Align 2-pyrone-4,6-dicarbaxylate hydrolase; PDC hydrolase; 2-pyrone-4,6-dicarboxylate lactonase; EC 3.1.1.57 (characterized)
to candidate BPHYT_RS35395 BPHYT_RS35395 membrane protein
Query= SwissProt::Q93PS7 (305 letters) >FitnessBrowser__BFirm:BPHYT_RS35395 Length = 289 Score = 119 bits (298), Expect = 8e-32 Identities = 88/274 (32%), Positives = 121/274 (44%), Gaps = 16/274 (5%) Query: 29 VDAHCHVFGPGNEFPFAPERKYTP-CDASKAQLYALRDHLGFARNVVVQATCHGADNRAM 87 VD H HVF P A ER+Y P DA+ L D V+VQ + G DN + Sbjct: 9 VDTHAHVFAKA--LPLADERRYAPDYDATLDAYRKLLDANDIGHAVLVQPSFLGTDNSYL 66 Query: 88 VDACKSSGGKARGVATVKRSISDAELQQLHDAGVRGVRFNFVKRLVDFTPKDELMEIAGR 147 + A + RGVA V IS+ +L QL+ GV GVR N + + + + R Sbjct: 67 LQALTRDRTRLRGVAVVSPDISEDDLAQLNGQGVTGVRLNLIGQTLPDLSAAPYTTLWRR 126 Query: 148 IAKLGWHVVIYFEAVDLPELWDFFTALPTTVVVDHMGRPDVTKGVDSEEFALFLKFMREH 207 ++KLGWHV ++ EA DL L + A+ VVVDH GRP G F L + Sbjct: 127 LSKLGWHVELHREASDLAPLINSLLAVGLPVVVDHFGRPAPDSGTSDPGFKDLLA-LGPS 185 Query: 208 QNVWSKVSCPERLSVTGPKALNGEQNAYRDVVPFARRVVEEF-PDRVLWGTDWPHPNLKD 266 VW K+S R S G N RD R++ F +R++WG+DWPH + Sbjct: 186 GRVWVKISGAYRCSKPG-------SNFMRDATD---RLINAFGTERLMWGSDWPHTQF-E 234 Query: 267 HMPDDGLLVDFIPHIAPTAELQQKLLVDNPMRLY 300 H D + + + L +L P Y Sbjct: 235 HATDFSQTLSALLDLGLAPSLVDAILCSTPHSFY 268 Lambda K H 0.322 0.138 0.445 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: 284 Number of extensions: 19 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: 305 Length of database: 289 Length adjustment: 26 Effective length of query: 279 Effective length of database: 263 Effective search space: 73377 Effective search space used: 73377 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