 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: 230 Number of extensions: 12 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: 264 Length of database: 348 Length adjustment: 27 Effective length of query: 237 Effective length of database: 321 Effective search space: 76077 Effective search space used: 76077 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: 48 (23.1 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